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This page was generated on 2023-10-16 11:37:06 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 852/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gmapR 1.42.0  (landing page)
Michael Lawrence
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/gmapR
git_branch: RELEASE_3_17
git_last_commit: 506bc70
git_last_commit_date: 2023-04-25 10:23:34 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.6.4 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

BUILD results for gmapR on merida1


To the developers/maintainers of the gmapR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gmapR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gmapR
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gmapR
StartedAt: 2023-10-15 18:37:49 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 18:43:15 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 325.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gmapR
###
##############################################################################
##############################################################################


* checking for file ‘gmapR/DESCRIPTION’ ... OK
* preparing ‘gmapR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘gmapR’ ...
** using staged installation
** libs
cd gstruct/; \
        CFLAGS="-g -O3" \
	./configure --enable-static --disable-shared \
	            --prefix=/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr --includedir=/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include/gstruct \
	            --libdir=/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib \
	            --with-samtools-lib=/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/bin
checking whether to link statically... not specified so disabled by default
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /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 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... 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 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 by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 306e4:200800:7fbee3ff:bfebfbff
checking whether mmx is enabled and supported by CPU... yes
checking whether sse is enabled and supported by CPU... yes
checking whether sse2 is enabled and supported by CPU... yes
checking whether sse3 is enabled and supported by CPU... yes
checking whether ssse3 is enabled and supported by CPU... yes
checking whether sse4.1 is enabled and supported by CPU... yes
checking whether sse4.2 is enabled and supported by CPU... yes
checking whether avx is enabled and supported by CPU... yes
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether avx is supported by operating system... yes
checking whether popcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x80000001 output... 0:0:1:2c100800
checking whether lzcnt is enabled and supported by CPU... no
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... /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o
mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo
/bin/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o
mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo
/bin/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin21.6.0\" -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o
mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo
/bin/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share\" -g -O3   -D_THREAD_SAFE  -version-info 1:0:0  -o libgstruct-1.0.la -rpath /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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 '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libgstruct-1.0.la '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib'
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib/libgstruct-1.0.la
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: chmod 644 /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: ranlib /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
 ../config/install-sh -c -d '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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 '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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 '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include/gstruct'
 ../config/install-sh -c -d '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib/pkgconfig'
 /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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 -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bamreader.c -o bamreader.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bamtally.c -o bamtally.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c iit.c -o iit.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c variantsummary.c -o variantsummary.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c genome.c -o genome.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_gmapR.c -o R_init_gmapR.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/x86_64/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cd gmap/; \
	 ./configure --with-gmapdb= --prefix=/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr \
	            --libdir=/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
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checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/bin
checking for a working version of perl... /usr/bin/perl
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checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
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checking how to print strings... printf
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checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop
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checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
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checking how to hardcode library paths into programs... immediate
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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
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checking for x86 cpuid 0x00000001 output... 306e4:11200800:7fbee3ff:bfebfbff
checking whether mmx is enabled and supported... yes
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checking whether C compiler accepts -msse4.1... yes
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checking whether C compiler accepts -mavx... yes
checking gmapdb... /private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/gmapR/src/../inst/usr/share
checking MAX_READLENGTH... 250
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
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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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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/MacOSX11.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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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/MacOSX11.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/MacOSX11.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/MacOSX11.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/MacOSX11.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/MacOSX11.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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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=\"/private/tmp/RtmpDcr5bk/Rbuilde0c27d20d661/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
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 ‘/private/tmp/RtmpDcr5bk/Rinste0c276daba74/gmapR’
      -----------------------------------
ERROR: package installation failed