############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL gmapR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘gmapR’ ... ** using staged installation ** libs ** arch - cd gstruct/; \ CFLAGS="-g -O3" \ ./configure --enable-static --disable-shared \ --prefix=/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr --includedir=/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct \ --libdir=/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib \ --with-samtools-lib=/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/samtools \ --disable-maintainer-mode \ --disable-binaries checking package version... 2017-01-01 checking whether to enable maintainer-specific portions of Makefiles... no loading default site script ./config.site checking CFLAGS... -g -O3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking bindir... /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin checking whether to link statically... not specified so disabled by default checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for qsub... no checking gmap program directory... checking for get-genome... false checking for iit_store... false checking for iit_get... false checking for gmap_build... false checking for gmap... false checking for gsnap... false checking for sam_sort... false checking for uniqscan... false checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for builtin popcount/clz/ctz features... not specified so enabled by default ./configure: line 13657: ACX_BUILTIN_POPCOUNT: command not found checking for bsr instruction in assembly... yes checking whether sse2 is enabled... not specified so enabled by default checking compiler is defective and requires an immediate in sse2 shift commands... no checking whether ssse3 is enabled... not specified so enabled by default checking whether sse4.1 is enabled... not specified so enabled by default checking whether sse4.2 is enabled... not specified so enabled by default checking whether avx is enabled... not specified so enabled by default checking whether avx2 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking for x86 cpuid 0x00000001 output... 50657:400800:7ffefbff:bfebfbff checking whether mmx is enabled and supported by CPU... yes checking whether sse is enabled and supported by CPU... yes checking whether sse2 is enabled and supported by CPU... yes checking whether sse3 is enabled and supported by CPU... yes checking whether ssse3 is enabled and supported by CPU... yes checking whether sse4.1 is enabled and supported by CPU... yes checking whether sse4.2 is enabled and supported by CPU... yes checking whether avx is enabled and supported by CPU... yes checking for x86-AVX xgetbv 0x00000000 output... 2ff:0 checking whether avx is supported by operating system... yes checking whether popcnt is enabled and supported by CPU... yes checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking whether lzcnt is enabled and supported by CPU... yes checking for x86 cpuid 0x00000007 output... 0:0:0:0 checking whether avx2 is enabled and supported by CPU... no checking whether bmi1 is enabled and supported by CPU... no checking whether bmi2 is enabled and supported by CPU... no checking whether C compiler accepts -mmmx... yes checking for mmintrin.h header file... yes checking whether C compiler accepts -msse... yes checking for xmmintrin.h header file... yes checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse3... yes checking for pmmintrin.h header file... yes checking whether C compiler accepts -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse4.2... yes checking for nmmintrin.h header file... yes checking whether C compiler accepts -mavx... yes checking for immintrin.h header file... yes checking gmapdb... /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share checking whether to make binaries... disabled checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for samtools program... checking for samtools library... provided by --with-samtools-lib checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating lib/gstruct-1.0.pc config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: WARNING: You don't seem to have gsnap specified. checking Standard compiler and flags to be used... gcc -g -O3 checking Standard linker flags to be used... checking pthread compiler flags to be used... -pthread checking popcnt compiler flags to be used... checking SIMD features available on computer... mmx sse sse2 sse3 ssse3 sse4.1 sse4.2 avx checking SIMD compiler flags to be used... -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bgzf.c -o samtools/bgzf.o samtools/bgzf.c: In function ‘worker_aux’: samtools/bgzf.c:412:9: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 412 | int i, tmp, stop = 0; | ^~~ samtools/bgzf.c: In function ‘bgzf_close’: samtools/bgzf.c:592:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 592 | int ret, count, block_length; | ^~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kstring.c -o samtools/kstring.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_aux.c -o samtools/bam_aux.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam.c -o samtools/bam.o samtools/bam.c: In function ‘bam_header_write’: samtools/bam.c:128:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 128 | strncpy(buf, "BAM\001", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_import.c -o samtools/bam_import.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/limits.h:26, from /usr/lib/gcc/x86_64-linux-gnu/9/include/limits.h:194, from /usr/lib/gcc/x86_64-linux-gnu/9/include/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/9/include/limits.h:34, from /usr/include/zconf.h:418, from /usr/include/zlib.h:34, from samtools/bam_import.c:3: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam.c -o samtools/sam.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from samtools/sam.c:3: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_index.c -o samtools/bam_index.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_md.c -o samtools/bam_md.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function ‘razf_open_w’: samtools/razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 178 | strncpy((char*)rz->header->extra, "RAZF", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/faidx.c -o samtools/faidx.o samtools/faidx.c: In function ‘fai_load0’: samtools/faidx.c:309:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 309 | else | ^~~~ samtools/faidx.c:312:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 312 | if (fp == 0) { | ^~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/knetfile.c -o samtools/knetfile.o In file included from /usr/include/time.h:25, from samtools/knetfile.c:33: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_sort.c -o samtools/bam_sort.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdlib.h:25, from samtools/bam_sort.c:3: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam_header.c -o samtools/sam_header.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/sam_header.c:3: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_reheader.c -o samtools/bam_reheader.o samtools/bam_reheader.c: In function ‘bam_reheader’: samtools/bam_reheader.c:12:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] 12 | bam_header_t *old; | ^~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kprobaln.c -o samtools/kprobaln.o samtools/kprobaln.c: In function ‘kpa_glocal’: samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] 78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/samtools_patch.c -o samtools/samtools_patch.o ar -crus samtools/libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') cd gstruct; \ make install make[1]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct' Making install in src make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct/src' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:296:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 296 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:457:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 457 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:758:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 758 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o access.c: In function ‘Access_file_exists_p’: access.c:59:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 59 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:39: access.c: In function ‘Access_allocated’: littleendian.h:18:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(unsigned int),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:125:3: note: in expansion of macro ‘FREAD_UINTS’ 125 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:15:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2353:5: note: in expansion of macro ‘FREAD_INT’ 2353 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:15:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1731:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1731 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1732:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1732 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1733:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1733 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1734:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1734 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1735:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1735 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1816:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1816 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1817:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1817 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1819:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1819 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1823:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1823 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:20:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1907:5: note: in expansion of macro ‘FREAD_UINT8’ 1907 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:16:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 16 | #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT’ 1913 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2257:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2257 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2263:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2263 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2268:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2268 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2279:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2279 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2285:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2285 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2290:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2290 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2301:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2301 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:15:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3019:5: note: in expansion of macro ‘FREAD_INT’ 3019 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:20:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2030:5: note: in expansion of macro ‘FREAD_UINT8’ 2030 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:16:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 16 | #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2035:5: note: in expansion of macro ‘FREAD_UINT’ 2035 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o chrom.c: In function ‘Chrom_from_string’: chrom.c:108:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 108 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:108:10: note: did you mean to dereference the pointer? 108 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o genome.c: In function ‘fill_buffer’: genome.c:1218:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1218 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:329:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 329 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:1374:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1374 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:1451:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1451 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:1554:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:1710:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1710 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT 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libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo `test -f 'expr.c' || echo './'`expr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -pthread -version-info 1:0:0 -o libgstruct-1.0.la -rpath /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-expr.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo -lz -lm libtool: link: ar cru .libs/libgstruct-1.0.a libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-expr.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libgstruct-1.0.a libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" ) make[3]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib' /bin/bash ../libtool --mode=install /usr/bin/install -c libgstruct-1.0.la '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib' libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.la libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: chmod 644 /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: ranlib /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: finish: PATH="/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' make[3]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct/src' make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct' make[3]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct' make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct' make[1]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gstruct' gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c bamreader.c -o bamreader.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c bamtally.c -o bamtally.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c iit.c -o iit.o iit.c: In function ‘R_iit_read’: iit.c:267:18: warning: ‘fields’ may be used uninitialized in this function [-Wmaybe-uninitialized] 267 | mkChar(IIT_fieldvalue(iit, i, fields[f]))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit.c:214:10: note: ‘fields’ was declared here 214 | int *fields; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c variantsummary.c -o variantsummary.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c genome.c -o genome.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c R_init_gmapR.c -o R_init_gmapR.o gcc -shared -L"/home/biocbuild/bbs-3.15-bioc/R/lib" -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -L"/home/biocbuild/bbs-3.15-bioc/R/lib" -lR cd gmap/; \ ./configure --with-gmapdb= --prefix=/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr \ --libdir=/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib --disable-maintainer-mode checking package version... 2013-11-01 checking whether to enable maintainer-specific portions of Makefiles... no checking CONFIG_SITE... ./config.site loading script ./config.site checking CFLAGS... not set by user so using default -O3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking bindir... /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for popcnt feature... not specified so enabled by default checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking whether sse2 is enabled... not specified so enabled by default checking whether user has declared a defective SSE2 compiler... no checking whether sse4.1 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking for x86 cpuid 0x00000001 output... 50657:10400800:7ffefbff:bfebfbff checking whether mmx is enabled and supported... yes checking whether sse is enabled and supported... yes checking whether sse2 is enabled and supported... yes checking whether sse3 is enabled and supported... yes checking whether ssse3 is enabled and supported... yes checking whether sse4.1 is enabled and supported... yes checking whether sse4.2 is enabled and supported... yes checking whether avx is enabled and supported... yes checking whether C compiler accepts -mmmx... yes checking whether C compiler accepts -msse... yes checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -msse3... yes checking whether C compiler accepts -mssse3... yes checking whether C compiler accepts -msse4.1... yes checking whether C compiler accepts -msse4.2... yes checking whether C compiler accepts -mavx... yes checking gmapdb... /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share checking MAX_READLENGTH... 250 checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking for goby library... disabled checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_setup.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands cd gmap; \ make install make[1]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap' Making install in src make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/src' gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-univinterval.o -MD -MP -MF .deps/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read-univ.o -MD -MP -MF .deps/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bzip2.o -MD -MP -MF .deps/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmap-bzip2.Tpo .deps/gmap-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress-write.o -MD -MP -MF .deps/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function ‘fill_buffer’: compress-write.c:73:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 73 | printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u compress-write.c: In function ‘write_compressed_one’: compress-write.c:251:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 251 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %u 252 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} compress-write.c: In function ‘put_compressed_one’: compress-write.c:299:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 299 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %u 300 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_sites.o -MD -MP -MF .deps/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gmap-genome_sites.Tpo .deps/gmap-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome-write.o -MD -MP -MF .deps/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function ‘genome_write_file’: genome-write.c:252:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 252 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 253 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:252:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 252 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 253 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:255:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 255 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 256 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:255:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 255 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 256 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c: In function ‘genome_writeraw_file’: genome-write.c:429:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 429 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 430 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:429:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 429 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 430 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:432:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 432 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 433 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:432:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 432 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 433 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c: In function ‘fill_circular_chromosomes’: genome-write.c:595:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome-write.c:595:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome-write.c:595:73: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome-write.c:595:78: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome-write.c: In function ‘genome_write_memory’: genome-write.c:642:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 642 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 643 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:642:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 642 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 643 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:645:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 645 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 646 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c:645:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 645 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %u 646 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka unsigned int} genome-write.c: In function ‘Genome_write’: genome-write.c:787:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 787 | fprintf(stderr,"Genome length is %lu nt\n",genomelength); | ~~^ ~~~~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bitpack64-read.o -MD -MP -MF .deps/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmap-bitpack64-read.Tpo .deps/gmap-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 593 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cmet.o -MD -MP -MF .deps/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmap-cmet.Tpo .deps/gmap-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-atoi.o -MD -MP -MF .deps/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmap-atoi.Tpo .deps/gmap-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:2419:20: warning: ‘%u’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~ pair.c:2419:18: note: directive argument in the range [1, 2147483647] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2478:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2478 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2478:18: note: directive argument in the range [1, 2147483647] 2478 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2474:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2474 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2474:18: note: directive argument in the range [1, 2147483647] 2474 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2455:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2455 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2455:20: note: directive argument in the range [1, 2147483647] 2455 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2451:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2451 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2451:20: note: directive argument in the range [1, 2147483647] 2451 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2444:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2444 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2444:20: note: directive argument in the range [1, 2147483647] 2444 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2439:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2439 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2439:20: note: directive argument in the range [1, 2147483647] 2439 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2389:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2389 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2389:20: note: directive argument in the range [1, 2147483647] 2389 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2386:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2386 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2386:20: note: directive argument in the range [1, 2147483647] 2386 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2383:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2383 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2383:20: note: directive argument in the range [1, 2147483647] 2383 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2537:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2537 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2537:21: note: directive argument in the range [1, 2147483647] 2537 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2534:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2534 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2534:21: note: directive argument in the range [1, 2147483647] 2534 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2531:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2531 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2531:21: note: directive argument in the range [1, 2147483647] 2531 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘compute_cigar.constprop’: pair.c:4587:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4587 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4591:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4591 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4689:21: warning: ‘N’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4689 | sprintf(token,"%uN",genome_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4706:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4706 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4754:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4754 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4750:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4750 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4736:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4736 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4732:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4732 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4724:23: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4719:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4719 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4625:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4625 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4622:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4622 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4619:21: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4619 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4783:22: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4783 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4780:22: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4780 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4777:22: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4777 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4806:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4806 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4810:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4810 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4800:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4800 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_sam’: pair.c:5195:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5195 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5145:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5145 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5218:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5218 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5086:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5086 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5046:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5046 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5111:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5111 