############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gmapR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘gmapR’ ... ** using staged installation ** libs ** arch - cd gstruct/; \ CFLAGS="-g -O3" \ ./configure --enable-static --disable-shared \ --prefix=/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr --includedir=/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include/gstruct \ --libdir=/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib \ --with-samtools-lib=/Users/biocbuild/bbs-3.16-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-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking target system type... x86_64-apple-darwin21.6.0 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... rm: conftest.dSYM: is a directory 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... config/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for style of include used by make... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/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... no 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... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes 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... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld 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 /usr/X11/lib, headers /usr/X11/include checking whether -R must be followed by a space... neither works 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... yes checking for joinable pthread attribute... 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(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... no 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... yes checking for pagesize via sysconf... yes checking for pagesize via sysctl... yes 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 16917: ACX_BUILTIN_POPCOUNT: command not found checking for bsr instruction in assembly... no 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 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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... /Users/biocbuild/bbs-3.16-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... -D_THREAD_SAFE 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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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:412:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int i, tmp, stop = 0; ^ samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable] int ret, count, block_length; ^ samtools/bgzf.c:83:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :35:1: note: expanded from here kh_clear_cache ^ 3 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 samtools/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :88:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :102:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :109:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :114:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :117:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :120:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :126:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :131:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 samtools/bam_import.c:20:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :417:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c:20:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :420:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c:20:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :431:1: note: expanded from here kh_del_ref ^ 3 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 samtools/bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :108:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :122:1: note: expanded from here kh_del_i ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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:14:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :415:1: note: expanded from here kh_clear_s ^ samtools/faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :429:1: note: expanded from here kh_del_s ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 samtools/sam_header.c:10:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :415:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c:10:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :429:1: note: expanded from here kh_del_str ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] bam_header_t *old; ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -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 cd gstruct; \ make install Making install in src /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:59:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] if (stat64(filename,&sb) == 0) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ access.c:79:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] stat64(filename,&sb); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ 2 warnings generated. mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 iit-read.c:1611:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1611:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1638:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1638:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1650:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1650:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1672:21: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,divno,offset,filesize); ^~~~~~ iit-read.c:1672:28: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,divno,offset,filesize); ^~~~~~~~ iit-read.c:1693:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1693:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1742:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1742:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1779:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1779:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1834:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1834:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2344:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2344:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2360:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2360:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2372:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2372:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2381:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2381:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2408:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2408:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2429:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2429:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2446:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2446:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2466:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2466:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2495:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2495:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2608:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2608:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2626:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2626:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2643:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2643:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2652:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2652:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2681:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2681:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2702:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2702:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2719:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2719:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2744:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2744:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2770:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2770:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2823:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2823:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3010:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3010:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3026:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3026:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3043:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3043:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3052:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3052:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3081:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3081:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3107:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3107:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3124:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3124:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3149:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3149:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3175:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3175:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3220:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3220:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ 74 warnings generated. mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:108:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. 