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Created October 17, 2012 20:40
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TMAP homebrew
Raw
gistfile1.txt
nilshomer$ ./bin/brew install -v tmap
==> Cloning https://github.com/iontorrent/TMAP.git
git clone --depth 1 --branch tmap.3.2.0 https://github.com/iontorrent/TMAP.git /Users/nilshomer/Library/Caches/Homebrew/tmap--git
Cloning into '/Users/nilshomer/Library/Caches/Homebrew/tmap--git'...
remote: Counting objects: 2272, done.
remote: Compressing objects: 100% (1182/1182), done.
remote: Total 2272 (delta 1681), reused 1564 (delta 1085)
Receiving objects: 100% (2272/2272), 6.20 MiB | 928 KiB/s, done.
Resolving deltas: 100% (1681/1681), done.
warning: Remote branch tmap.3.2.0 not found in upstream origin, using HEAD instead
==> Checking out tag tmap.3.2.0
git checkout tmap.3.2.0 --
Note: checking out 'tmap.3.2.0'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b new_branch_name
HEAD is now at 115c314... * moving master to 3.2.0
git checkout-index -a -f --prefix=/private/tmp/tmap-cSqp/
git submodule init
Submodule 'src/samtools' (http://github.com/nh13/samtools.git) registered for path 'src/samtools'
git submodule update
Cloning into 'src/samtools'...
remote: Counting objects: 5251, done.
remote: Compressing objects: 100% (1437/1437), done.
remote: Total 5251 (delta 3824), reused 5211 (delta 3804)
Receiving objects: 100% (5251/5251), 1.68 MiB | 2.57 MiB/s, done.
Resolving deltas: 100% (3824/3824), done.
Submodule path 'src/samtools': checked out '2c748fb1381cfc41f970e27a68a927ddc497a8ac'
git submodule --quiet foreach --recursive git checkout-index -a -f "--prefix=/private/tmp/tmap-cSqp/$path/"
==> sh autogen.sh
sh autogen.sh
running: aclocal
running: autoheader
running: automake -a
running: autoconf
==> ./configure --disable-dependency-tracking --disable-tcmalloc --prefix=/Users/nilshomer/git/homebrew/Cellar/tmap/3.2.0 --enable-intel64
./configure --disable-dependency-tracking --disable-tcmalloc --prefix=/Users/nilshomer/git/homebrew/Cellar/tmap/3.2.0 --enable-intel64
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 build system type... x86_64-apple-darwin11.4.2
checking for gcc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... none
checking whether cc understands -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... none
checking whether c++ understands -c and -o together... yes
checking how to run the C preprocessor... cc -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 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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether the git revision is available... no
checking for BZ2_bzRead in -lbz2... yes
configure: WARNING: "Using 64-bit SA intervals; Genome sizes greater than 4Gb are supported"
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for inline... inline
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for error_at_line... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for working memcmp... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking whether lstat correctly handles trailing slash... no
checking whether stat accepts an empty string... no
checking for working strtod... yes
checking for vprintf... yes
checking for _doprnt... no
checking for gzread in -lz... yes
checking for pow in -lm... yes
checking for pthread_create in -lpthread... yes
checking for pow... yes
checking for strdup... yes
checking for memset... yes
checking for strchr... yes
checking for strdup... (cached) yes
checking for strstr... yes
checking for memmove... yes
checking for getopt_long... yes
checking for gettimeofday... yes
checking for gethostbyaddr... yes
checking for gethostbyname... yes
checking for memchr... yes
checking for select... yes
checking for socket... yes
checking for sqrt... yes
checking for strerror... yes
checking for strtol... yes
checking for int8_t... yes
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for size_t... (cached) yes
checking for off_t... yes
checking return type of signal handlers... void
checking for ssize_t... yes
checking size of short int... 2
checking size of int... 4
checking size of long int... 8
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking emmintrin.h usability... yes
checking emmintrin.h presence... yes
checking for emmintrin.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for sys/socket.h... (cached) yes
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking curses.h usability... yes
checking curses.h presence... yes
checking for curses.h... yes
checking xcurses.h usability... no
checking xcurses.h presence... no
checking for xcurses.h... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
==> make
make
/usr/bin/make all-recursive
Making all in .
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_alloc.o src/util/tmap_alloc.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_definitions.o src/util/tmap_definitions.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_error.o src/util/tmap_error.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_rand.o src/util/tmap_rand.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_time.o src/util/tmap_time.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_fibheap.o src/util/tmap_fibheap.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_progress.o src/util/tmap_progress.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_string.o src/util/tmap_string.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_levenshtein.o src/util/tmap_levenshtein.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/util/tmap_sam_convert.o src/util/tmap_sam_convert.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/seq/tmap_fq.o src/seq/tmap_fq.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/seq/tmap_sff.o src/seq/tmap_sff.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/seq/tmap_sam.o src/seq/tmap_sam.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/seq/tmap_seq.o src/seq/tmap_seq.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/seq/tmap_seqs.o src/seq/tmap_seqs.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/io/tmap_file.o src/io/tmap_file.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/io/tmap_fq_io.o src/io/tmap_fq_io.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/io/tmap_sff_io.o src/io/tmap_sff_io.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/io/tmap_sam_io.o src/io/tmap_sam_io.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/io/tmap_seq_io.o src/io/tmap_seq_io.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/io/tmap_seqs_io.o src/io/tmap_seqs_io.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt.o src/index/tmap_bwt.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_aux.o src/index/tmap_bwt_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwtl.o src/index/tmap_bwtl.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_gen.o src/index/tmap_bwt_gen.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_match.o src/index/tmap_bwt_match.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_match_hash.o src/index/tmap_bwt_match_hash.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_smem.o src/index/tmap_bwt_smem.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_index.o src/index/tmap_index.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_refseq.o src/index/tmap_refseq.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_sa.o src/index/tmap_sa.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_sa_aux.o src/index/tmap_sa_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_index_size.o src/index/tmap_index_size.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sw/tmap_sw.o src/sw/tmap_sw.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sw/tmap_fsw.o src/sw/tmap_fsw.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sw/tmap_vsw_definitions.o src/sw/tmap_vsw_definitions.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sw/tmap_vsw.o src/sw/tmap_vsw.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/vsw.o src/sw/lib/vsw.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/vsw16.o src/sw/lib/vsw16.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/sw-vector.o src/sw/lib/sw-vector.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution.o src/sw/lib/Solution.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution1.o src/sw/lib/Solution1.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution2.o src/sw/lib/Solution2.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution3.o src/sw/lib/Solution3.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution4.o src/sw/lib/Solution4.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution5.o src/sw/lib/Solution5.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution6.o src/sw/lib/Solution6.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution7.o src/sw/lib/Solution7.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution8.o src/sw/lib/Solution8.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution9.o src/sw/lib/Solution9.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution10.o src/sw/lib/Solution10.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/AffineSWOptimization.o src/sw/lib/AffineSWOptimization.cpp
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c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/AffineSWOptimizationHash.o src/sw/lib/AffineSWOptimizationHash.cpp
brew: superenv removed: -Wall -g -O3
c++ -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/AffineSWOptimizationWrapper.o src/sw/lib/AffineSWOptimizationWrapper.cpp
brew: superenv removed: -Wall -g -O3
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sw/tmap_vsw_bm.o src/sw/tmap_vsw_bm.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam.o src/samtools/bam.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/sam.o src/samtools/sam.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/sam_header.o src/samtools/sam_header.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_import.o src/samtools/bam_import.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_aux.o src/samtools/bam_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_pileup.o src/samtools/bam_pileup.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_lpileup.o src/samtools/bam_lpileup.c
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cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_md.o src/samtools/bam_md.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/faidx.o src/samtools/faidx.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bedidx.o src/samtools/bedidx.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/razf.o src/samtools/razf.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bgzf.o src/samtools/bgzf.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/kstring.o src/samtools/kstring.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/knetfile.o src/samtools/knetfile.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/kaln.o src/samtools/kaln.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/kprobaln.o src/samtools/kprobaln.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_index.o src/samtools/bam_index.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_sort.o src/samtools/bam_sort.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_reheader.o src/samtools/bam_reheader.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_cat.o src/samtools/bam_cat.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_tview.o src/samtools/bam_tview.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_plcmd.o src/samtools/bam_plcmd.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/sam_view.o src/samtools/sam_view.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_rmdup.o src/samtools/bam_rmdup.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_rmdupse.o src/samtools/bam_rmdupse.c
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cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_mate.o src/samtools/bam_mate.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_stat.o src/samtools/bam_stat.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam_color.o src/samtools/bam_color.c
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cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam2bcf.o src/samtools/bam2bcf.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam2bcf_indel.o src/samtools/bam2bcf_indel.c
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cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/errmod.o src/samtools/errmod.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/sample.o src/samtools/sample.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/cut_target.o src/samtools/cut_target.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/phase.o src/samtools/phase.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bam2depth.o src/samtools/bam2depth.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/padding.o src/samtools/padding.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcf2qcall.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/bcfutils.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/call1.o src/samtools/bcftools/call1.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/em.o src/samtools/bcftools/em.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/fet.o src/samtools/bcftools/fet.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/index.o src/samtools/bcftools/index.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kfunc.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/kmin.o src/samtools/bcftools/kmin.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/main.o src/samtools/bcftools/main.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/mut.o src/samtools/bcftools/mut.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/prob1.o src/samtools/bcftools/prob1.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bcftools/vcf.o src/samtools/bcftools/vcf.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/samtools/bamtk.o src/samtools/bamtk.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/server/tmap_server.o src/server/tmap_server.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/server/tmap_shm.o src/server/tmap_shm.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/sam2fs/tmap_sam2fs.o src/sam2fs/tmap_sam2fs.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_index_speed.o src/index/tmap_index_speed.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_check.o src/index/tmap_bwt_check.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/index/tmap_bwt_compare.o src/index/tmap_bwt_compare.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/util/tmap_map_opt.o src/map/util/tmap_map_opt.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/util/tmap_map_stats.o src/map/util/tmap_map_stats.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/util/tmap_map_util.o src/map/util/tmap_map_util.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/pairing/tmap_map_pairing.o src/map/pairing/tmap_map_pairing.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map1/tmap_map1.o src/map/map1/tmap_map1.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map1/tmap_map1_aux.o src/map/map1/tmap_map1_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map2/tmap_map2.o src/map/map2/tmap_map2.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_chain.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_core.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map2/tmap_map2_mempool.o src/map/map2/tmap_map2_mempool.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map3/tmap_map3.o src/map/map3/tmap_map3.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map3/tmap_map3_aux.o src/map/map3/tmap_map3_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map4/tmap_map4.o src/map/map4/tmap_map4.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/map4/tmap_map4_aux.o src/map/map4/tmap_map4_aux.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/mapvsw/tmap_map_vsw.o src/map/mapvsw/tmap_map_vsw.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/mapall/tmap_map_all.o src/map/mapall/tmap_map_all.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/map/tmap_map_driver.o src/map/tmap_map_driver.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
cc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -mtune=nocona -c -o src/tmap_main.o src/tmap_main.c
brew: superenv removed: -Wall -g -O3 -mtune=nocona
c++ -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -Isrc/samtools -o tmap src/util/tmap_alloc.o src/util/tmap_definitions.o src/util/tmap_error.o src/util/tmap_rand.o src/util/tmap_time.o src/util/tmap_fibheap.o src/util/tmap_progress.o src/util/tmap_string.o src/util/tmap_levenshtein.o src/util/tmap_sam_convert.o src/seq/tmap_fq.o src/seq/tmap_sff.o src/seq/tmap_sam.o src/seq/tmap_seq.o src/seq/tmap_seqs.o src/io/tmap_file.o src/io/tmap_fq_io.o src/io/tmap_sff_io.o src/io/tmap_sam_io.o src/io/tmap_seq_io.o src/io/tmap_seqs_io.o src/index/tmap_bwt.o src/index/tmap_bwt_aux.o src/index/tmap_bwtl.o src/index/tmap_bwt_gen.o src/index/tmap_bwt_match.o src/index/tmap_bwt_match_hash.o src/index/tmap_bwt_smem.o src/index/tmap_index.o src/index/tmap_refseq.o src/index/tmap_sa.o src/index/tmap_sa_aux.o src/index/tmap_index_size.o src/sw/tmap_sw.o src/sw/tmap_fsw.o src/sw/tmap_vsw_definitions.o src/sw/tmap_vsw.o src/sw/lib/vsw.o src/sw/lib/vsw16.o src/sw/lib/sw-vector.o src/sw/lib/Solution.o src/sw/lib/Solution1.o src/sw/lib/Solution2.o src/sw/lib/Solution3.o src/sw/lib/Solution4.o src/sw/lib/Solution5.o src/sw/lib/Solution6.o src/sw/lib/Solution7.o src/sw/lib/Solution8.o src/sw/lib/Solution9.o src/sw/lib/Solution10.o src/sw/lib/AffineSWOptimization.o src/sw/lib/AffineSWOptimizationHash.o src/sw/lib/AffineSWOptimizationWrapper.o src/sw/tmap_vsw_bm.o src/samtools/bam.o src/samtools/sam.o src/samtools/sam_header.o src/samtools/bam_import.o src/samtools/bam_aux.o src/samtools/bam_pileup.o src/samtools/bam_lpileup.o src/samtools/bam_md.o src/samtools/faidx.o src/samtools/bedidx.o src/samtools/razf.o src/samtools/bgzf.o src/samtools/kstring.o src/samtools/knetfile.o src/samtools/kaln.o src/samtools/kprobaln.o src/samtools/bam_index.o src/samtools/bam_sort.o src/samtools/bam_reheader.o src/samtools/bam_cat.o src/samtools/bam_tview.o src/samtools/bam_plcmd.o src/samtools/sam_view.o src/samtools/bam_rmdup.o src/samtools/bam_rmdupse.o src/samtools/bam_mate.o src/samtools/bam_stat.o src/samtools/bam_color.o src/samtools/bam2bcf.o src/samtools/bam2bcf_indel.o src/samtools/errmod.o src/samtools/sample.o src/samtools/cut_target.o src/samtools/phase.o src/samtools/bam2depth.o src/samtools/padding.o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/call1.o src/samtools/bcftools/em.o src/samtools/bcftools/fet.o src/samtools/bcftools/index.o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kmin.o src/samtools/bcftools/main.o src/samtools/bcftools/mut.o src/samtools/bcftools/prob1.o src/samtools/bcftools/vcf.o src/samtools/bamtk.o src/server/tmap_server.o src/server/tmap_shm.o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs.o src/index/tmap_index_speed.o src/index/tmap_bwt_check.o src/index/tmap_bwt_compare.o src/map/util/tmap_map_opt.o src/map/util/tmap_map_stats.o src/map/util/tmap_map_util.o src/map/pairing/tmap_map_pairing.o src/map/map1/tmap_map1.o src/map/map1/tmap_map1_aux.o src/map/map2/tmap_map2.o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_mempool.o src/map/map3/tmap_map3.o src/map/map3/tmap_map3_aux.o src/map/map4/tmap_map4.o src/map/map4/tmap_map4_aux.o src/map/mapvsw/tmap_map_vsw.o src/map/mapall/tmap_map_all.o src/map/tmap_map_driver.o src/tmap_main.o -lpthread -lm -lz -lbz2
brew: superenv removed: -Wall -g -O3
Undefined symbols for architecture x86_64:
"___ks_insertsort_sort", referenced from:
_ks_combsort_sort in bam_sort.o
_ks_introsort_sort in bam_sort.o
"_tmap_bwt_2occ", referenced from:
_tmap_index_speed in tmap_index_speed.o
"_tmap_bwt_2occ4", referenced from:
_tmap_bwt_smem_extend in tmap_bwt_smem.o
_tmap_index_speed in tmap_index_speed.o
"_tmap_bwt_match_cal_width_reverse", referenced from:
_tmap_map1_thread_map in tmap_map1.o
"_tmap_bwt_match_hash_2occ", referenced from:
_tmap_bwt_match_hash_cal_width_forward in tmap_bwt_match_hash.o
_tmap_bwt_match_hash_cal_width_reverse in tmap_bwt_match_hash.o
_tmap_bwt_match_hash_exact in tmap_bwt_match_hash.o
_tmap_bwt_match_hash_exact_reverse in tmap_bwt_match_hash.o
_tmap_bwt_match_hash_exact_alt in tmap_bwt_match_hash.o
_tmap_bwt_match_hash_exact_alt_reverse in tmap_bwt_match_hash.o
_tmap_map3_aux_core_seed in tmap_map3_aux.o
...
"_tmap_bwt_match_hash_2occ4", referenced from:
_tmap_map1_aux_core in tmap_map1_aux.o
_tmap_map2_core_aln in tmap_map2_core.o
"_tmap_bwt_match_hash_occ", referenced from:
_tmap_bwt_match_hash_invPsi in tmap_bwt_match_hash.o
"_tmap_bwt_occ", referenced from:
_tmap_sa_bwt2sa in tmap_sa.o
_tmap_index_speed in tmap_index_speed.o
"_tmap_bwt_occ4", referenced from:
_tmap_index_speed in tmap_index_speed.o
"_tmap_bwtl_2occ4", referenced from:
_tmap_map2_core_aln in tmap_map2_core.o
"_tmap_compliment", referenced from:
_tmap_string_compliment in tmap_string.o
"_tmap_fq_clone", referenced from:
_tmap_seq_clone in tmap_seq.o
"_tmap_fq_destroy", referenced from:
_tmap_seq_destroy in tmap_seq.o
"_tmap_fq_init", referenced from:
_tmap_seq_init in tmap_seq.o
"_tmap_fsw_sub_core", referenced from:
_tmap_fsw_clipping_core in tmap_fsw.o
"_tmap_get_file_name", referenced from:
_tmap_bwt_read in tmap_bwt.o
_tmap_bwt_write in tmap_bwt.o
_tmap_bwt_shm_read_num_bytes in tmap_bwt.o
_tmap_bwt_pac2bwt in tmap_bwt_gen.o
_tmap_refseq_fasta2pac in tmap_refseq.o
_tmap_refseq_read in tmap_refseq.o
_tmap_refseq_write in tmap_refseq.o
...
"_tmap_interval_overlap", referenced from:
_tmap_refseq_pac2fasta_main in tmap_refseq.o
"_tmap_log2", referenced from:
_tmap_bwt_read in tmap_bwt.o
_tmap_bwt_shm_unpack in tmap_bwt.o
_tmap_bwt_update_occ_interval in tmap_bwt.o
_tmap_sa_read in tmap_sa.o
_tmap_sa_shm_unpack in tmap_sa.o
"_tmap_map2_mempool_pop", referenced from:
_tmap_map2_core_aln in tmap_map2_core.o
"_tmap_map2_stack_pop", referenced from:
_tmap_map2_core_aln in tmap_map2_core.o
"_tmap_map2_stack_push0", referenced from:
_tmap_map2_core_aln in tmap_map2_core.o
"_tmap_map_sam_copy", referenced from:
_tmap_map_sams_clone in tmap_map_util.o
_tmap_map_sams_merge in tmap_map_util.o
_tmap_map_pairing_read_rescue_helper in tmap_map_pairing.o
(maybe you meant: _tmap_map_sam_copy_and_nullify)
"_tmap_refseq_pac2real", referenced from:
_tmap_map1_aux_core in tmap_map1_aux.o
_tmap_map2_aux_core in tmap_map2_aux.o
_tmap_map3_aux_core in tmap_map3_aux.o
_tmap_map4_aux_core in tmap_map4_aux.o
"_tmap_refseq_subseq", referenced from:
_tmap_index_speed in tmap_index_speed.o
_tmap_map_util_fsw in tmap_map_util.o
"_tmap_refseq_subseq2", referenced from:
_tmap_map_util_sw_gen_score_helper in tmap_map_util.o
_tmap_map_util_sw_gen_cigar in tmap_map_util.o
"_tmap_reverse_compliment", referenced from:
_tmap_string_reverse_compliment in tmap_string.o
_tmap_sam2fs_aux_worker in tmap_sam2fs.o
"_tmap_reverse_compliment_int", referenced from:
_tmap_map_util_sw_gen_score_helper in tmap_map_util.o
_tmap_map_util_sw_gen_cigar in tmap_map_util.o
_tmap_map_util_fsw in tmap_map_util.o
"_tmap_reverse_int", referenced from:
_tmap_sw_clipping_core2 in tmap_sw.o
"_tmap_sam_clone", referenced from:
_tmap_seq_clone in tmap_seq.o
"_tmap_sam_convert_mapped", referenced from:
_tmap_map_sam_print in tmap_map_util.o
"_tmap_sam_convert_unmapped", referenced from:
_tmap_seqs_io_sff2sam_main in tmap_seqs_io.o
_tmap_map_sam_print in tmap_map_util.o
"_tmap_sam_io_init2", referenced from:
_tmap_seqs_io_sff2sam_main in tmap_seqs_io.o
_tmap_map_driver_core in tmap_map_driver.o
"_tmap_seq_get_bases", referenced from:
_tmap_fsw_flowseq_from_seq in tmap_fsw.o
_tmap_map_util_sw_gen_score in tmap_map_util.o
_tmap_map_util_sw_gen_score_helper in tmap_map_util.o
_tmap_map_util_sw_gen_cigar in tmap_map_util.o
_tmap_map1_thread_map in tmap_map1.o
_tmap_map1_aux_core in tmap_map1_aux.o
_tmap_map2_aux_core in tmap_map2_aux.o
...