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_compressed’: pair.c:7169:19: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7169 | sprintf(token,"%d:%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7162:19: warning: ‘x’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7162 | sprintf(token,"%dx%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7152:21: warning: ‘v’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7152 | sprintf(token,"%dv",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7150:21: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7150 | sprintf(token,"%d^%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7081:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7081 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7078:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7078 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7075:21: warning: ‘[’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7075 | sprintf(token,"%d[",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7073:21: warning: ‘]’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7073 | sprintf(token,"%d]",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7070:21: warning: ‘(’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7070 | sprintf(token,"%d(",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7068:21: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7068 | sprintf(token,"%d)",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7066:21: warning: ‘=’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7066 | sprintf(token,"%d=",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7063:21: warning: ‘<’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7063 | sprintf(token,"%d<",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7061:21: warning: ‘>’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7061 | sprintf(token,"%d>",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7206:20: warning: ‘*’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7206 | sprintf(token,"%d*",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cellpool.o -MD -MP -MF .deps/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmap-cellpool.Tpo .deps/gmap-cellpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-doublelist.o -MD -MP -MF .deps/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmap-doublelist.Tpo .deps/gmap-doublelist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicestringpool.o -MD -MP -MF .deps/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmap-splicestringpool.Tpo .deps/gmap-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-samheader.o -MD -MP -MF .deps/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmap-samheader.Tpo .deps/gmap-samheader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gmap-getopt.Tpo .deps/gmap-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt1.o -MD -MP -MF .deps/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gmap-getopt1.Tpo .deps/gmap-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gmap.o -MD -MP -MF .deps/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gmap.c: In function ‘apply_stage3’: gmap.c:3244:28: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Diagpool_T {aka struct Diagpool_T *} gmap.c:2672:61: note: expected ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} but argument is of type ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} 2672 | Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, | ~~~~~~~~~~~^~~~~~~~ gmap.c:3244:37: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Cellpool_T {aka struct Cellpool_T *} gmap.c:2673:17: note: expected ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} but argument is of type ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} 2673 | Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { | ~~~~~~~~~~~^~~~~~~~ mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-except.o -MD -MP -MF .deps/gmapl-except.Tpo -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapl-except.Tpo .deps/gmapl-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-assert.o -MD -MP -MF .deps/gmapl-assert.Tpo -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapl-assert.Tpo .deps/gmapl-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-mem.o -MD -MP -MF .deps/gmapl-mem.Tpo -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapl-mem.Tpo .deps/gmapl-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intlist.o -MD -MP -MF .deps/gmapl-intlist.Tpo -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapl-intlist.Tpo .deps/gmapl-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-list.o -MD -MP -MF .deps/gmapl-list.Tpo -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapl-list.Tpo .deps/gmapl-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-littleendian.o -MD -MP -MF .deps/gmapl-littleendian.Tpo -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/gmapl-littleendian.Tpo .deps/gmapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bigendian.o -MD -MP -MF .deps/gmapl-bigendian.Tpo -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/gmapl-bigendian.Tpo .deps/gmapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-univinterval.o -MD -MP -MF .deps/gmapl-univinterval.Tpo -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gmapl-univinterval.Tpo .deps/gmapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-interval.o -MD -MP -MF .deps/gmapl-interval.Tpo -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapl-interval.Tpo .deps/gmapl-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uintlist.o -MD -MP -MF .deps/gmapl-uintlist.Tpo -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapl-uintlist.Tpo .deps/gmapl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stopwatch.o -MD -MP -MF .deps/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapl-stopwatch.Tpo .deps/gmapl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-access.o -MD -MP -MF .deps/gmapl-access.Tpo -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/gmapl-access.Tpo .deps/gmapl-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read-univ.o -MD -MP -MF .deps/gmapl-iit-read-univ.Tpo -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gmapl-iit-read-univ.Tpo .deps/gmapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read.o -MD -MP -MF .deps/gmapl-iit-read.Tpo -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gmapl-iit-read.Tpo .deps/gmapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-md5.o -MD -MP -MF .deps/gmapl-md5.Tpo -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmapl-md5.Tpo .deps/gmapl-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bzip2.o -MD -MP -MF .deps/gmapl-bzip2.Tpo -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapl-bzip2.Tpo .deps/gmapl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-sequence.o -MD -MP -MF .deps/gmapl-sequence.Tpo -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapl-sequence.Tpo .deps/gmapl-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-reader.o -MD -MP -MF .deps/gmapl-reader.Tpo -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmapl-reader.Tpo .deps/gmapl-reader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genomicpos.o -MD -MP -MF .deps/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapl-genomicpos.Tpo .deps/gmapl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress.o -MD -MP -MF .deps/gmapl-compress.Tpo -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapl-compress.Tpo .deps/gmapl-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress-write.o -MD -MP -MF .deps/gmapl-compress-write.Tpo -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function ‘fill_buffer’: compress-write.c:73:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 73 | printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu compress-write.c: In function ‘write_compressed_one’: compress-write.c:251:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 251 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 252 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} compress-write.c: In function ‘put_compressed_one’: compress-write.c:299:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 299 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 300 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/gmapl-compress-write.Tpo .deps/gmapl-compress-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gbuffer.o -MD -MP -MF .deps/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmapl-gbuffer.Tpo .deps/gmapl-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome.o -MD -MP -MF .deps/gmapl-genome.Tpo -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmapl-genome.Tpo .deps/gmapl-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_hr.o -MD -MP -MF .deps/gmapl-genome_hr.Tpo -c -o gmapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmapl-genome_hr.Tpo .deps/gmapl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_sites.o -MD -MP -MF .deps/gmapl-genome_sites.Tpo -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome_sites.c: In function ‘Genome_print_blocks’: genome_sites.c:24729:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24729 | printf("%u\t",startblock/3*32U); | ~^ ~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu genome_sites.c:24744:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24744 | printf("%u\t",ptr/3*32U); | ~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | unsigned int | %llu genome_sites.c:24751:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24751 | printf("%u\t",(endblock+3)/3*32U); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gmapl-genome_sites.Tpo .deps/gmapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome-write.o -MD -MP -MF .deps/gmapl-genome-write.Tpo -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function ‘genome_write_file’: genome-write.c:252:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 252 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 253 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:252:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 252 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 253 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:255:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 255 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 256 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:255:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 255 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 256 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c: In function ‘genome_writeraw_file’: genome-write.c:429:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 429 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 430 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:429:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 429 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 430 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:432:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 432 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 433 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:432:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 432 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 433 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c: In function ‘fill_circular_chromosomes’: genome-write.c:595:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c:595:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c:595:73: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c:595:78: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c: In function ‘genome_write_memory’: genome-write.c:642:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 642 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 643 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:642:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 642 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 643 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:645:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 645 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 646 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:645:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 645 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 646 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c: In function ‘Genome_write’: genome-write.c:787:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 787 | fprintf(stderr,"Genome length is %lu nt\n",genomelength); | ~~^ ~~~~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/gmapl-genome-write.Tpo .deps/gmapl-genome-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bitpack64-read.o -MD -MP -MF .deps/gmapl-bitpack64-read.Tpo -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmapl-bitpack64-read.Tpo .deps/gmapl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb.o -MD -MP -MF .deps/gmapl-indexdb.Tpo -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmapl-indexdb.Tpo .deps/gmapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb_hr.o -MD -MP -MF .deps/gmapl-indexdb_hr.Tpo -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘Compoundpos_dump’: indexdb_hr.c:1008:31: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1008 | printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu indexdb_hr.c: In function ‘heap_even_dump’: indexdb_hr.c:1232:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1232 | printf("#%d--%d:%u ",i,batch->nentries,batch->position); | ~^ ~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 593 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmapl-indexdb_hr.Tpo .deps/gmapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligo.o -MD -MP -MF .deps/gmapl-oligo.Tpo -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmapl-oligo.Tpo .deps/gmapl-oligo.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-block.o -MD -MP -MF .deps/gmapl-block.Tpo -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmapl-block.Tpo .deps/gmapl-block.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrom.o -MD -MP -MF .deps/gmapl-chrom.Tpo -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gmapl-chrom.Tpo .deps/gmapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-segmentpos.o -MD -MP -MF .deps/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function ‘Segmentpos_print’: segmentpos.c:90:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 90 | fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gmapl-segmentpos.Tpo .deps/gmapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrnum.o -MD -MP -MF .deps/gmapl-chrnum.Tpo -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmapl-chrnum.Tpo .deps/gmapl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrsubset.o -MD -MP -MF .deps/gmapl-chrsubset.Tpo -c -o gmapl-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmapl-chrsubset.Tpo .deps/gmapl-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uinttable.o -MD -MP -MF .deps/gmapl-uinttable.Tpo -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmapl-uinttable.Tpo .deps/gmapl-uinttable.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gregion.o -MD -MP -MF .deps/gmapl-gregion.Tpo -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmapl-gregion.Tpo .deps/gmapl-gregion.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-match.o -MD -MP -MF .deps/gmapl-match.Tpo -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmapl-match.Tpo .deps/gmapl-match.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-matchpool.o -MD -MP -MF .deps/gmapl-matchpool.Tpo -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmapl-matchpool.Tpo .deps/gmapl-matchpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagnostic.o -MD -MP -MF .deps/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmapl-diagnostic.Tpo .deps/gmapl-diagnostic.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage1.o -MD -MP -MF .deps/gmapl-stage1.Tpo -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmapl-stage1.Tpo .deps/gmapl-stage1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diag.o -MD -MP -MF .deps/gmapl-diag.Tpo -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmapl-diag.Tpo .deps/gmapl-diag.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagpool.o -MD -MP -MF .deps/gmapl-diagpool.Tpo -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmapl-diagpool.Tpo .deps/gmapl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cmet.o -MD -MP -MF .deps/gmapl-cmet.Tpo -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmapl-cmet.Tpo .deps/gmapl-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-atoi.o -MD -MP -MF .deps/gmapl-atoi.Tpo -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmapl-atoi.Tpo .deps/gmapl-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-orderstat.o -MD -MP -MF .deps/gmapl-orderstat.Tpo -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmapl-orderstat.Tpo .deps/gmapl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligoindex_hr.o -MD -MP -MF .deps/gmapl-oligoindex_hr.Tpo -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmapl-oligoindex_hr.Tpo .deps/gmapl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intron.o -MD -MP -MF .deps/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmapl-intron.Tpo .deps/gmapl-intron.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent.o -MD -MP -MF .deps/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmapl-maxent.Tpo .deps/gmapl-maxent.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent_hr.o -MD -MP -MF .deps/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmapl-maxent_hr.Tpo .deps/gmapl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pair.o -MD -MP -MF .deps/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_genomic_sequence’: pair.c:546:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 546 | sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘print_genomicalt_sequence’: pair.c:573:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 573 | sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘compute_margin’: pair.c:600:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 600 | sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c:607:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 607 | sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘Pair_print_coordinates’: pair.c:1272:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1272 | fprintf(fp,"%u %u %c",this->genomepos + ONEBASEDP, | ~^ | | | unsigned int | %llu pair.c:1276:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1276 | fprintf(fp,"%s:%u %u %c",chrstring, | ~^ | | | unsigned int | %llu pair.c: In function ‘Pair_print_exonsummary’: pair.c:1790:19: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1790 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1790:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1790 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1799:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1799 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1799:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1799 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1913:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1913 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1913:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1913 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1922:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1922 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1922:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1922 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c: In function ‘Pair_print_compressed’: pair.c:6986:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6986 | fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c:6986:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6986 | fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:2419:20: warning: ‘%u’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~ pair.c:2419:18: note: directive argument in the range [1, 2147483647] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2478:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2478 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2478:18: note: directive argument in the range [1, 2147483647] 2478 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2474:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2474 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2474:18: note: directive argument in the range [1, 2147483647] 2474 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2455:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2455 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2455:20: note: directive argument in the range [1, 2147483647] 2455 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2451:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2451 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2451:20: note: directive argument in the range [1, 2147483647] 2451 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2444:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2444 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2444:20: note: directive argument in the range [1, 2147483647] 2444 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2439:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2439 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2439:20: note: directive argument in the range [1, 2147483647] 2439 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2389:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2389 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2389:20: note: directive argument in the range [1, 2147483647] 2389 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2386:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2386 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2386:20: note: directive argument in the range [1, 2147483647] 2386 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2383:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2383 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2383:20: note: directive argument in the range [1, 2147483647] 2383 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2537:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2537 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2537:21: note: directive argument in the range [1, 2147483647] 2537 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2534:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2534 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2534:21: note: directive argument in the range [1, 2147483647] 2534 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2531:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2531 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2531:21: note: directive argument in the range [1, 2147483647] 2531 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘compute_cigar.constprop’: pair.c:4587:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4587 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4591:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4591 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4689:21: warning: ‘N’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4689 | sprintf(token,"%uN",genome_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4706:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4706 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4754:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4754 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4750:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4750 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4736:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4736 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4732:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4732 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4724:23: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4719:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4719 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4625:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4625 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4622:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4622 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4619:21: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4619 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4783:22: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4783 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4780:22: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4780 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4777:22: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4777 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4806:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4806 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4810:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4810 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4800:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4800 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_sam’: pair.c:5195:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5195 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5145:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5145 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5218:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5218 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5086:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5086 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5046:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5046 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5111:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5111 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_compressed’: pair.c:7169:19: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7169 | sprintf(token,"%d:%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7162:19: warning: ‘x’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7162 | sprintf(token,"%dx%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7152:21: warning: ‘v’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7152 | sprintf(token,"%dv",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7150:21: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7150 | sprintf(token,"%d^%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7081:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7081 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7078:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7078 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7075:21: warning: ‘[’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7075 | sprintf(token,"%d[",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7073:21: warning: ‘]’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7073 | sprintf(token,"%d]",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7070:21: warning: ‘(’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7070 | sprintf(token,"%d(",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7068:21: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7068 | sprintf(token,"%d)",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7066:21: warning: ‘=’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7066 | sprintf(token,"%d=",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7063:21: warning: ‘<’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7063 | sprintf(token,"%d<",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7061:21: warning: ‘>’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7061 | sprintf(token,"%d>",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7206:20: warning: ‘*’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7206 | sprintf(token,"%d*",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pairpool.o -MD -MP -MF .deps/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmapl-pairpool.Tpo .deps/gmapl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cellpool.o -MD -MP -MF .deps/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmapl-cellpool.Tpo .deps/gmapl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage2.o -MD -MP -MF .deps/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-doublelist.o -MD -MP -MF .deps/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmapl-doublelist.Tpo .deps/gmapl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-smooth.o -MD -MP -MF .deps/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmapl-smooth.Tpo .deps/gmapl-smooth.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicestringpool.o -MD -MP -MF .deps/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmapl-splicestringpool.Tpo .deps/gmapl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie_build.o -MD -MP -MF .deps/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function ‘Splicetrie_dump’: splicetrie_build.c:132:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 132 | printf("%d %u",(int) leaf,position); | ~^ ~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu splicetrie_build.c:146:19: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 146 | printf("%d %u",(int) leaf,position); | ~^ ~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gmap.c: In function ‘apply_stage3’: gmap.c:3244:28: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Diagpool_T {aka struct Diagpool_T *} gmap.c:2672:61: note: expected ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} but argument is of type ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} 2672 | Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, | ~~~~~~~~~~~^~~~~~~~ gmap.c:3244:37: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Cellpool_T {aka struct Cellpool_T *} gmap.c:2673:17: note: expected ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} but argument is of type ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} 2673 | Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { | ~~~~~~~~~~~^~~~~~~~ mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrsubset.o -MD -MP -MF .deps/get_genome-chrsubset.Tpo -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/get_genome-chrsubset.Tpo .deps/get_genome-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c: In function ‘translate_chromosomepos_universal’: parserange.c:186:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 186 | fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", | ~~^ | | | long unsigned int | %llu 187 | Univinterval_low(interval),left,*genomicstart); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} parserange.c:186:31: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 186 | fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", | ~~^ | | | long unsigned int | %llu 187 | Univinterval_low(interval),left,*genomicstart); | ~~~~ | | | Univcoord_T {aka long long unsigned int} parserange.c:186:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 186 | fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", | ~~^ | | | long unsigned int | %llu 187 | Univinterval_low(interval),left,*genomicstart); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c get-genome.c: In function ‘print_two_coords’: get-genome.c:194:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 194 | printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu get-genome.c:194:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 194 | printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu get-genome.c: In function ‘print_sequence’: get-genome.c:410:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 410 | printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu get-genome.c:410:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 410 | printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); | ~~^ ~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu get-genome.c:428:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 428 | printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); | ~~^ ~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu get-genome.c:428:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 428 | printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function ‘fill_buffer’: compress-write.c:73:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 73 | printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu compress-write.c: In function ‘write_compressed_one’: compress-write.c:251:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 251 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 252 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} compress-write.c: In function ‘put_compressed_one’: compress-write.c:299:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 299 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 300 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function ‘genome_write_file’: genome-write.c:252:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 252 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 253 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:252:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 252 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 253 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:255:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 255 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 256 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:255:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 255 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 256 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c: In function ‘genome_writeraw_file’: genome-write.c:429:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 429 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 430 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:429:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 429 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 430 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:432:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 432 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 433 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:432:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 432 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 433 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c: In function ‘fill_circular_chromosomes’: genome-write.c:595:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c:595:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c:595:73: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c:595:78: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 595 | fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); | ~~^ ~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome-write.c: In function ‘genome_write_memory’: genome-write.c:642:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 642 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 643 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:642:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 642 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 643 | accession,startposition,endposition,fileroot); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:645:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 645 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 646 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c:645:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 645 | fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n", | ~~^ | | | long unsigned int | %llu 646 | accession,startposition+1U,endposition+1U,fileroot); | ~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} genome-write.c: In function ‘Genome_write’: genome-write.c:787:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 787 | fprintf(stderr,"Genome length is %lu nt\n",genomelength); | ~~^ ~~~~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-genome_hr.o -MD -MP -MF .deps/gmapindex-genome_hr.Tpo -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmapindex-genome_hr.Tpo .deps/gmapindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c mv -f .deps/gmapindex-bitpack64-write.Tpo .deps/gmapindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-indexdb-write.o -MD -MP -MF .deps/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘check_offsets_from_bitpack’: indexdb-write.c:2494:50: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~^ | | | int | %lld 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘check_offsets_from_gammas’: indexdb-write.c:2726:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2726 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2727 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2737:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2737 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2738 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2760:54: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2760 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2761 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2787:55: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2787 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2788 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2798:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2798 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2799 | oligok,offsets[oligok],*ptr); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘Indexdb_write_offsets’: indexdb-write.c:2888:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2888 | fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2895:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2895 | fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2972:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 2972 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c:3094:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 3094 | fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~ | | | | long unsigned int Oligospace_T {aka long long unsigned int} | %llu indexdb-write.c:3127:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3127 | fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:3171:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3171 | fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_file’: indexdb-write.c:3371:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3371 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_memory’: indexdb-write.c:3601:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3601 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/gmapindex-indexdb-write.Tpo .deps/gmapindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c table.c: In function ‘Table_gc’: table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types] 283 | (*keyfree)(&p->key); | ^~~~~~~ | | | const void ** table.c:283:18: note: expected ‘void **’ but argument is of type ‘const void **’ mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-tableuint.o -MD -MP -MF .deps/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c mv -f .deps/gmapindex-tableuint.Tpo .deps/gmapindex-tableuint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-tableuint8.o -MD -MP -MF .deps/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c mv -f .deps/gmapindex-tableuint8.Tpo .deps/gmapindex-tableuint8.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-chrom.o -MD -MP -MF .deps/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function ‘Segmentpos_print’: segmentpos.c:90:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 90 | fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-saca-k.o -MD -MP -MF .deps/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c mv -f .deps/gmapindex-saca-k.Tpo .deps/gmapindex-saca-k.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-sarray-write.o -MD -MP -MF .deps/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c mv -f .deps/gmapindex-sarray-write.Tpo .deps/gmapindex-sarray-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c gmapindex.c: In function ‘process_sequence_aux’: gmapindex.c:305:35: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 5 has type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wformat=] 305 | nitems = sscanf(Buffer,"%s %s %lu",accession_p,chrpos_string,&universal_coord); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int * Univcoord_T * {aka long long unsigned int *} | %llu gmapindex.c: In function ‘write_chromosome_file’: gmapindex.c:509:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 509 | fprintf(stderr,"Chromosome %s has universal coordinates %lu..%lu\n", | ~~^ | | | long unsigned int | %llu 510 | chr_string,chroffset+1,chroffset+1+chrlength-1); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c:509:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 509 | fprintf(stderr,"Chromosome %s has universal coordinates %lu..%lu\n", | ~~^ | | | long unsigned int | %llu 510 | chr_string,chroffset+1,chroffset+1+chrlength-1); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c:520:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 520 | fprintf(textfp,"%s\t%lu..%lu\t%u", | ~~^ | | | long unsigned int | %llu 521 | chr_string,chroffset+1,chroffset+chrlength,chrlength); | ~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c:520:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 520 | fprintf(textfp,"%s\t%lu..%lu\t%u", | ~~^ | | | long unsigned int | %llu 521 | chr_string,chroffset+1,chroffset+chrlength,chrlength); | ~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c: In function ‘write_contig_file’: gmapindex.c:695:29: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 695 | fprintf(textfp,"%s\t%lu..%lu\t%s:%u..%u\t%u", | ~~^ | | | long unsigned int | %llu 696 | accessions[i],universalpos2+1U,universalpos1, | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c:695:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 695 | fprintf(textfp,"%s\t%lu..%lu\t%s:%u..%u\t%u", | ~~^ | | | long unsigned int | %llu 696 | accessions[i],universalpos2+1U,universalpos1, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c:700:29: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | fprintf(textfp,"%s\t%lu..%lu\t%s:%u..%u\t%u", | ~~^ | | | long unsigned int | %llu 701 | accessions[i],universalpos1+1U,universalpos2, | ~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c:700:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | fprintf(textfp,"%s\t%lu..%lu\t%s:%u..%u\t%u", | ~~^ | | | long unsigned int | %llu 701 | accessions[i],universalpos1+1U,universalpos2, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} gmapindex.c: In function ‘main’: gmapindex.c:1061:46: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1061 | fprintf(stderr,"Total genomic length = %lu bp\n",totalnts); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-except.o -MD -MP -MF .deps/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_store-except.Tpo .deps/iit_store-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-assert.o -MD -MP -MF .deps/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_store-assert.Tpo .deps/iit_store-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-mem.o -MD -MP -MF .deps/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_store-mem.Tpo .deps/iit_store-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-intlist.o -MD -MP -MF .deps/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_store-intlist.Tpo .deps/iit_store-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-list.o -MD -MP -MF .deps/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_store-list.Tpo .deps/iit_store-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-littleendian.o -MD -MP -MF .deps/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-bigendian.o -MD -MP -MF .deps/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-univinterval.o -MD -MP -MF .deps/iit_store-univinterval.Tpo -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/iit_store-univinterval.Tpo .deps/iit_store-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-interval.o -MD -MP -MF .deps/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_store-interval.Tpo .deps/iit_store-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-uintlist.o -MD -MP -MF .deps/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_store-uintlist.Tpo .deps/iit_store-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-stopwatch.o -MD -MP -MF .deps/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_store-stopwatch.Tpo .deps/iit_store-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-access.o -MD -MP -MF .deps/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-iit-write-univ.o -MD -MP -MF .deps/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c mv -f .deps/iit_store-iit-write-univ.Tpo .deps/iit_store-iit-write-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-iit-write.o -MD -MP -MF .deps/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c mv -f .deps/iit_store-iit-write.Tpo .deps/iit_store-iit-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-tableint.o -MD -MP -MF .deps/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c mv -f .deps/iit_store-tableint.Tpo .deps/iit_store-tableint.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-table.o -MD -MP -MF .deps/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c table.c: In function ‘Table_gc’: table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types] 283 | (*keyfree)(&p->key); | ^~~~~~~ | | | const void ** table.c:283:18: note: expected ‘void **’ but argument is of type ‘const void **’ mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-chrom.o -MD -MP -MF .deps/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/iit_store-chrom.Tpo .deps/iit_store-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-getopt.o -MD -MP -MF .deps/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/iit_store-getopt.Tpo .deps/iit_store-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-getopt1.o -MD -MP -MF .deps/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/iit_store-getopt1.Tpo .deps/iit_store-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_store-iit_store.o -MD -MP -MF .deps/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c iit_store.c: In function ‘scan_header_spaces’: iit_store.c:371:35: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 4 has type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wformat=] 371 | nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end)); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T * {aka long long unsigned int *} | long unsigned int * | %llu iit_store.c:371:39: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 5 has type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wformat=] 371 | nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end)); | ~~^ ~~~~~~~ | | | | long unsigned int * Univcoord_T * {aka long long unsigned int *} | %llu iit_store.c: In function ‘parse_fasta’: iit_store.c:596:41: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 596 | fprintf(stderr,"Maximum coordinate: %lu\n",*max_coordinate); | ~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit_store.c:597:41: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 597 | fprintf(stderr,"Total label length: %lu + %d separators\n",*label_totallength,nentries); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit_store.c:598:46: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 598 | fprintf(stderr,"Total annotation length: %lu + %d separators\n",*annot_totallength,nentries); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit_store.c: In function ‘parse_fieldlist’: iit_store.c:447:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 447 | fgets(&(Buffer[1]),LINELENGTH-1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit_store.c: In function ‘parse_fasta’: iit_store.c:482:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 482 | fgets(Buffer,LINELENGTH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit_store.c:485:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 485 | fgets(&(Buffer[1]),LINELENGTH-1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-except.o -MD -MP -MF .deps/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_get-except.Tpo .deps/iit_get-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-assert.o -MD -MP -MF .deps/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_get-assert.Tpo .deps/iit_get-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-mem.o -MD -MP -MF .deps/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_get-mem.Tpo .deps/iit_get-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-intlist.o -MD -MP -MF .deps/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_get-intlist.Tpo .deps/iit_get-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-list.o -MD -MP -MF .deps/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_get-list.Tpo .deps/iit_get-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-littleendian.o -MD -MP -MF .deps/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-bigendian.o -MD -MP -MF .deps/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-univinterval.o -MD -MP -MF .deps/iit_get-univinterval.Tpo -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/iit_get-univinterval.Tpo .deps/iit_get-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-interval.o -MD -MP -MF .deps/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_get-interval.Tpo .deps/iit_get-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-uintlist.o -MD -MP -MF .deps/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_get-uintlist.Tpo .deps/iit_get-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-stopwatch.o -MD -MP -MF .deps/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_get-stopwatch.Tpo .deps/iit_get-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-access.o -MD -MP -MF .deps/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-iit-read-univ.o -MD -MP -MF .deps/iit_get-iit-read-univ.Tpo -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/iit_get-iit-read-univ.Tpo .deps/iit_get-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-iit-read.o -MD -MP -MF .deps/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-parserange.o -MD -MP -MF .deps/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c: In function ‘translate_chromosomepos_universal’: parserange.c:186:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 186 | fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", | ~~^ | | | long unsigned int | %llu 187 | Univinterval_low(interval),left,*genomicstart); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} parserange.c:186:31: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 186 | fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", | ~~^ | | | long unsigned int | %llu 187 | Univinterval_low(interval),left,*genomicstart); | ~~~~ | | | Univcoord_T {aka long long unsigned int} parserange.c:186:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 186 | fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", | ~~^ | | | long unsigned int | %llu 187 | Univinterval_low(interval),left,*genomicstart); | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-getopt.o -MD -MP -MF .deps/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/iit_get-getopt.Tpo .deps/iit_get-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-getopt1.o -MD -MP -MF .deps/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/iit_get-getopt1.Tpo .deps/iit_get-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_get-iit_get.o -MD -MP -MF .deps/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c iit_get.c: In function ‘print_interval_univ’: iit_get.c:619:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 619 | printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit_get.c:619:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 619 | printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-except.o -MD -MP -MF .deps/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_dump-except.Tpo .deps/iit_dump-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-assert.o -MD -MP -MF .deps/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_dump-assert.Tpo .deps/iit_dump-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-mem.o -MD -MP -MF .deps/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_dump-mem.Tpo .deps/iit_dump-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-littleendian.o -MD -MP -MF .deps/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-bigendian.o -MD -MP -MF .deps/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-intlist.o -MD -MP -MF .deps/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_dump-intlist.Tpo .deps/iit_dump-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-list.o -MD -MP -MF .deps/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_dump-list.Tpo .deps/iit_dump-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-univinterval.o -MD -MP -MF .deps/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/iit_dump-univinterval.Tpo .deps/iit_dump-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-interval.o -MD -MP -MF .deps/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_dump-interval.Tpo .deps/iit_dump-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-uintlist.o -MD -MP -MF .deps/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_dump-uintlist.Tpo .deps/iit_dump-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-stopwatch.o -MD -MP -MF .deps/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_dump-stopwatch.Tpo .deps/iit_dump-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-access.o -MD -MP -MF .deps/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-iit-read-univ.o -MD -MP -MF .deps/iit_dump-iit-read-univ.Tpo -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/iit_dump-iit-read-univ.Tpo .deps/iit_dump-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-iit-read.o -MD -MP -MF .deps/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-getopt.o -MD -MP -MF .deps/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/iit_dump-getopt.Tpo .deps/iit_dump-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-getopt1.o -MD -MP -MF .deps/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/iit_dump-getopt1.Tpo .deps/iit_dump-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O3 -MT iit_dump-iit_dump.o -MD -MP -MF .deps/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c mv -f .deps/iit_dump-iit_dump.Tpo .deps/iit_dump-iit_dump.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-except.o -MD -MP -MF .deps/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gsnap-except.Tpo .deps/gsnap-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-assert.o -MD -MP -MF .deps/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gsnap-assert.Tpo .deps/gsnap-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mem.o -MD -MP -MF .deps/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gsnap-mem.Tpo .deps/gsnap-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intlist.o -MD -MP -MF .deps/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gsnap-intlist.Tpo .deps/gsnap-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-list.o -MD -MP -MF .deps/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gsnap-list.Tpo .deps/gsnap-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-littleendian.o -MD -MP -MF .deps/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bigendian.o -MD -MP -MF .deps/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-univinterval.o -MD -MP -MF .deps/gsnap-univinterval.Tpo -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u mv -f .deps/gsnap-univinterval.Tpo .deps/gsnap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-interval.o -MD -MP -MF .deps/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gsnap-interval.Tpo .deps/gsnap-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-uintlist.o -MD -MP -MF .deps/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gsnap-uintlist.Tpo .deps/gsnap-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stopwatch.o -MD -MP -MF .deps/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gsnap-stopwatch.Tpo .deps/gsnap-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-access.o -MD -MP -MF .deps/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read-univ.o -MD -MP -MF .deps/gsnap-iit-read-univ.Tpo -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gsnap-iit-read-univ.Tpo .deps/gsnap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read.o -MD -MP -MF .deps/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-md5.o -MD -MP -MF .deps/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gsnap-md5.Tpo .deps/gsnap-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bzip2.o -MD -MP -MF .deps/gsnap-bzip2.Tpo -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gsnap-bzip2.Tpo .deps/gsnap-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sequence.o -MD -MP -MF .deps/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gsnap-sequence.Tpo .deps/gsnap-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-reader.o -MD -MP -MF .deps/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gsnap-reader.Tpo .deps/gsnap-reader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genomicpos.o -MD -MP -MF .deps/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gsnap-genomicpos.Tpo .deps/gsnap-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-compress.o -MD -MP -MF .deps/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gsnap-compress.Tpo .deps/gsnap-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome.o -MD -MP -MF .deps/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_hr.o -MD -MP -MF .deps/gsnap-genome_hr.Tpo -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gsnap-genome_hr.Tpo .deps/gsnap-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_sites.o -MD -MP -MF .deps/gsnap-genome_sites.Tpo -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gsnap-genome_sites.Tpo .deps/gsnap-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-read.o -MD -MP -MF .deps/gsnap-bitpack64-read.Tpo -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gsnap-bitpack64-read.Tpo .deps/gsnap-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb.o -MD -MP -MF .deps/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb_hr.o -MD -MP -MF .deps/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 593 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligo.o -MD -MP -MF .deps/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gsnap-oligo.Tpo .deps/gsnap-oligo.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrom.o -MD -MP -MF .deps/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gsnap-chrom.Tpo .deps/gsnap-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-segmentpos.o -MD -MP -MF .deps/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gsnap-segmentpos.Tpo .deps/gsnap-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrnum.o -MD -MP -MF .deps/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gsnap-chrnum.Tpo .deps/gsnap-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent_hr.o -MD -MP -MF .deps/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gsnap-maxent_hr.Tpo .deps/gsnap-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samprint.o -MD -MP -MF .deps/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c samprint.c: In function ‘compute_cigar’: samprint.c:989:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 989 | sprintf(token,"%dH",cliplength); | ^ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:996:19: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 996 | sprintf(token,"%d%c",matchlength,type); | ^~ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:1007:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 1007 | sprintf(token,"%dH",cliplength); | ^ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:947:19: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 947 | sprintf(token,"%d%c",matchlength,type); | ^~ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:959:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 959 | sprintf(token,"%dH",cliplength); | ^ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnap-samprint.Tpo .deps/gsnap-samprint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mapq.o -MD -MP -MF .deps/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/gsnap-mapq.Tpo .deps/gsnap-mapq.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-shortread.o -MD -MP -MF .deps/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/gsnap-shortread.Tpo .deps/gsnap-shortread.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-substring.o -MD -MP -MF .deps/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/gsnap-substring.Tpo .deps/gsnap-substring.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3hr.o -MD -MP -MF .deps/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/gsnap-stage3hr.Tpo .deps/gsnap-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-goby.o -MD -MP -MF .deps/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c mv -f .deps/gsnap-goby.Tpo .deps/gsnap-goby.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-spanningelt.o -MD -MP -MF .deps/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/gsnap-spanningelt.Tpo .deps/gsnap-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cmet.o -MD -MP -MF .deps/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gsnap-cmet.Tpo .deps/gsnap-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-atoi.o -MD -MP -MF .deps/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gsnap-atoi.Tpo .deps/gsnap-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent.o -MD -MP -MF .deps/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gsnap-maxent.Tpo .deps/gsnap-maxent.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pair.o -MD -MP -MF .deps/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:2419:20: warning: ‘%u’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~ pair.c:2419:18: note: directive argument in the range [1, 2147483647] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2478:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2478 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2478:18: note: directive argument in the range [1, 2147483647] 2478 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2474:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2474 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2474:18: note: directive argument in the range [1, 2147483647] 2474 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2455:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2455 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2455:20: note: directive argument in the range [1, 2147483647] 2455 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2451:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2451 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2451:20: note: directive argument in the range [1, 2147483647] 2451 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2444:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2444 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2444:20: note: directive argument in the range [1, 2147483647] 2444 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2439:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2439 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2439:20: note: directive argument in the range [1, 2147483647] 2439 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2389:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2389 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2389:20: note: directive argument in the range [1, 2147483647] 2389 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2386:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2386 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2386:20: note: directive argument in the range [1, 2147483647] 2386 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2383:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2383 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2383:20: note: directive argument in the range [1, 2147483647] 2383 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2537:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2537 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2537:21: note: directive argument in the range [1, 2147483647] 2537 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2534:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2534 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2534:21: note: directive argument in the range [1, 2147483647] 2534 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2531:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2531 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2531:21: note: directive argument in the range [1, 2147483647] 2531 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘compute_cigar.constprop’: pair.c:4587:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4587 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4591:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4591 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4689:21: warning: ‘N’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4689 | sprintf(token,"%uN",genome_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4706:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4706 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4754:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4754 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4750:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4750 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4736:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4736 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4732:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4732 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4724:23: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4719:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4719 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4625:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4625 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4622:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4622 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4619:21: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4619 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4783:22: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4783 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4780:22: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4780 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4777:22: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4777 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4806:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4806 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4810:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4810 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4800:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4800 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_sam’: pair.c:5195:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5195 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5145:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5145 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5218:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5218 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5086:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5086 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5046:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5046 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5111:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5111 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_compressed’: pair.c:7169:19: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7169 | sprintf(token,"%d:%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7162:19: warning: ‘x’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7162 | sprintf(token,"%dx%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7152:21: warning: ‘v’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7152 | sprintf(token,"%dv",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7150:21: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7150 | sprintf(token,"%d^%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7081:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7081 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7078:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7078 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7075:21: warning: ‘[’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7075 | sprintf(token,"%d[",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7073:21: warning: ‘]’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7073 | sprintf(token,"%d]",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7070:21: warning: ‘(’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7070 | sprintf(token,"%d(",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7068:21: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7068 | sprintf(token,"%d)",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7066:21: warning: ‘=’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7066 | sprintf(token,"%d=",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7063:21: warning: ‘<’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7063 | sprintf(token,"%d<",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7061:21: warning: ‘>’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7061 | sprintf(token,"%d>",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7206:20: warning: ‘*’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7206 | sprintf(token,"%d*",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnap-pair.Tpo .deps/gsnap-pair.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pairpool.o -MD -MP -MF .deps/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gsnap-pairpool.Tpo .deps/gsnap-pairpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diag.o -MD -MP -MF .deps/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gsnap-diag.Tpo .deps/gsnap-diag.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diagpool.o -MD -MP -MF .deps/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gsnap-diagpool.Tpo .deps/gsnap-diagpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-orderstat.o -MD -MP -MF .deps/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gsnap-orderstat.Tpo .deps/gsnap-orderstat.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligoindex_hr.o -MD -MP -MF .deps/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gsnap-oligoindex_hr.Tpo .deps/gsnap-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cellpool.o -MD -MP -MF .deps/gsnap-cellpool.Tpo -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gsnap-cellpool.Tpo .deps/gsnap-cellpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage2.o -MD -MP -MF .deps/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gsnap-stage2.Tpo .deps/gsnap-stage2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intron.o -MD -MP -MF .deps/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gsnap-intron.Tpo .deps/gsnap-intron.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-boyer-moore.o -MD -MP -MF .deps/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gsnap-boyer-moore.Tpo .deps/gsnap-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-changepoint.o -MD -MP -MF .deps/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gsnap-changepoint.Tpo .deps/gsnap-changepoint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pbinom.o -MD -MP -MF .deps/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gsnap-pbinom.Tpo .deps/gsnap-pbinom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-dynprog.o -MD -MP -MF .deps/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gsnap-dynprog.Tpo .deps/gsnap-dynprog.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gbuffer.o -MD -MP -MF .deps/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gsnap-gbuffer.Tpo .deps/gsnap-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-translation.o -MD -MP -MF .deps/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gsnap-translation.Tpo .deps/gsnap-translation.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-doublelist.o -MD -MP -MF .deps/gsnap-doublelist.Tpo -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gsnap-doublelist.Tpo .deps/gsnap-doublelist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-smooth.o -MD -MP -MF .deps/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gsnap-smooth.Tpo .deps/gsnap-smooth.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chimera.o -MD -MP -MF .deps/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gsnap-chimera.Tpo .deps/gsnap-chimera.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3.o -MD -MP -MF .deps/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gsnap-stage3.Tpo .deps/gsnap-stage3.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicestringpool.o -MD -MP -MF .deps/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gsnap-splicestringpool.Tpo .deps/gsnap-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie_build.o -MD -MP -MF .deps/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gsnap-splicetrie_build.Tpo .deps/gsnap-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie.o -MD -MP -MF .deps/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gsnap-splicetrie.Tpo .deps/gsnap-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splice.o -MD -MP -MF .deps/gsnap-splice.Tpo -c -o gsnap-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/gsnap-splice.Tpo .deps/gsnap-splice.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indel.o -MD -MP -MF .deps/gsnap-indel.Tpo -c -o gsnap-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/gsnap-indel.Tpo .deps/gsnap-indel.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-access.o -MD -MP -MF .deps/gsnap-bitpack64-access.Tpo -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gsnap-bitpack64-access.Tpo .deps/gsnap-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sarray-read.o -MD -MP -MF .deps/gsnap-sarray-read.Tpo -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c mv -f .deps/gsnap-sarray-read.Tpo .deps/gsnap-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage1hr.o -MD -MP -MF .deps/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/gsnap-stage1hr.Tpo .deps/gsnap-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-request.o -MD -MP -MF .deps/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gsnap-request.Tpo .deps/gsnap-request.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-resulthr.o -MD -MP -MF .deps/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/gsnap-resulthr.Tpo .deps/gsnap-resulthr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-inbuffer.o -MD -MP -MF .deps/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gsnap-inbuffer.Tpo .deps/gsnap-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samheader.o -MD -MP -MF .deps/gsnap-samheader.Tpo -c -o gsnap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gsnap-samheader.Tpo .deps/gsnap-samheader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-outbuffer.o -MD -MP -MF .deps/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gsnap-outbuffer.Tpo .deps/gsnap-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-datadir.o -MD -MP -MF .deps/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gsnap-datadir.Tpo .deps/gsnap-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt.o -MD -MP -MF .deps/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gsnap-getopt.Tpo .deps/gsnap-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt1.o -MD -MP -MF .deps/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gsnap-getopt1.Tpo .deps/gsnap-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gsnap.o -MD -MP -MF .deps/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c mv -f .deps/gsnap-gsnap.Tpo .deps/gsnap-gsnap.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-except.o -MD -MP -MF .deps/gsnapl-except.Tpo -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gsnapl-except.Tpo .deps/gsnapl-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-assert.o -MD -MP -MF .deps/gsnapl-assert.Tpo -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gsnapl-assert.Tpo .deps/gsnapl-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mem.o -MD -MP -MF .deps/gsnapl-mem.Tpo -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gsnapl-mem.Tpo .deps/gsnapl-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intlist.o -MD -MP -MF .deps/gsnapl-intlist.Tpo -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gsnapl-intlist.Tpo .deps/gsnapl-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-list.o -MD -MP -MF .deps/gsnapl-list.Tpo -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gsnapl-list.Tpo .deps/gsnapl-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-littleendian.o -MD -MP -MF .deps/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/gsnapl-littleendian.Tpo .deps/gsnapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bigendian.o -MD -MP -MF .deps/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/gsnapl-bigendian.Tpo .deps/gsnapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-univinterval.o -MD -MP -MF .deps/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gsnapl-univinterval.Tpo .deps/gsnapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-interval.o -MD -MP -MF .deps/gsnapl-interval.Tpo -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gsnapl-interval.Tpo .deps/gsnapl-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uintlist.o -MD -MP -MF .deps/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gsnapl-uintlist.Tpo .deps/gsnapl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uint8list.o -MD -MP -MF .deps/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:202:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 202 | sprintf(Buffer,"%u,",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu uint8list.c:205:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 205 | sprintf(Buffer,"%u",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu uint8list.c:211:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 211 | sprintf(Buffer,"%u,",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu uint8list.c:214:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 214 | sprintf(Buffer,"%u",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu mv -f .deps/gsnapl-uint8list.Tpo .deps/gsnapl-uint8list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stopwatch.o -MD -MP -MF .deps/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gsnapl-stopwatch.Tpo .deps/gsnapl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-access.o -MD -MP -MF .deps/gsnapl-access.Tpo -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/gsnapl-access.Tpo .deps/gsnapl-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read-univ.o -MD -MP -MF .deps/gsnapl-iit-read-univ.Tpo -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gsnapl-iit-read-univ.Tpo .deps/gsnapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read.o -MD -MP -MF .deps/gsnapl-iit-read.Tpo -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/gsnapl-iit-read.Tpo .deps/gsnapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-md5.o -MD -MP -MF .deps/gsnapl-md5.Tpo -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gsnapl-md5.Tpo .deps/gsnapl-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bzip2.o -MD -MP -MF .deps/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gsnapl-bzip2.Tpo .deps/gsnapl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sequence.o -MD -MP -MF .deps/gsnapl-sequence.Tpo -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gsnapl-sequence.Tpo .deps/gsnapl-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-reader.o -MD -MP -MF .deps/gsnapl-reader.Tpo -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gsnapl-reader.Tpo .deps/gsnapl-reader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genomicpos.o -MD -MP -MF .deps/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gsnapl-genomicpos.Tpo .deps/gsnapl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-compress.o -MD -MP -MF .deps/gsnapl-compress.Tpo -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gsnapl-compress.Tpo .deps/gsnapl-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome.o -MD -MP -MF .deps/gsnapl-genome.Tpo -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnapl-genome.Tpo .deps/gsnapl-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_hr.o -MD -MP -MF .deps/gsnapl-genome_hr.Tpo -c -o gsnapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gsnapl-genome_hr.Tpo .deps/gsnapl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_sites.o -MD -MP -MF .deps/gsnapl-genome_sites.Tpo -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome_sites.c: In function ‘Genome_print_blocks’: genome_sites.c:24729:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24729 | printf("%u\t",startblock/3*32U); | ~^ ~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu genome_sites.c:24744:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24744 | printf("%u\t",ptr/3*32U); | ~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | unsigned int | %llu genome_sites.c:24751:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24751 | printf("%u\t",(endblock+3)/3*32U); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gsnapl-genome_sites.Tpo .deps/gsnapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-read.o -MD -MP -MF .deps/gsnapl-bitpack64-read.Tpo -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gsnapl-bitpack64-read.Tpo .deps/gsnapl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb.o -MD -MP -MF .deps/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnapl-indexdb.Tpo .deps/gsnapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb_hr.o -MD -MP -MF .deps/gsnapl-indexdb_hr.Tpo -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘Compoundpos_dump’: indexdb_hr.c:1008:31: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1008 | printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu indexdb_hr.c: In function ‘heap_even_dump’: indexdb_hr.c:1232:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1232 | printf("#%d--%d:%u ",i,batch->nentries,batch->position); | ~^ ~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 593 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnapl-indexdb_hr.Tpo .deps/gsnapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligo.o -MD -MP -MF .deps/gsnapl-oligo.Tpo -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gsnapl-oligo.Tpo .deps/gsnapl-oligo.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrom.o -MD -MP -MF .deps/gsnapl-chrom.Tpo -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gsnapl-chrom.Tpo .deps/gsnapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-segmentpos.o -MD -MP -MF .deps/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function ‘Segmentpos_print’: segmentpos.c:90:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 90 | fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gsnapl-segmentpos.Tpo .deps/gsnapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrnum.o -MD -MP -MF .deps/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gsnapl-chrnum.Tpo .deps/gsnapl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent_hr.o -MD -MP -MF .deps/gsnapl-maxent_hr.Tpo -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gsnapl-maxent_hr.Tpo .deps/gsnapl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samprint.o -MD -MP -MF .deps/gsnapl-samprint.Tpo -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c samprint.c: In function ‘compute_cigar’: samprint.c:989:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 989 | sprintf(token,"%dH",cliplength); | ^ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:996:19: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 996 | sprintf(token,"%d%c",matchlength,type); | ^~ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:1007:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 1007 | sprintf(token,"%dH",cliplength); | ^ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:947:19: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 947 | sprintf(token,"%d%c",matchlength,type); | ^~ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samprint.c:959:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 959 | sprintf(token,"%dH",cliplength); | ^ In file included from /usr/include/stdio.h:867, from samprint.h:5, from samprint.c:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnapl-samprint.Tpo .deps/gsnapl-samprint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mapq.o -MD -MP -MF .deps/gsnapl-mapq.Tpo -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/gsnapl-mapq.Tpo .deps/gsnapl-mapq.