gistfile1.txt

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
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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
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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
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checking fcntl.h usability... yes
checking fcntl.h presence... yes
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checking limits.h usability... yes
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checking stddef.h usability... yes
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checking for inline... inline
checking whether byte ordering is bigendian... no
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checking size of unsigned long... 8
checking size of unsigned long long... 8
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checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether alloca is enabled... not specified so disabled by default
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checking for working mmap with MAP_FIXED... no
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checking for MADV_DONTNEED in madvise... yes
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checking for SHM_NORESERVE in shmget... no
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checking for struct stat64... no
checking for pagesize via sysconf... yes
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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
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checking for whether simd is enabled... not specified so enabled by default
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checking for avx512 support... no
checking for avx512bw and avx512vl support... no
checking for user-selected SIMD level... sse42
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
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checking if zlib package is complete... working
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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... sse42
checking SSE4.2 compiler flags to be used... 
==> 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
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-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.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-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/gmap-gmap_select.Tpo .deps/gmap-gmap_select.Po
mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.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-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
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-filestring.o -MD -MP -MF .deps/get_genome-filestring.Tpo -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.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-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-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-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-semaphore.Tpo .deps/get_genome-semaphore.Po
mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po
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-fopen.o -MD -MP -MF .deps/get_genome-fopen.Tpo -c -o get_genome-fopen.o `test -f 'fopen.c' || echo './'`fopen.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-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.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-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-bzip2.Tpo .deps/get_genome-bzip2.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-fopen.Tpo .deps/get_genome-fopen.Po
mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.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
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
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-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-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.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-chrnum.Tpo .deps/get_genome-chrnum.Po
mv -f .deps/get_genome-getline.Tpo .deps/get_genome-getline.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-datadir.Tpo .deps/get_genome-datadir.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
mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po
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
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-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-getopt1.Tpo .deps/get_genome-getopt1.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-getopt.Tpo .deps/get_genome-getopt.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
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
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-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
mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.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
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-bigendian.Tpo .deps/gmapindex-bigendian.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
mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.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-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
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
mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
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/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
mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po
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
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
mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po
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-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
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
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
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-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-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-popcount.o -MD -MP -MF .deps/gmapindex-popcount.Tpo -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.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-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
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/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
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-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
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-genome-write.Tpo .deps/gmapindex-genome-write.Po
mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.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-sequence.Tpo .deps/gmapindex-sequence.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
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:2233:33: error: use of undeclared identifier 'clz_table'
    firstbit = ((value >> 16) ? clz_table[value >> 16] : 16 + clz_table[value]);
                                ^
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.
mv -f .deps/gmapindex-genome128_consec.Tpo .deps/gmapindex-genome128_consec.Po
make[2]: *** [gmapindex-bitpack64-access.o] Error 1
make[2]: *** Waiting for unfinished jobs....
mv -f .deps/gmapindex-bitpack64-readtwo.Tpo .deps/gmapindex-bitpack64-readtwo.Po
mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po
mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.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-iit-read.Tpo .deps/gmapindex-iit-read.Po
mv -f .deps/gmapindex-bitpack64-incr.Tpo .deps/gmapindex-bitpack64-incr.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: 3.6.3-3-g520d9c3
ORIGIN: https://github.com/Homebrew/brew
HEAD: 520d9c3ab8cf377fab055a099889862e60033ede
Last commit: 13 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: ba43f699b8ef8ba44b33b377b4cbee10cb657b25
Core tap last commit: 23 minutes 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.HKxAHPuIsJ/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: 2.37.3 => /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
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