"_tmap_seq_get_bases_length", referenced from:
_tmap_map_util_sw_gen_score in tmap_map_util.o
_tmap_map_util_sw_gen_score_helper in tmap_map_util.o
_tmap_map_util_sw_gen_cigar in tmap_map_util.o
_tmap_map_pairing_pick_pairs in tmap_map_pairing.o
_tmap_map_pairing_read_rescue_helper in tmap_map_pairing.o
_tmap_map1_thread_map in tmap_map1.o
_tmap_map2_thread_map in tmap_map2.o
...
"_tmap_seq_io_destroy", referenced from:
_tmap_seq_io_sff2fq_main in tmap_seq_io.o
_tmap_seqs_io_sff2sam_main in tmap_seqs_io.o
_tmap_refseq_fasta2pac in tmap_refseq.o
"_tmap_seq_io_init", referenced from:
_tmap_seq_io_sff2fq_main in tmap_seq_io.o
_tmap_refseq_fasta2pac in tmap_refseq.o
"_tmap_seq_io_read", referenced from:
_tmap_seq_io_read_buffer in tmap_seq_io.o
_tmap_seq_io_sff2fq_main in tmap_seq_io.o
_tmap_refseq_fasta2pac in tmap_refseq.o
(maybe you meant: _tmap_seq_io_read_buffer)
"_tmap_seqs_io_destroy", referenced from:
_tmap_map_driver_core in tmap_map_driver.o
"_tmap_seqs_io_init", referenced from:
_tmap_seqs_io_sff2sam_main in tmap_seqs_io.o
_tmap_map_driver_core in tmap_map_driver.o
"_tmap_seqs_io_read", referenced from:
_tmap_seqs_io_read_buffer in tmap_seqs_io.o
_tmap_seqs_io_sff2sam_main in tmap_seqs_io.o
(maybe you meant: _tmap_seqs_io_read_buffer)
"_tmap_shm_add_listing", referenced from:
_tmap_server_start in tmap_server.o
"_tmap_shm_get_buffer", referenced from:
_tmap_index_init in tmap_index.o
"_tmap_shm_get_state", referenced from:
_tmap_server_start in tmap_server.o
"_tmap_shm_set_dead", referenced from:
_tmap_server_sigint in tmap_server.o
_tmap_server_stop in tmap_server.o
_tmap_server_kill in tmap_server.o
"_tmap_shm_set_ready", referenced from:
_tmap_server_start in tmap_server.o
"_tmap_string_clone", referenced from:
_tmap_sff_clone in tmap_sff.o
_tmap_refseq_fasta2pac in tmap_refseq.o
"_tmap_string_clone2", referenced from:
_tmap_refseq_fasta2pac in tmap_refseq.o
"_tmap_string_copy", referenced from:
_tmap_seq_sff2fq in tmap_seq.o
"_tmap_string_destroy", referenced from:
_tmap_sff_header_destroy in tmap_sff.o
_tmap_sff_read_header_destroy in tmap_sff.o
_tmap_sff_read_destroy in tmap_sff.o
_tmap_sam_destroy in tmap_sam.o
_tmap_sam_io_update_string in tmap_sam_io.o
_tmap_refseq_destroy in tmap_refseq.o
"_tmap_string_init", referenced from:
_tmap_sff_header_read in tmap_sff.o
_tmap_sff_read_header_read in tmap_sff.o
_tmap_sff_read_read in tmap_sff.o
_tmap_sam_io_update_string in tmap_sam_io.o
_tmap_refseq_read_anno in tmap_refseq.o
_tmap_refseq_shm_unpack in tmap_refseq.o
"_tmap_string_reverse", referenced from:
_tmap_fq_reverse in tmap_fq.o
_tmap_fq_reverse_compliment in tmap_fq.o
_tmap_sff_reverse in tmap_sff.o
_tmap_sff_reverse_compliment in tmap_sff.o
_tmap_sam_reverse in tmap_sam.o
_tmap_sam_reverse_compliment in tmap_sam.o
(maybe you meant: _tmap_string_reverse_compliment)
"_tmap_to_int", referenced from:
_tmap_map_util_fsw in tmap_map_util.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]: *** [tmap] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Error: Failure while executing: make
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