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-shortread.o -MD -MP -MF .deps/gsnapl-shortread.Tpo -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/gsnapl-shortread.Tpo .deps/gsnapl-shortread.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-substring.o -MD -MP -MF .deps/gsnapl-substring.Tpo -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c: In function ‘Substring_print_ends’: substring.c:1005:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1005 | printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); | ~^ ~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:1005:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1005 | printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); | ~^ ~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c: In function ‘print_coordinates’: substring.c:3536:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3536 | fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3536:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3536 | fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U, | ~^ | | | unsigned int | %llu 3537 | substring->alignend_trim - substring->chroffset); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} substring.c:3539:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3539 | fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3539:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3539 | fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset, | ~^ | | | unsigned int | %llu 3540 | substring->alignstart_trim - substring->chroffset + 1U); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} substring.c:3544:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3544 | fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3544:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3544 | fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset, | ~^ | | | unsigned int | %llu 3545 | substring->alignend_trim - substring->chroffset + 1U); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} substring.c:3547:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3547 | fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3547:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3547 | fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U, | ~^ | | | unsigned int | %llu 3548 | substring->alignstart_trim - substring->chroffset); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/gsnapl-substring.Tpo .deps/gsnapl-substring.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3hr.o -MD -MP -MF .deps/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/gsnapl-stage3hr.Tpo .deps/gsnapl-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-goby.o -MD -MP -MF .deps/gsnapl-goby.Tpo -c -o gsnapl-goby.o `test -f 'goby.c' || echo './'`goby.c mv -f .deps/gsnapl-goby.Tpo .deps/gsnapl-goby.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-spanningelt.o -MD -MP -MF .deps/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/gsnapl-spanningelt.Tpo .deps/gsnapl-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cmet.o -MD -MP -MF .deps/gsnapl-cmet.Tpo -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gsnapl-cmet.Tpo .deps/gsnapl-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-atoi.o -MD -MP -MF .deps/gsnapl-atoi.Tpo -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gsnapl-atoi.Tpo .deps/gsnapl-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent.o -MD -MP -MF .deps/gsnapl-maxent.Tpo -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gsnapl-maxent.Tpo .deps/gsnapl-maxent.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pair.o -MD -MP -MF .deps/gsnapl-pair.Tpo -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_genomic_sequence’: pair.c:546:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 546 | sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘print_genomicalt_sequence’: pair.c:573:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 573 | sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘compute_margin’: pair.c:600:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 600 | sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c:607:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 607 | sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘Pair_print_coordinates’: pair.c:1272:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1272 | fprintf(fp,"%u %u %c",this->genomepos + ONEBASEDP, | ~^ | | | unsigned int | %llu pair.c:1276:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1276 | fprintf(fp,"%s:%u %u %c",chrstring, | ~^ | | | unsigned int | %llu pair.c: In function ‘Pair_print_exonsummary’: pair.c:1790:19: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1790 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1790:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1790 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1799:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1799 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1799:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1799 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1913:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1913 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1913:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1913 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1922:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1922 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1922:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1922 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c: In function ‘Pair_print_compressed’: pair.c:6986:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6986 | fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c:6986:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6986 | fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:2419:20: warning: ‘%u’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~ pair.c:2419:18: note: directive argument in the range [1, 2147483647] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2478:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2478 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2478:18: note: directive argument in the range [1, 2147483647] 2478 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2474:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2474 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2474:18: note: directive argument in the range [1, 2147483647] 2474 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2455:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2455 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2455:20: note: directive argument in the range [1, 2147483647] 2455 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2451:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2451 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2451:20: note: directive argument in the range [1, 2147483647] 2451 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2444:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2444 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2444:20: note: directive argument in the range [1, 2147483647] 2444 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2439:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2439 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2439:20: note: directive argument in the range [1, 2147483647] 2439 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2389:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2389 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2389:20: note: directive argument in the range [1, 2147483647] 2389 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2386:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2386 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2386:20: note: directive argument in the range [1, 2147483647] 2386 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2383:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2383 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2383:20: note: directive argument in the range [1, 2147483647] 2383 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2537:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2537 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2537:21: note: directive argument in the range [1, 2147483647] 2537 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2534:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2534 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2534:21: note: directive argument in the range [1, 2147483647] 2534 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2531:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2531 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2531:21: note: directive argument in the range [1, 2147483647] 2531 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘compute_cigar.constprop’: pair.c:4587:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4587 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4591:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4591 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4689:21: warning: ‘N’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4689 | sprintf(token,"%uN",genome_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4706:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4706 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4754:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4754 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4750:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4750 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4736:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4736 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4732:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4732 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4724:23: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4719:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4719 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4625:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4625 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4622:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4622 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4619:21: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4619 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4783:22: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4783 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4780:22: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4780 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4777:22: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4777 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4806:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4806 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4810:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4810 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4800:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4800 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_sam’: pair.c:5195:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5195 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5145:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5145 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5218:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5218 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5086:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5086 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5046:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5046 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5111:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5111 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_compressed’: pair.c:7169:19: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7169 | sprintf(token,"%d:%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7162:19: warning: ‘x’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7162 | sprintf(token,"%dx%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7152:21: warning: ‘v’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7152 | sprintf(token,"%dv",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7150:21: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7150 | sprintf(token,"%d^%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7081:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7081 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7078:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7078 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7075:21: warning: ‘[’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7075 | sprintf(token,"%d[",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7073:21: warning: ‘]’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7073 | sprintf(token,"%d]",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7070:21: warning: ‘(’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7070 | sprintf(token,"%d(",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7068:21: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7068 | sprintf(token,"%d)",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7066:21: warning: ‘=’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7066 | sprintf(token,"%d=",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7063:21: warning: ‘<’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7063 | sprintf(token,"%d<",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7061:21: warning: ‘>’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7061 | sprintf(token,"%d>",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7206:20: warning: ‘*’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7206 | sprintf(token,"%d*",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gsnapl-pair.Tpo .deps/gsnapl-pair.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pairpool.o -MD -MP -MF .deps/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gsnapl-pairpool.Tpo .deps/gsnapl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diag.o -MD -MP -MF .deps/gsnapl-diag.Tpo -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gsnapl-diag.Tpo .deps/gsnapl-diag.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diagpool.o -MD -MP -MF .deps/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gsnapl-diagpool.Tpo .deps/gsnapl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-orderstat.o -MD -MP -MF .deps/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gsnapl-orderstat.Tpo .deps/gsnapl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligoindex_hr.o -MD -MP -MF .deps/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gsnapl-oligoindex_hr.Tpo .deps/gsnapl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cellpool.o -MD -MP -MF .deps/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gsnapl-cellpool.Tpo .deps/gsnapl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage2.o -MD -MP -MF .deps/gsnapl-stage2.Tpo -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gsnapl-stage2.Tpo .deps/gsnapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intron.o -MD -MP -MF .deps/gsnapl-intron.Tpo -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gsnapl-intron.Tpo .deps/gsnapl-intron.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-boyer-moore.o -MD -MP -MF .deps/gsnapl-boyer-moore.Tpo -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gsnapl-boyer-moore.Tpo .deps/gsnapl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-changepoint.o -MD -MP -MF .deps/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gsnapl-changepoint.Tpo .deps/gsnapl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pbinom.o -MD -MP -MF .deps/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gsnapl-pbinom.Tpo .deps/gsnapl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-dynprog.o -MD -MP -MF .deps/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gsnapl-dynprog.Tpo .deps/gsnapl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gbuffer.o -MD -MP -MF .deps/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gsnapl-gbuffer.Tpo .deps/gsnapl-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-translation.o -MD -MP -MF .deps/gsnapl-translation.Tpo -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gsnapl-translation.Tpo .deps/gsnapl-translation.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-doublelist.o -MD -MP -MF .deps/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gsnapl-doublelist.Tpo .deps/gsnapl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-smooth.o -MD -MP -MF .deps/gsnapl-smooth.Tpo -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gsnapl-smooth.Tpo .deps/gsnapl-smooth.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chimera.o -MD -MP -MF .deps/gsnapl-chimera.Tpo -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gsnapl-chimera.Tpo .deps/gsnapl-chimera.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3.o -MD -MP -MF .deps/gsnapl-stage3.Tpo -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gsnapl-stage3.Tpo .deps/gsnapl-stage3.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicestringpool.o -MD -MP -MF .deps/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gsnapl-splicestringpool.Tpo .deps/gsnapl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie_build.o -MD -MP -MF .deps/gsnapl-splicetrie_build.Tpo -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function ‘Splicetrie_dump’: splicetrie_build.c:132:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 132 | printf("%d %u",(int) leaf,position); | ~^ ~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu splicetrie_build.c:146:19: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 146 | printf("%d %u",(int) leaf,position); | ~^ ~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/gsnapl-splicetrie_build.Tpo .deps/gsnapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie.o -MD -MP -MF .deps/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gsnapl-splicetrie.Tpo .deps/gsnapl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splice.o -MD -MP -MF .deps/gsnapl-splice.Tpo -c -o gsnapl-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/gsnapl-splice.Tpo .deps/gsnapl-splice.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indel.o -MD -MP -MF .deps/gsnapl-indel.Tpo -c -o gsnapl-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/gsnapl-indel.Tpo .deps/gsnapl-indel.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-access.o -MD -MP -MF .deps/gsnapl-bitpack64-access.Tpo -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gsnapl-bitpack64-access.Tpo .deps/gsnapl-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sarray-read.o -MD -MP -MF .deps/gsnapl-sarray-read.Tpo -c -o gsnapl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c sarray-read.c: In function ‘Sarray_new’: sarray-read.c:302:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 302 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:368:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 368 | new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2, | ^ sarray-read.c:434:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 434 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T), | ^ sarray-read.c:526:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 526 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:653:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 653 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len, | ^ sarray-read.c: In function ‘Elt_dump_list’: sarray-read.c:1667:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1667 | printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]); | ~^ ~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu sarray-read.c: In function ‘Elt_dump’: sarray-read.c:1682:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1682 | printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]); | ~^ ~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu sarray-read.c: In function ‘collect_elt_matches’: sarray-read.c:2170:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2170 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:2442:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2442:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2456:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2456 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2499:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2499:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2513:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2513 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2643:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2643:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2656:36: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2656 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2699:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2699:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2712:12: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2712 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2752:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2752 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:3024:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3024:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3038:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3038 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3082:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3082:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3096:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3096 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:3217:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3217:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3231:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3231 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3274:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3274:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3288:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3288 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ mv -f .deps/gsnapl-sarray-read.Tpo .deps/gsnapl-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage1hr.o -MD -MP -MF .deps/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c: In function ‘find_singlesplices_plus’: stage1hr.c:6629:54: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6629 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6630 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6629:75: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6629 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6630 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6629:99: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6629 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6630 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:62: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:67: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:101: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 6 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), 6770 | Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:106: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 7 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), 6770 | Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:135: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 9 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu ...... 6771 | segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c: In function ‘find_singlesplices_minus’: stage1hr.c:7145:54: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7145 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7146 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7145:75: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7145 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7146 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7145:99: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7145 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7146 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7284:54: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7284 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7285 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7284:75: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7284 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7285 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7284:99: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7284 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7285 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/gsnapl-stage1hr.Tpo .deps/gsnapl-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-request.o -MD -MP -MF .deps/gsnapl-request.Tpo -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gsnapl-request.Tpo .deps/gsnapl-request.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-resulthr.o -MD -MP -MF .deps/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/gsnapl-resulthr.Tpo .deps/gsnapl-resulthr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-inbuffer.o -MD -MP -MF .deps/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gsnapl-inbuffer.Tpo .deps/gsnapl-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samheader.o -MD -MP -MF .deps/gsnapl-samheader.Tpo -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gsnapl-samheader.Tpo .deps/gsnapl-samheader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-outbuffer.o -MD -MP -MF .deps/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gsnapl-outbuffer.Tpo .deps/gsnapl-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-datadir.o -MD -MP -MF .deps/gsnapl-datadir.Tpo -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gsnapl-datadir.Tpo .deps/gsnapl-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt.o -MD -MP -MF .deps/gsnapl-getopt.Tpo -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gsnapl-getopt.Tpo .deps/gsnapl-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt1.o -MD -MP -MF .deps/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gsnapl-getopt1.Tpo .deps/gsnapl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gsnap.o -MD -MP -MF .deps/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c mv -f .deps/gsnapl-gsnap.Tpo .deps/gsnapl-gsnap.