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-msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" 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-DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -D_THREAD_SAFE -version-info 1:0:0 -o libgstruct-1.0.la -rpath /Users/biocbuild/bbs-3.16-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 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" ) ../config/install-sh -c -d '/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libgstruct-1.0.la '/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib' libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.la libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: chmod 644 /Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: ranlib /Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a ../config/install-sh -c -d '/Users/biocbuild/bbs-3.16-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 '/Users/biocbuild/bbs-3.16-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 '/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include/gstruct' ../config/install-sh -c -d '/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -c bamreader.c -o bamreader.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -c bamtally.c -o bamtally.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -c iit.c -o iit.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -c variantsummary.c -o variantsummary.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -c genome.c -o genome.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_gmapR.c -o R_init_gmapR.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-bamread.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-bamtally.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-datadir.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-genome.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-iit-read.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-interval.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-access.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-chrom.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-tally.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-expr.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-iit-write.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-intlist.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-list.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-mem.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-sequence.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-table.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-tableuint.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-translation.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-ucharlist.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-uintlist.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-uinttable.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-except.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-md5.o)) was built for newer macOS version (12.0) than being linked (10.13) ld: warning: object file (/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a(libgstruct_1.0_la-stopwatch.o)) was built for newer macOS version (12.0) than being linked (10.13) cd gmap/; \ ./configure --with-gmapdb= --prefix=/Users/biocbuild/bbs-3.16-bioc/meat/gmapR/src/../inst/usr \ --libdir=/Users/biocbuild/bbs-3.16-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-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking target system type... x86_64-apple-darwin21.6.0 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... config/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk 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... /Users/biocbuild/bbs-3.16-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... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no 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... 786432 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/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... no 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... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes 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... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld 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... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE 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... no 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... yes checking for pagesize via sysconf... yes checking for pagesize via sysctl... yes 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... no 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... 50657:3a400800:7ffefbff: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... /Users/biocbuild/bbs-3.16-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 configure: WARNING: WARNING: You don't seem to have memory mapping. GMAP will work without this, but the program can run faster if memory mapping is available. If you wish to enable memory mapping, please specify the appropriate values for CC, PTHREAD_CFLAGS, and PTHREAD_LIBS in the config.site file and run configure again. Otherwise, you may proceed with the rest of the installation. cd gmap; \ make install Making install in src gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %u univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %u 2 warnings generated. mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] if (stat64(filename,&sb) == 0) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] stat64(filename,&sb); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ 2 warnings generated. mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u 10 warnings generated. mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %u compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u 4 warnings generated. mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~~ %u genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~ %u genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~~~ %u genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~ %u genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %u 17 warnings generated. mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ 2 warnings generated. mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2672:61: note: passing argument to parameter 'cellpool' here Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, ^ gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2673:17: note: passing argument to parameter 'diagpool' here Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { ^ 2 warnings generated. mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmapl-littleendian.Tpo .deps/gmapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmapl-bigendian.Tpo .deps/gmapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapl-univinterval.Tpo .deps/gmapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] if (stat64(filename,&sb) == 0) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] stat64(filename,&sb); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ 2 warnings generated. mv -f .deps/gmapl-access.Tpo .deps/gmapl-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/gmapl-iit-read-univ.Tpo .deps/gmapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/gmapl-iit-read.Tpo .deps/gmapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmapl-compress-write.Tpo .deps/gmapl-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/gmapl-genome.Tpo .deps/gmapl-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] printf("%u\t",startblock/3*32U); ~~ ^~~~~~~~~~~~~~~~ %llu genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] printf("%u\t",ptr/3*32U); ~~ ^~~~~~~~~ %llu genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] printf("%u\t",(endblock+3)/3*32U); ~~ ^~~~~~~~~~~~~~~~~~ %llu 3 warnings generated. mv -f .deps/gmapl-genome_sites.Tpo .deps/gmapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~~ %llu genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~ %llu genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~~~ %llu genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~ %llu genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %llu 17 warnings generated. mv -f .deps/gmapl-genome-write.Tpo .deps/gmapl-genome-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmapl-indexdb.Tpo .deps/gmapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ~~ ^~~~~~~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapl-indexdb_hr.Tpo .deps/gmapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmapl-chrom.Tpo .deps/gmapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:90:41: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %llu 1 warning generated. mv -f .deps/gmapl-segmentpos.Tpo .deps/gmapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:546:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %llu /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~~~~~~~~~ pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] chroffset + this->genomepos + ONEBASEDP, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %llu pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ~~ ^~~~~~~~~~~~~~~~~~~~~ %llu 18 warnings generated. mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%d %u",(int) leaf,position); ~~ ^~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2672:61: note: passing argument to parameter 'cellpool' here Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, ^ gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types] matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); ^~~~~~~~ gmap.c:2673:17: note: passing argument to parameter 'diagpool' here Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { ^ 2 warnings generated. mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] if (stat64(filename,&sb) == 0) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] stat64(filename,&sb); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ 2 warnings generated. mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:187:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~ parserange.c:187:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~ parserange.c:187:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~ 3 warnings generated. mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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:194:23: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); ~~~ ^~~~~~ %llu get-genome.c:194:40: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); ~~~ ^~~~~~~~~~~ %llu get-genome.c:410:41: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu get-genome.c:410:78: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); ~~~ ^~~~~~~~~~~~~~~ %llu get-genome.c:428:41: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); ~~~ ^~~~~~~~~~~~~~~ %llu get-genome.c:428:67: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %llu 6 warnings generated. mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.16-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 gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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 mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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 mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %llu univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %llu 2 warnings generated. mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] if (stat64(filename,&sb) == 0) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations] stat64(filename,&sb); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:427:9: note: 'stat64' has been explicitly marked deprecated here int stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA); ^ 2 warnings generated. mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %llu iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %llu iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %llu iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %llu iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %llu 10 warnings generated. mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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 mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %llu 4 warnings generated. mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %llu compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~~ %llu genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~ %llu genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~~~ %llu genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 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); ~~~ ^~~~~~~~~~~~~~~ %llu genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %llu 17 warnings generated. mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~ indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^ indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]); ^~~~~~~~ indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] oligok-1UL,offsets[oligok-1],cum); ^~~~~~~~~~ indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsetscomp[gammaptrs[p-1]],cum); ^~~~~~ indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] oligok,offsets[oligok],*ptr); ^~~~~~ indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]); ~~~ ^~~~~~~~~~~~ %llu indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]); ~~~ ^~~~~~~~~~~~~~ %llu indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset); ~~~ ^~~~~~ %lld indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ~~~ ^~~~~~~~ %llu indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT8),filesize); ^~~~~~~~ indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] positionsfile,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~ 24 warnings generated. mv -f .deps/gmapindex-indexdb-write.Tpo .deps/gmapindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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:283:18: warning: passing 'const void **' to parameter of type 'void **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] (*keyfree)(&p->key); ^~~~~~~ 1 warning generated. mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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:90:41: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %llu 1 warning generated. mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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:305:64: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat] nitems = sscanf(Buffer,"%s %s %lu",accession_p,chrpos_string,&universal_coord); ~~~ ^~~~~~~~~~~~~~~~ %llu gmapindex.c:510:19: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] chr_string,chroffset+1,chroffset+1+chrlength-1); ^~~~~~~~~~~ gmapindex.c:510:31: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] chr_string,chroffset+1,chroffset+1+chrlength-1); ^~~~~~~~~~~~~~~~~~~~~~~ gmapindex.c:521:17: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] chr_string,chroffset+1,chroffset+chrlength,chrlength); ^~~~~~~~~~~ gmapindex.c:521:29: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] chr_string,chroffset+1,chroffset+chrlength,chrlength); ^~~~~~~~~~~~~~~~~~~ gmapindex.c:696:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accessions[i],universalpos2+1U,universalpos1, ^~~~~~~~~~~~~~~~ gmapindex.c:696:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accessions[i],universalpos2+1U,universalpos1, ^~~~~~~~~~~~~ gmapindex.c:701:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] accessions[i],universalpos1+1U,universalpos2, ^~~~~~~~~~~~~~~~ gmapindex.c:701:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] accessions[i],universalpos1+1U,universalpos2, ^~~~~~~~~~~~~ gmapindex.c:1061:54: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Total genomic length = %lu bp\n",totalnts); ~~~ ^~~~~~~~ %llu 10 warnings generated. mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -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 -D_THREAD_SAFE -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 Undefined symbols for architecture x86_64: "_Access_mmap", referenced from: _Sarray_write_lcp in gmapindex-sarray-write.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [gmapindex] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [gmap] Error 2 ERROR: compilation failed for package ‘gmapR’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR’