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Created October 17, 2022 19:54
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a
==> Downloading http://research-pub.gene.com/gmap/src/gmap-gsnap-2021-12-17.tar.gz
Already downloaded: /Library/Caches/Homebrew/downloads/25acee6a0370db6d646e1462f8472c2d52b755641091ba1d9e4d858f5ae2ae8d--gmap-gsnap-2021-12-17.tar.gz
==> Verifying checksum for '25acee6a0370db6d646e1462f8472c2d52b755641091ba1d9e4d858f5ae2ae8d--gmap-gsnap-2021-12-17.tar.gz'
==> Installing gmap-gsnap from brewsci/bio
tar --extract --no-same-owner --file /Library/Caches/Homebrew/downloads/25acee6a0370db6d646e1462f8472c2d52b755641091ba1d9e4d858f5ae2ae8d--gmap-gsnap-2021-12-17.tar.gz --directory /private/tmp/d20221017-50389-1j5us08
cp -pR /private/tmp/d20221017-50389-1j5us08/gmap-2021-12-17/. /private/tmp/gmap-gsnap-20221017-50389-12q4ecj/gmap-2021-12-17
chmod -Rf +w /private/tmp/d20221017-50389-1j5us08
==> ./configure --prefix=/opt/homebrew/Cellar/gmap-gsnap/2021-12-17
checking package version... 2021-12-17
loading default site script ./config.site
checking CFLAGS... not set by user so using default -O3 -fomit-frame-pointer
checking build system type... arm-apple-darwin21.6.0
checking host system type... arm-apple-darwin21.6.0
checking target system type... arm-apple-darwin21.6.0
checking for non-Intel CPU... no
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
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 clang... gcc3
checking whether to enable maintainer-specific portions of Makefiles... no
checking bindir... /opt/homebrew/Cellar/gmap-gsnap/2021-12-17/bin
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) clang
checking whether we are using the GNU C compiler... (cached) yes
checking whether clang accepts -g... (cached) yes
checking for clang option to accept ISO C89... (cached) none needed
checking whether clang and cc understand -c and -o together... yes
checking for C compiler vendor... clang
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... clang
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
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 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 for inline... inline
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether alloca is enabled... not specified so disabled by default
checking whether mmap is enabled... not specified so enabled by default
checking for working mmap with MAP_FIXED... no
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for SHM_NORESERVE in shmget... no
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 shmget... yes
checking for shmctl... yes
checking for shmat... yes
checking for shmdt... yes
checking for semget... yes
checking for semctl... yes
checking for semop... yes
checking for struct stat64... no
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 whether C compiler accepts -O3 -fomit-frame-pointer -mpopcnt... yes
checking whether __builtin_popcount is declared... no
checking whether __builtin_clz is declared... no
checking whether __builtin_ctz is declared... no
checking for bsr instruction in assembly... no
checking compiler is defective and requires an immediate in sse2 shift commands... yes
checking for _mm_extract_epi64... no
checking for _mm_popcnt_u64... no
checking for whether simd is enabled... not specified so enabled by default
checking for sse2 support... no
checking for ssse3 support... no
checking for sse4.1 support... no
checking for sse4.2 support... no
checking for popcnt support... no
checking for bmi1 support... no
checking for avx2 support... no
checking for bmi2 support... no
checking for avx512 support... no
checking for avx512bw and avx512vl support... no
checking gmapdb... /opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share
checking MAX_STACK_READLENGTH... 300
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for bzlib support... enabled
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for BZ2_bzReadOpen in -lbz2... yes
checking for BZ2_bzRead in -lbz2... yes
checking for BZ2_bzReadClose in -lbz2... yes
checking if bzlib package is complete... working
checking 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_process.pl
config.status: creating util/gmap_build.pl
config.status: creating util/gmap_cat.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/ensembl_genes.pl
config.status: creating util/gtf_splicesites.pl
config.status: creating util/gtf_transcript_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
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.
configure: WARNING:
WARNING: Your C compiler does not know how to handle a particular
form of the SSE2 shift commands, and must be somewhat old (probably
gcc 4.1 or gcc 4.2). The configure script has therefore substituted
alternate C code that your compiler can handle. However, for
optimal performance, you may want to obtain a more recent C compiler
and build the code with that.
checking standard compiler and flags to be used... clang -O3 -fomit-frame-pointer
checking standard linker flags to be used...
checking pthread compiler flags to be used... -D_THREAD_SAFE
checking popcnt flags to be used... -mpopcnt
checking compile level... none
==> make
Making all in src
/Library/Developer/CommandLineTools/usr/bin/make all-am
clang -DHAVE_CONFIG_H -I. -DMAIN=1 -O3 -fomit-frame-pointer -MT cpuid-cpuid.o -MD -MP -MF .deps/cpuid-cpuid.Tpo -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
clang -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -MT gmap-cpuid.o -MD -MP -MF .deps/gmap-cpuid.Tpo -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
clang -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -MT gmap-gmap_select.o -MD -MP -MF .deps/gmap-gmap_select.Tpo -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo './'`gmap_select.c
clang -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -MT gmapl-cpuid.o -MD -MP -MF .deps/gmapl-cpuid.Tpo -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
clang -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -MT gmapl-gmapl_select.o -MD -MP -MF .deps/gmapl-gmapl_select.Tpo -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo './'`gmapl_select.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-assert.Tpo .deps/get_genome-assert.Po
mv -f .deps/gmapl-cpuid.Tpo .deps/gmapl-cpuid.Po
mv -f .deps/cpuid-cpuid.Tpo .deps/cpuid-cpuid.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/gmap-cpuid.Tpo .deps/gmap-cpuid.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-except.Tpo .deps/get_genome-except.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-mem.Tpo .deps/get_genome-mem.Po
mv -f .deps/gmap-gmap_select.Tpo .deps/gmap-gmap_select.Po
mv -f .deps/gmapl-gmapl_select.Tpo .deps/gmapl-gmapl_select.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -MT get_genome-semaphore.o -MD -MP -MF .deps/get_genome-semaphore.Tpo -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-list.Tpo .deps/get_genome-list.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -MT get_genome-filestring.o -MD -MP -MF .deps/get_genome-filestring.Tpo -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-univinterval.Tpo .deps/get_genome-univinterval.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-bigendian.Tpo .deps/get_genome-bigendian.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-stopwatch.Tpo .deps/get_genome-stopwatch.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -MT get_genome-fopen.o -MD -MP -MF .deps/get_genome-fopen.Tpo -c -o get_genome-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
mv -f .deps/get_genome-semaphore.Tpo .deps/get_genome-semaphore.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-interval.Tpo .deps/get_genome-interval.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-access.Tpo .deps/get_genome-access.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/get_genome-fopen.Tpo .deps/get_genome-fopen.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-bzip2.Tpo .deps/get_genome-bzip2.Po
mv -f .deps/get_genome-filestring.Tpo .deps/get_genome-filestring.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po
mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -MT get_genome-getline.o -MD -MP -MF .deps/get_genome-getline.Tpo -c -o get_genome-getline.o `test -f 'getline.c' || echo './'`getline.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-chrom.Tpo .deps/get_genome-chrom.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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-chrnum.Tpo .deps/get_genome-chrnum.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share\" -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po
mv -f .deps/get_genome-getline.Tpo .deps/get_genome-getline.Po
mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po
mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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/get_genome-getopt.Tpo .deps/get_genome-getopt.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-assert.Tpo .deps/gmapindex-assert.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po
mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-littleendian.Tpo .deps/gmapindex-littleendian.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-list.Tpo .deps/gmapindex-list.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-semaphore.o -MD -MP -MF .deps/gmapindex-semaphore.Tpo -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-bigendian.Tpo .deps/gmapindex-bigendian.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-filestring.o -MD -MP -MF .deps/gmapindex-filestring.Tpo -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po
mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-uintlist.Tpo .deps/gmapindex-uintlist.Po
mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
mv -f .deps/gmapindex-semaphore.Tpo .deps/gmapindex-semaphore.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-fopen.o -MD -MP -MF .deps/gmapindex-fopen.Tpo -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-filestring.Tpo .deps/gmapindex-filestring.Po
mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-fopen.Tpo .deps/gmapindex-fopen.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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
mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po
mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-bzip2.Tpo .deps/gmapindex-bzip2.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-popcount.o -MD -MP -MF .deps/gmapindex-popcount.Tpo -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-genome128_hr.o -MD -MP -MF .deps/gmapindex-genome128_hr.Tpo -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-genome128_consec.o -MD -MP -MF .deps/gmapindex-genome128_consec.Tpo -c -o gmapindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-compress.Tpo .deps/gmapindex-compress.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-bitpack64-readtwo.o -MD -MP -MF .deps/gmapindex-bitpack64-readtwo.Tpo -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
mv -f .deps/gmapindex-popcount.Tpo .deps/gmapindex-popcount.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-bitpack64-access.o -MD -MP -MF .deps/gmapindex-bitpack64-access.Tpo -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-bitpack64-incr.o -MD -MP -MF .deps/gmapindex-bitpack64-incr.Tpo -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -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-compress-write.Tpo .deps/gmapindex-compress-write.Po
bitpack64-access.c:2233:33: error: use of undeclared identifier 'clz_table'
firstbit = ((value >> 16) ? clz_table[value >> 16] : 16 + clz_table[value]);
^
clang -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DUTILITYP=1 -O3 -fomit-frame-pointer -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
bitpack64-access.c:2233:63: error: use of undeclared identifier 'clz_table'
firstbit = ((value >> 16) ? clz_table[value >> 16] : 16 + clz_table[value]);
^
2 errors generated.
make[2]: *** [gmapindex-bitpack64-access.o] Error 1
make[2]: *** Waiting for unfinished jobs....
mv -f .deps/gmapindex-genome128_consec.Tpo .deps/gmapindex-genome128_consec.Po
mv -f .deps/gmapindex-bitpack64-readtwo.Tpo .deps/gmapindex-bitpack64-readtwo.Po
mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po
mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po
mv -f .deps/gmapindex-genome128_hr.Tpo .deps/gmapindex-genome128_hr.Po
mv -f .deps/gmapindex-bitpack64-write.Tpo .deps/gmapindex-bitpack64-write.Po
mv -f .deps/gmapindex-bitpack64-incr.Tpo .deps/gmapindex-bitpack64-incr.Po
mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po
mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/gmap-gsnap.rb
==> Configuration
HOMEBREW_VERSION: 3.6.5-1-g2919ab0
ORIGIN: https://github.com/Homebrew/brew
HEAD: 2919ab0206250ea119ea403f76291d0e5c8c18b6
Last commit: 9 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 9ec6fb16b3acfa926fabdfe14f399108d8b5ef6c
Core tap last commit: 3 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_BROWSER: open -a Firefox.app
HOMEBREW_CACHE: /Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.jAXNwUkjFX/org.xquartz:0
HOMEBREW_EDITOR: mate_wait
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_LOGS: /var/log/homebrew
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 2.6.8 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: 10-core 64-bit arm_firestorm_icestorm
Clang: 14.0.0 build 1400
Git: 2.38.0 => /opt/homebrew/bin/git
Curl: 7.79.1 => /usr/bin/curl
macOS: 12.6-arm64
CLT: 14.0.0.0.1.1661618636
Xcode: 13.4.1
Error: brewsci/bio/gmap-gsnap 2021-12-17 did not build
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j10
CMAKE_PREFIX_PATH: /opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH: /opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/htslib/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/12
HOMEBREW_GIT: git
HOMEBREW_SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
ACLOCAL_PATH: /opt/homebrew/share/aclocal
PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew/opt/xz/bin:/opt/homebrew/opt/htslib/bin:/opt/homebrew/opt/samtools/bin:/usr/bin:/bin:/usr/sbin:/sbin
Logs:
/var/log/homebrew/gmap-gsnap/00.options.out
/var/log/homebrew/gmap-gsnap/01.configure.cc
/var/log/homebrew/gmap-gsnap/02.make.cc
/var/log/homebrew/gmap-gsnap/config.log
/var/log/homebrew/gmap-gsnap/01.configure
/var/log/homebrew/gmap-gsnap/02.make
Do not report this issue to Homebrew/brew or Homebrew/core!
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