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-except.o -MD -MP -MF .deps/uniqscan-except.Tpo -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/uniqscan-except.Tpo .deps/uniqscan-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-assert.o -MD -MP -MF .deps/uniqscan-assert.Tpo -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/uniqscan-assert.Tpo .deps/uniqscan-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mem.o -MD -MP -MF .deps/uniqscan-mem.Tpo -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/uniqscan-mem.Tpo .deps/uniqscan-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intlist.o -MD -MP -MF .deps/uniqscan-intlist.Tpo -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/uniqscan-intlist.Tpo .deps/uniqscan-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-list.o -MD -MP -MF .deps/uniqscan-list.Tpo -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/uniqscan-list.Tpo .deps/uniqscan-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-littleendian.o -MD -MP -MF .deps/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/uniqscan-littleendian.Tpo .deps/uniqscan-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bigendian.o -MD -MP -MF .deps/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/uniqscan-bigendian.Tpo .deps/uniqscan-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-univinterval.o -MD -MP -MF .deps/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u mv -f .deps/uniqscan-univinterval.Tpo .deps/uniqscan-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-interval.o -MD -MP -MF .deps/uniqscan-interval.Tpo -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/uniqscan-interval.Tpo .deps/uniqscan-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uintlist.o -MD -MP -MF .deps/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/uniqscan-uintlist.Tpo .deps/uniqscan-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stopwatch.o -MD -MP -MF .deps/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/uniqscan-stopwatch.Tpo .deps/uniqscan-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-access.o -MD -MP -MF .deps/uniqscan-access.Tpo -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/uniqscan-access.Tpo .deps/uniqscan-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read-univ.o -MD -MP -MF .deps/uniqscan-iit-read-univ.Tpo -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/uniqscan-iit-read-univ.Tpo .deps/uniqscan-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read.o -MD -MP -MF .deps/uniqscan-iit-read.Tpo -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/uniqscan-iit-read.Tpo .deps/uniqscan-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-md5.o -MD -MP -MF .deps/uniqscan-md5.Tpo -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/uniqscan-md5.Tpo .deps/uniqscan-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bzip2.o -MD -MP -MF .deps/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/uniqscan-bzip2.Tpo .deps/uniqscan-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sequence.o -MD -MP -MF .deps/uniqscan-sequence.Tpo -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/uniqscan-sequence.Tpo .deps/uniqscan-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-reader.o -MD -MP -MF .deps/uniqscan-reader.Tpo -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/uniqscan-reader.Tpo .deps/uniqscan-reader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genomicpos.o -MD -MP -MF .deps/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/uniqscan-genomicpos.Tpo .deps/uniqscan-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-compress.o -MD -MP -MF .deps/uniqscan-compress.Tpo -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/uniqscan-compress.Tpo .deps/uniqscan-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome.o -MD -MP -MF .deps/uniqscan-genome.Tpo -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka unsigned int} | %u genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka unsigned int} | long unsigned int | %u genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscan-genome.Tpo .deps/uniqscan-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_hr.o -MD -MP -MF .deps/uniqscan-genome_hr.Tpo -c -o uniqscan-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/uniqscan-genome_hr.Tpo .deps/uniqscan-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_sites.o -MD -MP -MF .deps/uniqscan-genome_sites.Tpo -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/uniqscan-genome_sites.Tpo .deps/uniqscan-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-read.o -MD -MP -MF .deps/uniqscan-bitpack64-read.Tpo -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/uniqscan-bitpack64-read.Tpo .deps/uniqscan-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb.o -MD -MP -MF .deps/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscan-indexdb.Tpo .deps/uniqscan-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb_hr.o -MD -MP -MF .deps/uniqscan-indexdb_hr.Tpo -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 593 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscan-indexdb_hr.Tpo .deps/uniqscan-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligo.o -MD -MP -MF .deps/uniqscan-oligo.Tpo -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/uniqscan-oligo.Tpo .deps/uniqscan-oligo.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrom.o -MD -MP -MF .deps/uniqscan-chrom.Tpo -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/uniqscan-chrom.Tpo .deps/uniqscan-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-segmentpos.o -MD -MP -MF .deps/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/uniqscan-segmentpos.Tpo .deps/uniqscan-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrnum.o -MD -MP -MF .deps/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/uniqscan-chrnum.Tpo .deps/uniqscan-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent_hr.o -MD -MP -MF .deps/uniqscan-maxent_hr.Tpo -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/uniqscan-maxent_hr.Tpo .deps/uniqscan-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mapq.o -MD -MP -MF .deps/uniqscan-mapq.Tpo -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/uniqscan-mapq.Tpo .deps/uniqscan-mapq.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-shortread.o -MD -MP -MF .deps/uniqscan-shortread.Tpo -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/uniqscan-shortread.Tpo .deps/uniqscan-shortread.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-substring.o -MD -MP -MF .deps/uniqscan-substring.Tpo -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/uniqscan-substring.Tpo .deps/uniqscan-substring.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3hr.o -MD -MP -MF .deps/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/uniqscan-stage3hr.Tpo .deps/uniqscan-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-spanningelt.o -MD -MP -MF .deps/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/uniqscan-spanningelt.Tpo .deps/uniqscan-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cmet.o -MD -MP -MF .deps/uniqscan-cmet.Tpo -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/uniqscan-cmet.Tpo .deps/uniqscan-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-atoi.o -MD -MP -MF .deps/uniqscan-atoi.Tpo -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/uniqscan-atoi.Tpo .deps/uniqscan-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent.o -MD -MP -MF .deps/uniqscan-maxent.Tpo -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/uniqscan-maxent.Tpo .deps/uniqscan-maxent.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pair.o -MD -MP -MF .deps/uniqscan-pair.Tpo -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:2419:20: warning: ‘%u’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~ pair.c:2419:18: note: directive argument in the range [1, 2147483647] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2478:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2478 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2478:18: note: directive argument in the range [1, 2147483647] 2478 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2474:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2474 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2474:18: note: directive argument in the range [1, 2147483647] 2474 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2455:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2455 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2455:20: note: directive argument in the range [1, 2147483647] 2455 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2451:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2451 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2451:20: note: directive argument in the range [1, 2147483647] 2451 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2444:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2444 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2444:20: note: directive argument in the range [1, 2147483647] 2444 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2439:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2439 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2439:20: note: directive argument in the range [1, 2147483647] 2439 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2389:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2389 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2389:20: note: directive argument in the range [1, 2147483647] 2389 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2386:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2386 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2386:20: note: directive argument in the range [1, 2147483647] 2386 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2383:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2383 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2383:20: note: directive argument in the range [1, 2147483647] 2383 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2537:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2537 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2537:21: note: directive argument in the range [1, 2147483647] 2537 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2534:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2534 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2534:21: note: directive argument in the range [1, 2147483647] 2534 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2531:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2531 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2531:21: note: directive argument in the range [1, 2147483647] 2531 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘compute_cigar.constprop’: pair.c:4587:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4587 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4591:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4591 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4689:21: warning: ‘N’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4689 | sprintf(token,"%uN",genome_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4706:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4706 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4754:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4754 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4750:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4750 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4736:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4736 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4732:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4732 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4724:23: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4719:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4719 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4625:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4625 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4622:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4622 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4619:21: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4619 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4783:22: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4783 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4780:22: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4780 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4777:22: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4777 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4806:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4806 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4810:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4810 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4800:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4800 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_sam’: pair.c:5195:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5195 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5145:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5145 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5218:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5218 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5086:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5086 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5046:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5046 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5111:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5111 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_compressed’: pair.c:7169:19: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7169 | sprintf(token,"%d:%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7162:19: warning: ‘x’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7162 | sprintf(token,"%dx%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7152:21: warning: ‘v’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7152 | sprintf(token,"%dv",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7150:21: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7150 | sprintf(token,"%d^%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7081:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7081 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7078:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7078 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7075:21: warning: ‘[’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7075 | sprintf(token,"%d[",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7073:21: warning: ‘]’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7073 | sprintf(token,"%d]",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7070:21: warning: ‘(’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7070 | sprintf(token,"%d(",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7068:21: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7068 | sprintf(token,"%d)",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7066:21: warning: ‘=’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7066 | sprintf(token,"%d=",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7063:21: warning: ‘<’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7063 | sprintf(token,"%d<",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7061:21: warning: ‘>’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7061 | sprintf(token,"%d>",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7206:20: warning: ‘*’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7206 | sprintf(token,"%d*",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscan-pair.Tpo .deps/uniqscan-pair.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pairpool.o -MD -MP -MF .deps/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/uniqscan-pairpool.Tpo .deps/uniqscan-pairpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diag.o -MD -MP -MF .deps/uniqscan-diag.Tpo -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/uniqscan-diag.Tpo .deps/uniqscan-diag.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diagpool.o -MD -MP -MF .deps/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/uniqscan-diagpool.Tpo .deps/uniqscan-diagpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-orderstat.o -MD -MP -MF .deps/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/uniqscan-orderstat.Tpo .deps/uniqscan-orderstat.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligoindex_hr.o -MD -MP -MF .deps/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/uniqscan-oligoindex_hr.Tpo .deps/uniqscan-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cellpool.o -MD -MP -MF .deps/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/uniqscan-cellpool.Tpo .deps/uniqscan-cellpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage2.o -MD -MP -MF .deps/uniqscan-stage2.Tpo -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/uniqscan-stage2.Tpo .deps/uniqscan-stage2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intron.o -MD -MP -MF .deps/uniqscan-intron.Tpo -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/uniqscan-intron.Tpo .deps/uniqscan-intron.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-boyer-moore.o -MD -MP -MF .deps/uniqscan-boyer-moore.Tpo -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/uniqscan-boyer-moore.Tpo .deps/uniqscan-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-changepoint.o -MD -MP -MF .deps/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/uniqscan-changepoint.Tpo .deps/uniqscan-changepoint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pbinom.o -MD -MP -MF .deps/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/uniqscan-pbinom.Tpo .deps/uniqscan-pbinom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-dynprog.o -MD -MP -MF .deps/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/uniqscan-dynprog.Tpo .deps/uniqscan-dynprog.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-translation.o -MD -MP -MF .deps/uniqscan-translation.Tpo -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/uniqscan-translation.Tpo .deps/uniqscan-translation.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-doublelist.o -MD -MP -MF .deps/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/uniqscan-doublelist.Tpo .deps/uniqscan-doublelist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-smooth.o -MD -MP -MF .deps/uniqscan-smooth.Tpo -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/uniqscan-smooth.Tpo .deps/uniqscan-smooth.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chimera.o -MD -MP -MF .deps/uniqscan-chimera.Tpo -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/uniqscan-chimera.Tpo .deps/uniqscan-chimera.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3.o -MD -MP -MF .deps/uniqscan-stage3.Tpo -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/uniqscan-stage3.Tpo .deps/uniqscan-stage3.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicestringpool.o -MD -MP -MF .deps/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/uniqscan-splicestringpool.Tpo .deps/uniqscan-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie_build.o -MD -MP -MF .deps/uniqscan-splicetrie_build.Tpo -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/uniqscan-splicetrie_build.Tpo .deps/uniqscan-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie.o -MD -MP -MF .deps/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/uniqscan-splicetrie.Tpo .deps/uniqscan-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splice.o -MD -MP -MF .deps/uniqscan-splice.Tpo -c -o uniqscan-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/uniqscan-splice.Tpo .deps/uniqscan-splice.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indel.o -MD -MP -MF .deps/uniqscan-indel.Tpo -c -o uniqscan-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/uniqscan-indel.Tpo .deps/uniqscan-indel.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-access.o -MD -MP -MF .deps/uniqscan-bitpack64-access.Tpo -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/uniqscan-bitpack64-access.Tpo .deps/uniqscan-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sarray-read.o -MD -MP -MF .deps/uniqscan-sarray-read.Tpo -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c mv -f .deps/uniqscan-sarray-read.Tpo .deps/uniqscan-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage1hr.o -MD -MP -MF .deps/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/uniqscan-stage1hr.Tpo .deps/uniqscan-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-resulthr.o -MD -MP -MF .deps/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/uniqscan-resulthr.Tpo .deps/uniqscan-resulthr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-datadir.o -MD -MP -MF .deps/uniqscan-datadir.Tpo -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/uniqscan-datadir.Tpo .deps/uniqscan-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt.o -MD -MP -MF .deps/uniqscan-getopt.Tpo -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/uniqscan-getopt.Tpo .deps/uniqscan-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt1.o -MD -MP -MF .deps/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/uniqscan-getopt1.Tpo .deps/uniqscan-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uniqscan.o -MD -MP -MF .deps/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c mv -f .deps/uniqscan-uniqscan.Tpo .deps/uniqscan-uniqscan.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-except.o -MD -MP -MF .deps/uniqscanl-except.Tpo -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/uniqscanl-except.Tpo .deps/uniqscanl-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-assert.o -MD -MP -MF .deps/uniqscanl-assert.Tpo -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/uniqscanl-assert.Tpo .deps/uniqscanl-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mem.o -MD -MP -MF .deps/uniqscanl-mem.Tpo -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/uniqscanl-mem.Tpo .deps/uniqscanl-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intlist.o -MD -MP -MF .deps/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/uniqscanl-intlist.Tpo .deps/uniqscanl-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-list.o -MD -MP -MF .deps/uniqscanl-list.Tpo -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/uniqscanl-list.Tpo .deps/uniqscanl-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-littleendian.o -MD -MP -MF .deps/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-littleendian.Tpo .deps/uniqscanl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bigendian.o -MD -MP -MF .deps/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/uniqscanl-bigendian.Tpo .deps/uniqscanl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-univinterval.o -MD -MP -MF .deps/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/uniqscanl-univinterval.Tpo .deps/uniqscanl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-interval.o -MD -MP -MF .deps/uniqscanl-interval.Tpo -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/uniqscanl-interval.Tpo .deps/uniqscanl-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uintlist.o -MD -MP -MF .deps/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/uniqscanl-uintlist.Tpo .deps/uniqscanl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uint8list.o -MD -MP -MF .deps/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:202:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 202 | sprintf(Buffer,"%u,",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu uint8list.c:205:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 205 | sprintf(Buffer,"%u",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu uint8list.c:211:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 211 | sprintf(Buffer,"%u,",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu uint8list.c:214:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 214 | sprintf(Buffer,"%u",Uint8list_head(p)); | ~^ ~~~~~~~~~~~~~~~~~ | | | | | UINT8 {aka long long unsigned int} | unsigned int | %llu mv -f .deps/uniqscanl-uint8list.Tpo .deps/uniqscanl-uint8list.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stopwatch.o -MD -MP -MF .deps/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/uniqscanl-stopwatch.Tpo .deps/uniqscanl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-access.o -MD -MP -MF .deps/uniqscanl-access.Tpo -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/uniqscanl-access.Tpo .deps/uniqscanl-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read-univ.o -MD -MP -MF .deps/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/uniqscanl-iit-read-univ.Tpo .deps/uniqscanl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read.o -MD -MP -MF .deps/uniqscanl-iit-read.Tpo -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/uniqscanl-iit-read.Tpo .deps/uniqscanl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-md5.o -MD -MP -MF .deps/uniqscanl-md5.Tpo -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/uniqscanl-md5.Tpo .deps/uniqscanl-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bzip2.o -MD -MP -MF .deps/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/uniqscanl-bzip2.Tpo .deps/uniqscanl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sequence.o -MD -MP -MF .deps/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/uniqscanl-sequence.Tpo .deps/uniqscanl-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-reader.o -MD -MP -MF .deps/uniqscanl-reader.Tpo -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/uniqscanl-reader.Tpo .deps/uniqscanl-reader.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genomicpos.o -MD -MP -MF .deps/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/uniqscanl-genomicpos.Tpo .deps/uniqscanl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-compress.o -MD -MP -MF .deps/uniqscanl-compress.Tpo -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/uniqscanl-compress.Tpo .deps/uniqscanl-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome.o -MD -MP -MF .deps/uniqscanl-genome.Tpo -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-genome.Tpo .deps/uniqscanl-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_hr.o -MD -MP -MF .deps/uniqscanl-genome_hr.Tpo -c -o uniqscanl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/uniqscanl-genome_hr.Tpo .deps/uniqscanl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_sites.o -MD -MP -MF .deps/uniqscanl-genome_sites.Tpo -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome_sites.c: In function ‘Genome_print_blocks’: genome_sites.c:24729:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24729 | printf("%u\t",startblock/3*32U); | ~^ ~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu genome_sites.c:24744:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24744 | printf("%u\t",ptr/3*32U); | ~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | unsigned int | %llu genome_sites.c:24751:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 24751 | printf("%u\t",(endblock+3)/3*32U); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/uniqscanl-genome_sites.Tpo .deps/uniqscanl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-read.o -MD -MP -MF .deps/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/uniqscanl-bitpack64-read.Tpo .deps/uniqscanl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb.o -MD -MP -MF .deps/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-indexdb.Tpo .deps/uniqscanl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb_hr.o -MD -MP -MF .deps/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘Compoundpos_dump’: indexdb_hr.c:1008:31: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1008 | printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu indexdb_hr.c: In function ‘heap_even_dump’: indexdb_hr.c:1232:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1232 | printf("#%d--%d:%u ",i,batch->nentries,batch->position); | ~^ ~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 593 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-indexdb_hr.Tpo .deps/uniqscanl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligo.o -MD -MP -MF .deps/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/uniqscanl-oligo.Tpo .deps/uniqscanl-oligo.