install.log

$ brew install -vd tmap
/usr/local/bin/brew: loading /usr/local/Library/Formula/tmap.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/automake.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/autoconf.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/libtool.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/automake.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/autoconf.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/libtool.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/python.rb
==> Cloning https://github.com/iontorrent/TMAP.git
git clone --depth 1 --branch tmap.3.2.0 https://github.com/iontorrent/TMAP.git /Library/Caches/Homebrew/tmap--git
Cloning into '/Library/Caches/Homebrew/tmap--git'...
remote: Counting objects: 264, done.
remote: Compressing objects: 100% (240/240), done.
remote: Total 264 (delta 42), reused 88 (delta 22)
Receiving objects: 100% (264/264), 817.10 KiB | 71 KiB/s, done.
Resolving deltas: 100% (42/42), done.
Note: checking out '115c3149c64ef808fad8908e37aca0023f032cff'.

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

==> Checking out tag tmap.3.2.0
git checkout tmap.3.2.0 --
HEAD is now at 115c314... * moving master to 3.2.0
git checkout-index -a -f --prefix=/private/tmp/tmap-E4HN/
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% (1451/1451), done.
remote: Total 5251 (delta 3824), reused 5211 (delta 3790)
Receiving objects: 100% (5251/5251), 1.69 MiB | 47 KiB/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-E4HN/$path/"
==> sh autogen.sh
sh autogen.sh
running: aclocal
running: autoheader
running: automake -a
running: autoconf
==> ./configure --disable-dependency-tracking --disable-tcmalloc --prefix=/usr/local/Cellar/tmap/3.2.0 --enable-intel64
./configure --disable-dependency-tracking --disable-tcmalloc --prefix=/usr/local/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
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checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-apple-darwin12.2.0
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
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checking whether it is safe to define __EXTENSIONS__... yes
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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
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checking return type of signal handlers... void
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checking size of short int... 2
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checking size of long int... 8
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
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checking whether time.h and sys/time.h may both be included... yes
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checking stdio.h usability... yes
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checking float.h usability... yes
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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
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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/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
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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/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
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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_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
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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_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
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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_stat.o src/samtools/bam_stat.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_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
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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_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
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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/sample.o src/samtools/sample.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/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