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrom.o -MD -MP -MF .deps/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/uniqscanl-chrom.Tpo .deps/uniqscanl-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-segmentpos.o -MD -MP -MF .deps/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function ‘Segmentpos_print’: segmentpos.c:90:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 90 | fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/uniqscanl-segmentpos.Tpo .deps/uniqscanl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrnum.o -MD -MP -MF .deps/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/uniqscanl-chrnum.Tpo .deps/uniqscanl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent_hr.o -MD -MP -MF .deps/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/uniqscanl-maxent_hr.Tpo .deps/uniqscanl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mapq.o -MD -MP -MF .deps/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/uniqscanl-mapq.Tpo .deps/uniqscanl-mapq.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-shortread.o -MD -MP -MF .deps/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/uniqscanl-shortread.Tpo .deps/uniqscanl-shortread.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-substring.o -MD -MP -MF .deps/uniqscanl-substring.Tpo -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c: In function ‘Substring_print_ends’: substring.c:1005:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1005 | printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); | ~^ ~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:1005:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1005 | printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); | ~^ ~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c: In function ‘print_coordinates’: substring.c:3536:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3536 | fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3536:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3536 | fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U, | ~^ | | | unsigned int | %llu 3537 | substring->alignend_trim - substring->chroffset); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} substring.c:3539:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3539 | fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3539:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3539 | fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset, | ~^ | | | unsigned int | %llu 3540 | substring->alignstart_trim - substring->chroffset + 1U); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} substring.c:3544:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3544 | fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3544:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3544 | fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset, | ~^ | | | unsigned int | %llu 3545 | substring->alignend_trim - substring->chroffset + 1U); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} substring.c:3547:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3547 | fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U, | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu substring.c:3547:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3547 | fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U, | ~^ | | | unsigned int | %llu 3548 | substring->alignstart_trim - substring->chroffset); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/uniqscanl-substring.Tpo .deps/uniqscanl-substring.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3hr.o -MD -MP -MF .deps/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/uniqscanl-stage3hr.Tpo .deps/uniqscanl-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-spanningelt.o -MD -MP -MF .deps/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/uniqscanl-spanningelt.Tpo .deps/uniqscanl-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cmet.o -MD -MP -MF .deps/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/uniqscanl-cmet.Tpo .deps/uniqscanl-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-atoi.o -MD -MP -MF .deps/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/uniqscanl-atoi.Tpo .deps/uniqscanl-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent.o -MD -MP -MF .deps/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/uniqscanl-maxent.Tpo .deps/uniqscanl-maxent.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pair.o -MD -MP -MF .deps/uniqscanl-pair.Tpo -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_genomic_sequence’: pair.c:546:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 546 | sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘print_genomicalt_sequence’: pair.c:573:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 573 | sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘compute_margin’: pair.c:600:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 600 | sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c:607:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 607 | sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘Pair_print_coordinates’: pair.c:1272:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1272 | fprintf(fp,"%u %u %c",this->genomepos + ONEBASEDP, | ~^ | | | unsigned int | %llu pair.c:1276:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1276 | fprintf(fp,"%s:%u %u %c",chrstring, | ~^ | | | unsigned int | %llu pair.c: In function ‘Pair_print_exonsummary’: pair.c:1790:19: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1790 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1790:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1790 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1799:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1799 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1799:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1799 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1913:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1913 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1913:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1913 | fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1922:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1922 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c:1922:24: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1922 | fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu pair.c: In function ‘Pair_print_compressed’: pair.c:6986:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6986 | fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c:6986:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6986 | fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); | ~^ | | | unsigned int | %llu pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:2419:20: warning: ‘%u’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~ pair.c:2419:18: note: directive argument in the range [1, 2147483647] 2419 | sprintf(token,"N%u",abs(intron_end - intron_start) + 1); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2478:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2478 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2478:18: note: directive argument in the range [1, 2147483647] 2478 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2474:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2474 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2474:18: note: directive argument in the range [1, 2147483647] 2474 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2455:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2455 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2455:20: note: directive argument in the range [1, 2147483647] 2455 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2451:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2451 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2451:20: note: directive argument in the range [1, 2147483647] 2451 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2444:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2444 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2444:20: note: directive argument in the range [1, 2147483647] 2444 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2439:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2439 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2439:20: note: directive argument in the range [1, 2147483647] 2439 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2389:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2389 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2389:20: note: directive argument in the range [1, 2147483647] 2389 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2386:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2386 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2386:20: note: directive argument in the range [1, 2147483647] 2386 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2383:22: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2383 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2383:20: note: directive argument in the range [1, 2147483647] 2383 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2537:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2537 | sprintf(token,"D%d",Dlength); | ^~ pair.c:2537:21: note: directive argument in the range [1, 2147483647] 2537 | sprintf(token,"D%d",Dlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2534:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2534 | sprintf(token,"I%d",Ilength); | ^~ pair.c:2534:21: note: directive argument in the range [1, 2147483647] 2534 | sprintf(token,"I%d",Ilength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:2531:23: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2531 | sprintf(token,"M%d",Mlength); | ^~ pair.c:2531:21: note: directive argument in the range [1, 2147483647] 2531 | sprintf(token,"M%d",Mlength); | ^~~~~ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘compute_cigar.constprop’: pair.c:4587:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4587 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4591:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4591 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4689:21: warning: ‘N’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4689 | sprintf(token,"%uN",genome_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4706:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4706 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4754:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4754 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4750:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4750 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4736:23: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4736 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4732:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4732 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4724:23: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4719:23: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4719 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4625:21: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4625 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4622:21: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4622 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4619:21: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4619 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4783:22: warning: ‘D’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4783 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4780:22: warning: ‘I’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4780 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4777:22: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4777 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4806:24: warning: ‘S’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4806 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4810:24: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4810 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:4800:19: warning: ‘H’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 4800 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_sam’: pair.c:5195:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5195 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5145:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5145 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5218:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5218 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5086:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5086 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5046:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5046 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5111:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5111 | sprintf(token,"%d",nmatches); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c: In function ‘Pair_print_compressed’: pair.c:7169:19: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7169 | sprintf(token,"%d:%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7162:19: warning: ‘x’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7162 | sprintf(token,"%dx%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7152:21: warning: ‘v’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7152 | sprintf(token,"%dv",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7150:21: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7150 | sprintf(token,"%d^%c",runlength,this->cdna); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7081:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7081 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7078:21: warning: ‘#’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7078 | sprintf(token,"%d#",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7075:21: warning: ‘[’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7075 | sprintf(token,"%d[",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7073:21: warning: ‘]’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7073 | sprintf(token,"%d]",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7070:21: warning: ‘(’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7070 | sprintf(token,"%d(",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7068:21: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7068 | sprintf(token,"%d)",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7066:21: warning: ‘=’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7066 | sprintf(token,"%d=",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7063:21: warning: ‘<’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7063 | sprintf(token,"%d<",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7061:21: warning: ‘>’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7061 | sprintf(token,"%d>",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:7206:20: warning: ‘*’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 7206 | sprintf(token,"%d*",runlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:4, from chrnum.h:5, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-pair.Tpo .deps/uniqscanl-pair.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pairpool.o -MD -MP -MF .deps/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/uniqscanl-pairpool.Tpo .deps/uniqscanl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diag.o -MD -MP -MF .deps/uniqscanl-diag.Tpo -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/uniqscanl-diag.Tpo .deps/uniqscanl-diag.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diagpool.o -MD -MP -MF .deps/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/uniqscanl-diagpool.Tpo .deps/uniqscanl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-orderstat.o -MD -MP -MF .deps/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/uniqscanl-orderstat.Tpo .deps/uniqscanl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligoindex_hr.o -MD -MP -MF .deps/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/uniqscanl-oligoindex_hr.Tpo .deps/uniqscanl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cellpool.o -MD -MP -MF .deps/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/uniqscanl-cellpool.Tpo .deps/uniqscanl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage2.o -MD -MP -MF .deps/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/uniqscanl-stage2.Tpo .deps/uniqscanl-stage2.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intron.o -MD -MP -MF .deps/uniqscanl-intron.Tpo -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/uniqscanl-intron.Tpo .deps/uniqscanl-intron.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-boyer-moore.o -MD -MP -MF .deps/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/uniqscanl-boyer-moore.Tpo .deps/uniqscanl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-changepoint.o -MD -MP -MF .deps/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/uniqscanl-changepoint.Tpo .deps/uniqscanl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pbinom.o -MD -MP -MF .deps/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/uniqscanl-pbinom.Tpo .deps/uniqscanl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-dynprog.o -MD -MP -MF .deps/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/uniqscanl-dynprog.Tpo .deps/uniqscanl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-translation.o -MD -MP -MF .deps/uniqscanl-translation.Tpo -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/uniqscanl-translation.Tpo .deps/uniqscanl-translation.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-doublelist.o -MD -MP -MF .deps/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/uniqscanl-doublelist.Tpo .deps/uniqscanl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-smooth.o -MD -MP -MF .deps/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/uniqscanl-smooth.Tpo .deps/uniqscanl-smooth.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chimera.o -MD -MP -MF .deps/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/uniqscanl-chimera.Tpo .deps/uniqscanl-chimera.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3.o -MD -MP -MF .deps/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/uniqscanl-stage3.Tpo .deps/uniqscanl-stage3.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicestringpool.o -MD -MP -MF .deps/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/uniqscanl-splicestringpool.Tpo .deps/uniqscanl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie_build.o -MD -MP -MF .deps/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function ‘Splicetrie_dump’: splicetrie_build.c:132:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 132 | printf("%d %u",(int) leaf,position); | ~^ ~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu splicetrie_build.c:146:19: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 146 | printf("%d %u",(int) leaf,position); | ~^ ~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/uniqscanl-splicetrie_build.Tpo .deps/uniqscanl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie.o -MD -MP -MF .deps/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/uniqscanl-splicetrie.Tpo .deps/uniqscanl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splice.o -MD -MP -MF .deps/uniqscanl-splice.Tpo -c -o uniqscanl-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/uniqscanl-splice.Tpo .deps/uniqscanl-splice.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indel.o -MD -MP -MF .deps/uniqscanl-indel.Tpo -c -o uniqscanl-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/uniqscanl-indel.Tpo .deps/uniqscanl-indel.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-access.o -MD -MP -MF .deps/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/uniqscanl-bitpack64-access.Tpo .deps/uniqscanl-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sarray-read.o -MD -MP -MF .deps/uniqscanl-sarray-read.Tpo -c -o uniqscanl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c sarray-read.c: In function ‘Sarray_new’: sarray-read.c:302:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 302 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:368:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 368 | new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2, | ^ sarray-read.c:434:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 434 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T), | ^ sarray-read.c:526:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 526 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:653:15: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 653 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len, | ^ sarray-read.c: In function ‘Elt_dump_list’: sarray-read.c:1667:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1667 | printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]); | ~^ ~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu sarray-read.c: In function ‘Elt_dump’: sarray-read.c:1682:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1682 | printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]); | ~^ ~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu sarray-read.c: In function ‘collect_elt_matches’: sarray-read.c:2170:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2170 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:2442:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2442:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2456:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2456 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2499:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2499:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2513:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2513 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2643:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2643:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2656:36: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2656 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2699:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2699:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2712:12: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2712 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2752:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2752 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:3024:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3024:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3038:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3038 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3082:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3082:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3096:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3096 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:3217:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3217:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3231:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3231 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:50: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3274:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3274:13: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3288:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3288 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:21: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-sarray-read.Tpo .deps/uniqscanl-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage1hr.o -MD -MP -MF .deps/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c: In function ‘find_singlesplices_plus’: stage1hr.c:6629:54: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6629 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6630 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6629:75: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6629 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6630 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6629:99: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6629 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6630 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:62: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:67: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:101: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 6 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), 6770 | Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:106: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 7 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 6769 | Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor), 6770 | Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:6768:135: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 9 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 6768 | fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu ...... 6771 | segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c: In function ‘find_singlesplices_minus’: stage1hr.c:7145:54: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7145 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7146 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7145:75: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7145 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7146 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7145:99: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7145 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7146 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7284:54: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7284 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7285 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7284:75: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7284 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7285 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} stage1hr.c:7284:99: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 7284 | fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n", | ~^ | | | unsigned int | %llu 7285 | Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/uniqscanl-stage1hr.Tpo .deps/uniqscanl-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-resulthr.o -MD -MP -MF .deps/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/uniqscanl-resulthr.Tpo .deps/uniqscanl-resulthr.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-datadir.o -MD -MP -MF .deps/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/uniqscanl-datadir.Tpo .deps/uniqscanl-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt.o -MD -MP -MF .deps/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/uniqscanl-getopt.Tpo .deps/uniqscanl-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt1.o -MD -MP -MF .deps/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/uniqscanl-getopt1.Tpo .deps/uniqscanl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uniqscan.o -MD -MP -MF .deps/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c mv -f .deps/uniqscanl-uniqscan.Tpo .deps/uniqscanl-uniqscan.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-except.o -MD -MP -MF .deps/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/snpindex-except.Tpo .deps/snpindex-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-assert.o -MD -MP -MF .deps/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/snpindex-assert.Tpo .deps/snpindex-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-mem.o -MD -MP -MF .deps/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/snpindex-mem.Tpo .deps/snpindex-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-intlist.o -MD -MP -MF .deps/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/snpindex-intlist.Tpo .deps/snpindex-intlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-list.o -MD -MP -MF .deps/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/snpindex-list.Tpo .deps/snpindex-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-univinterval.o -MD -MP -MF .deps/snpindex-univinterval.Tpo -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/snpindex-univinterval.Tpo .deps/snpindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-interval.o -MD -MP -MF .deps/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/snpindex-interval.Tpo .deps/snpindex-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-uintlist.o -MD -MP -MF .deps/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/snpindex-uintlist.Tpo .deps/snpindex-uintlist.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-stopwatch.o -MD -MP -MF .deps/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/snpindex-stopwatch.Tpo .deps/snpindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read-univ.o -MD -MP -MF .deps/snpindex-iit-read-univ.Tpo -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/snpindex-iit-read-univ.Tpo .deps/snpindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read.o -MD -MP -MF .deps/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genomicpos.o -MD -MP -MF .deps/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/snpindex-genomicpos.Tpo .deps/snpindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress.o -MD -MP -MF .deps/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/snpindex-compress.Tpo .deps/snpindex-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress-write.o -MD -MP -MF .deps/snpindex-compress-write.Tpo -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function ‘fill_buffer’: compress-write.c:73:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 73 | printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu compress-write.c: In function ‘write_compressed_one’: compress-write.c:251:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 251 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 252 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} compress-write.c: In function ‘put_compressed_one’: compress-write.c:299:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 299 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 300 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/snpindex-compress-write.Tpo .deps/snpindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome_hr.o -MD -MP -MF .deps/snpindex-genome_hr.Tpo -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/snpindex-genome_hr.Tpo .deps/snpindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-read.o -MD -MP -MF .deps/snpindex-bitpack64-read.Tpo -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/snpindex-bitpack64-read.Tpo .deps/snpindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-write.o -MD -MP -MF .deps/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c mv -f .deps/snpindex-bitpack64-write.Tpo .deps/snpindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb-write.o -MD -MP -MF .deps/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘check_offsets_from_bitpack’: indexdb-write.c:2494:50: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~^ | | | int | %lld 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘check_offsets_from_gammas’: indexdb-write.c:2726:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2726 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2727 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2737:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2737 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2738 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2760:54: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2760 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2761 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2787:55: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2787 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2788 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2798:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2798 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2799 | oligok,offsets[oligok],*ptr); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘Indexdb_write_offsets’: indexdb-write.c:2888:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2888 | fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2895:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2895 | fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2972:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 2972 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c:3094:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 3094 | fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~ | | | | long unsigned int Oligospace_T {aka long long unsigned int} | %llu indexdb-write.c:3127:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3127 | fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:3171:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3171 | fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_file’: indexdb-write.c:3371:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3371 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_memory’: indexdb-write.c:3601:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3601 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/snpindex-indexdb-write.Tpo .deps/snpindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-chrom.o -MD -MP -MF .deps/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/snpindex-chrom.Tpo .deps/snpindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-md5.o -MD -MP -MF .deps/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/snpindex-md5.Tpo .deps/snpindex-md5.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bzip2.o -MD -MP -MF .deps/snpindex-bzip2.Tpo -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/snpindex-bzip2.Tpo .deps/snpindex-bzip2.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-sequence.o -MD -MP -MF .deps/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/snpindex-sequence.Tpo .deps/snpindex-sequence.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10292:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10292:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10292 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10392:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu genome.c:10392:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 10392 | fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); | ~~^ ~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu genome.c: In function ‘fill_buffer’: genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10185 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 377 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10320 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10417 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10583 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10857 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-datadir.o -MD -MP -MF .deps/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/snpindex-datadir.Tpo .deps/snpindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt.o -MD -MP -MF .deps/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/snpindex-getopt.Tpo .deps/snpindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt1.o -MD -MP -MF .deps/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/snpindex-getopt1.Tpo .deps/snpindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c snpindex.c: In function ‘merge_positions8’: snpindex.c:889:58: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘UINT8’ {aka ‘long long unsigned int’} [-Wformat=] 889 | fprintf(stderr,"Problem: saw duplicate positions %lu in oligo %s\n",*ptr1,nt); | ~~^ ~~~~~ | | | | | UINT8 {aka long long unsigned int} | long unsigned int | %llu snpindex.c: In function ‘main’: snpindex.c:1143:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 1143 | fprintf(stderr,"Allocating %lu*3*%lu bytes for compressed genome\n",nblocks,sizeof(Genomecomp_T)); | ~~^ ~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu snpindex.c:1270:29: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 1270 | fprintf(stderr,"Writing %lu offsets with %u total positions\n",oligospace+1,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~ | | | | long unsigned int Oligospace_T {aka long long unsigned int} | %llu mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-except.o -MD -MP -MF .deps/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/cmetindex-except.Tpo .deps/cmetindex-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-assert.o -MD -MP -MF .deps/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/cmetindex-assert.Tpo .deps/cmetindex-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-mem.o -MD -MP -MF .deps/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/cmetindex-mem.Tpo .deps/cmetindex-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genomicpos.o -MD -MP -MF .deps/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/cmetindex-genomicpos.Tpo .deps/cmetindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-stopwatch.o -MD -MP -MF .deps/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/cmetindex-stopwatch.Tpo .deps/cmetindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-univinterval.o -MD -MP -MF .deps/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/cmetindex-univinterval.Tpo .deps/cmetindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-interval.o -MD -MP -MF .deps/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/cmetindex-interval.Tpo .deps/cmetindex-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read-univ.o -MD -MP -MF .deps/cmetindex-iit-read-univ.Tpo -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/cmetindex-iit-read-univ.Tpo .deps/cmetindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read.o -MD -MP -MF .deps/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress.o -MD -MP -MF .deps/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/cmetindex-compress.Tpo .deps/cmetindex-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress-write.o -MD -MP -MF .deps/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function ‘fill_buffer’: compress-write.c:73:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 73 | printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu compress-write.c: In function ‘write_compressed_one’: compress-write.c:251:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 251 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 252 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} compress-write.c: In function ‘put_compressed_one’: compress-write.c:299:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 299 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 300 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/cmetindex-compress-write.Tpo .deps/cmetindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genome_hr.o -MD -MP -MF .deps/cmetindex-genome_hr.Tpo -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/cmetindex-genome_hr.Tpo .deps/cmetindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-read.o -MD -MP -MF .deps/cmetindex-bitpack64-read.Tpo -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/cmetindex-bitpack64-read.Tpo .deps/cmetindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-write.o -MD -MP -MF .deps/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c mv -f .deps/cmetindex-bitpack64-write.Tpo .deps/cmetindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb-write.o -MD -MP -MF .deps/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘check_offsets_from_bitpack’: indexdb-write.c:2494:50: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~^ | | | int | %lld 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘check_offsets_from_gammas’: indexdb-write.c:2726:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2726 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2727 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2737:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2737 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2738 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2760:54: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2760 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2761 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2787:55: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2787 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2788 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2798:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2798 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2799 | oligok,offsets[oligok],*ptr); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘Indexdb_write_offsets’: indexdb-write.c:2888:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2888 | fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2895:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2895 | fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2972:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 2972 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c:3094:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 3094 | fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~ | | | | long unsigned int Oligospace_T {aka long long unsigned int} | %llu indexdb-write.c:3127:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3127 | fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:3171:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3171 | fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_file’: indexdb-write.c:3371:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3371 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_memory’: indexdb-write.c:3601:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3601 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/cmetindex-indexdb-write.Tpo .deps/cmetindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmet.o -MD -MP -MF .deps/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/cmetindex-cmet.Tpo .deps/cmetindex-cmet.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-list.o -MD -MP -MF .deps/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/cmetindex-list.Tpo .deps/cmetindex-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-datadir.o -MD -MP -MF .deps/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/cmetindex-datadir.Tpo .deps/cmetindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt.o -MD -MP -MF .deps/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/cmetindex-getopt.Tpo .deps/cmetindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt1.o -MD -MP -MF .deps/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/cmetindex-getopt1.Tpo .deps/cmetindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmetindex.o -MD -MP -MF .deps/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c mv -f .deps/cmetindex-cmetindex.Tpo .deps/cmetindex-cmetindex.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-except.o -MD -MP -MF .deps/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/atoiindex-except.Tpo .deps/atoiindex-except.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-assert.o -MD -MP -MF .deps/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/atoiindex-assert.Tpo .deps/atoiindex-assert.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-mem.o -MD -MP -MF .deps/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/atoiindex-mem.Tpo .deps/atoiindex-mem.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 17 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 34 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 47 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 53 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 285 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 445 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 527 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 781 | read(fd,buf,8); | ^~~~~~~~~~~~~~ mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genomicpos.o -MD -MP -MF .deps/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-stopwatch.o -MD -MP -MF .deps/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/atoiindex-stopwatch.Tpo .deps/atoiindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat In file included from access.c:41: access.c: In function ‘Access_allocated’: littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 20 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’ 235 | FREAD_UINTS(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~ littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 23 | #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’ 237 | FREAD_UINT8S(memory,(*len)/eltsize,fp); | ^~~~~~~~~~~~ mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function ‘Univinterval_print’: univinterval.c:71:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu univinterval.c:71:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 71 | printf("%lu %lu %d",this->low,this->high,this->type); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function ‘Univ_IIT_dump’: iit-read-univ.c:507:16: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:507:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 507 | printf(" %lu..%lu",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_table’: iit-read-univ.c:544:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:544:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 544 | printf("%lu..%lu\t",startpos,endpos); | ~~^ ~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’: iit-read-univ.c:694:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:694:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 694 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:700:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu iit-read-univ.c:700:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 700 | printf("%lu..%lu\t",endpos+1U,startpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu iit-read-univ.c:703:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 703 | printf("%lu..%lu\t",startpos+1U,endpos+1U); | ~~^ ~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’ 873 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’ 875 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’ 876 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’ 877 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’ 878 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’ 920 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’ 921 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’ 922 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’ 927 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’ 929 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’ 931 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’ 991 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1213 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1217 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1221 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1225 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1229 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:11: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’ 1073 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’ 2237 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’ 2495 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1604 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1605 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1606 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1607 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1608 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1689 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1692 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1696 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’ 1785 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’ 1791 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2141 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2147 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2152 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2163 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2169 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2174 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2185 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 17 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’ 2898 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’ 1913 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 18 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’ 1918 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function ‘fill_buffer’: compress-write.c:73:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 73 | printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); | ~~^ ~~~~~~~~~~ | | | | long unsigned int Univcoord_T {aka long long unsigned int} | %llu compress-write.c: In function ‘write_compressed_one’: compress-write.c:251:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 251 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 252 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} compress-write.c: In function ‘put_compressed_one’: compress-write.c:299:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 299 | fprintf(stderr,"Don't recognize character %c at position %lu. Using N instead\n", | ~~^ | | | long unsigned int | %llu 300 | Buffer[i],position+i); | ~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genome_hr.o -MD -MP -MF .deps/atoiindex-genome_hr.Tpo -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/atoiindex-genome_hr.Tpo .deps/atoiindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_offsets_from_bitpack’: indexdb.c:1934:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 1934 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘Indexdb_offsets_from_gammas’: indexdb.c:2026:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2026 | fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1842 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘check_offsets_from_bitpack’: indexdb-write.c:2494:50: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~^ | | | int | %lld 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2494:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2494 | fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2495 | oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); | ~~~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘check_offsets_from_gammas’: indexdb-write.c:2726:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2726 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2727 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2737:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2737 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2738 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2760:54: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2760 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2761 | oligok-1UL,offsets[oligok-1],cum); | ~~~~~~~~~~ | | | long long unsigned int indexdb-write.c:2787:55: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2787 | fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2788 | oligok,offsetscomp[gammaptrs[p-1]],cum); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c:2798:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 2798 | fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u. Please inform twu@gene.com\n", | ~~^ | | | long unsigned int | %llu 2799 | oligok,offsets[oligok],*ptr); | ~~~~~~ | | | Oligospace_T {aka long long unsigned int} indexdb-write.c: In function ‘Indexdb_write_offsets’: indexdb-write.c:2888:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2888 | fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2895:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 2895 | fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:2972:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 2972 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c:3094:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long long unsigned int’} [-Wformat=] 3094 | fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~ | | | | long unsigned int Oligospace_T {aka long long unsigned int} | %llu indexdb-write.c:3127:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3127 | fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c:3171:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 3171 | fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_file’: indexdb-write.c:3371:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3371 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu indexdb-write.c: In function ‘compute_positions_in_memory’: indexdb-write.c:3601:49: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3601 | fprintf(stderr,"Bad character %c at position %lu\n",c,position); | ~~^ ~~~~~~~~ | | | | | Univcoord_T {aka long long unsigned int} | long unsigned int | %llu mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm -pthread make[3]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin' libtool: install: /usr/bin/install -c gmap /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gmap libtool: install: /usr/bin/install -c gmapl /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gmapl libtool: install: /usr/bin/install -c get-genome /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/get-genome libtool: install: /usr/bin/install -c gmapindex /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gmapindex libtool: install: /usr/bin/install -c iit_store /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/iit_store libtool: install: /usr/bin/install -c iit_get /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/iit_get libtool: install: /usr/bin/install -c iit_dump /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/iit_dump libtool: install: /usr/bin/install -c gsnap /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gsnap libtool: install: /usr/bin/install -c gsnapl /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gsnapl libtool: install: /usr/bin/install -c uniqscan /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/uniqscan libtool: install: /usr/bin/install -c uniqscanl /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/uniqscanl libtool: install: /usr/bin/install -c snpindex /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/snpindex libtool: install: /usr/bin/install -c cmetindex /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/cmetindex libtool: install: /usr/bin/install -c atoiindex /home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/atoiindex make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/src' Making install in util make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/util' cp gmap_compress.pl gmap_compress chmod +x gmap_compress cp gmap_uncompress.pl gmap_uncompress chmod +x gmap_uncompress cp gmap_process.pl gmap_process chmod +x gmap_process cp gmap_setup.pl gmap_setup chmod +x gmap_setup cp gmap_build.pl gmap_build chmod +x gmap_build cp gmap_reassemble.pl gmap_reassemble chmod +x gmap_reassemble cp md_coords.pl md_coords chmod +x md_coords cp fa_coords.pl fa_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/util' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin' /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/util' make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/util' Making install in tests make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/tests' make[3]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/tests' make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap/tests' make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap' make[3]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap' make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap' make[1]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/gmapR/src/gmap' installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-gmapR/00new/gmapR/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘directory’ in package ‘gmapR’ Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’ Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gmapR)