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alexreg/# vcflib - 2021-12-26_22-54-06.txt

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vcflib (brewsci/bio/vcflib) on macOS 12 - Homebrew build logs
Raw
# vcflib - 2021-12-26_22-54-06.txt
Homebrew build logs for brewsci/bio/vcflib on macOS 12
Build date: 2021-12-26 22:54:06
Raw
00.config.out
HOMEBREW_VERSION: 3.3.9
ORIGIN: https://github.com/Homebrew/brew
HEAD: 96137bc19e68398ebbb7033379df288cd8b9a3f9
Last commit: 9 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 37b1ec5189d5d75b439837bc3547d5134ba0d935
Core tap last commit: 4 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_BROWSER: open -a Firefox.app
HOMEBREW_CASK_OPTS: []
HOMEBREW_CORE_GIT_REMOTE: https://github.com/Homebrew/homebrew-core
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.tFZwW8Plls/org.xquartz:0
HOMEBREW_EDITOR: mate_wait
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 2.6.8 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: 10-core 64-bit arm_firestorm_icestorm
Clang: 13.0.0 build 1300
Git: 2.34.1 => /opt/homebrew/bin/git
Curl: 7.77.0 => /usr/bin/curl
macOS: 12.1-arm64
CLT: 13.2.0.0.1.1638488800
Xcode: 13.2.1
Rosetta 2: false
Raw
00.doctor.out
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
archey
lua@5.1
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and which additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew-provided
script of the same name. We found the following "config" scripts:
/Users/alex/.cargo/bin/cargo-install-update-config
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libblosc.1.21.1.dylib
/usr/local/lib/libblosc.1.dylib
/usr/local/lib/libblosc.dylib
/usr/local/lib/libfirm.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/blosc-export.h
/usr/local/include/blosc.h
/usr/local/include/libfirm/adt/array.h
/usr/local/include/libfirm/adt/bipartite.h
/usr/local/include/libfirm/adt/funcattr.h
/usr/local/include/libfirm/adt/gaussjordan.h
/usr/local/include/libfirm/adt/gaussseidel.h
/usr/local/include/libfirm/adt/hashptr.h
/usr/local/include/libfirm/adt/hungarian.h
/usr/local/include/libfirm/adt/list.h
/usr/local/include/libfirm/adt/obst.h
/usr/local/include/libfirm/adt/obstack.h
/usr/local/include/libfirm/adt/pmap.h
/usr/local/include/libfirm/adt/pqueue.h
/usr/local/include/libfirm/adt/pset.h
/usr/local/include/libfirm/adt/set.h
/usr/local/include/libfirm/adt/unionfind.h
/usr/local/include/libfirm/adt/xmalloc.h
/usr/local/include/libfirm/analyze_irg_args.h
/usr/local/include/libfirm/be.h
/usr/local/include/libfirm/begin.h
/usr/local/include/libfirm/callgraph.h
/usr/local/include/libfirm/cdep.h
/usr/local/include/libfirm/cgana.h
/usr/local/include/libfirm/dbginfo.h
/usr/local/include/libfirm/end.h
/usr/local/include/libfirm/execfreq.h
/usr/local/include/libfirm/firm.h
/usr/local/include/libfirm/firm_common.h
/usr/local/include/libfirm/firm_types.h
/usr/local/include/libfirm/heights.h
/usr/local/include/libfirm/ident.h
/usr/local/include/libfirm/ircgopt.h
/usr/local/include/libfirm/ircons.h
/usr/local/include/libfirm/irconsconfirm.h
/usr/local/include/libfirm/irdom.h
/usr/local/include/libfirm/irdump.h
/usr/local/include/libfirm/iredgekinds.h
/usr/local/include/libfirm/iredges.h
/usr/local/include/libfirm/irflag.h
/usr/local/include/libfirm/irgmod.h
/usr/local/include/libfirm/irgopt.h
/usr/local/include/libfirm/irgraph.h
/usr/local/include/libfirm/irgwalk.h
/usr/local/include/libfirm/irio.h
/usr/local/include/libfirm/irloop.h
/usr/local/include/libfirm/irmemory.h
/usr/local/include/libfirm/irmode.h
/usr/local/include/libfirm/irnode.h
/usr/local/include/libfirm/irop.h
/usr/local/include/libfirm/iropt.h
/usr/local/include/libfirm/iroptimize.h
/usr/local/include/libfirm/irouts.h
/usr/local/include/libfirm/irprintf.h
/usr/local/include/libfirm/irprog.h
/usr/local/include/libfirm/irverify.h
/usr/local/include/libfirm/jit.h
/usr/local/include/libfirm/lowering.h
/usr/local/include/libfirm/nodes.h
/usr/local/include/libfirm/statev.h
/usr/local/include/libfirm/target.h
/usr/local/include/libfirm/timing.h
/usr/local/include/libfirm/tv.h
/usr/local/include/libfirm/typerep.h
/usr/local/include/libfirm/vrp.h
/usr/local/include/python3.9/persistent/cPersistence.h
/usr/local/include/python3.9/persistent/ring.h
/usr/local/include/python3.9/zope.proxy/proxy.h
Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected '.pc' files:
/usr/local/lib/pkgconfig/blosc.pc
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libblosc.a
/usr/local/lib/libfirm.a
Raw
00.options.out
brewsci/bio/vcflib
Raw
00.tap.out
Formula: vcflib
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/vcflib.rb
Raw
01.make
2021-12-26 22:54:06 +0000
make
objc[94902]: Class AMSupportURLConnectionDelegate is implemented in both /usr/lib/libauthinstall.dylib (0x220b2eb90) and /Library/Apple/System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x1081dc2c8). One of the two will be used. Which one is undefined.
objc[94902]: Class AMSupportURLSession is implemented in both /usr/lib/libauthinstall.dylib (0x220b2ebe0) and /Library/Apple/System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x1081dc318). One of the two will be used. Which one is undefined.
if [ ! -d bin ]; then mkdir -p bin; fi
g++-11 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw.o src/ssw.cpp
g++-11 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw_cpp.o src/ssw_cpp.cpp
if [ ! -d lib ]; then mkdir -p lib; fi
if [ ! -d include ]; then mkdir -p include; fi
if [ ! -d obj ]; then mkdir -p obj; fi
cd tabixpp && INCLUDES="-I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib" LIBPATH="-L. -L/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread" HTSLIB="/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib/libhts.a" /Applications/Xcode.app/Contents/Developer/usr/bin/make && cp -f *.h* /private/tmp/vcflib-20211226-94802-xp20zo/include/
cd multichoose && /Applications/Xcode.app/Contents/Developer/usr/bin/make && cp -f *.h* /private/tmp/vcflib-20211226-94802-xp20zo/include/
cd smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make && cp -f *.h* /private/tmp/vcflib-20211226-94802-xp20zo/include/ && cp -f *.o /private/tmp/vcflib-20211226-94802-xp20zo/obj/
cd filevercmp && make && cp -f *.h* /private/tmp/vcflib-20211226-94802-xp20zo/include/ && cp -f *.o /private/tmp/vcflib-20211226-94802-xp20zo/include/
cd fastahack && /Applications/Xcode.app/Contents/Developer/usr/bin/make && cp -f *.h* /private/tmp/vcflib-20211226-94802-xp20zo/include/ && cp -f Fasta.o /private/tmp/vcflib-20211226-94802-xp20zo/obj/
cd intervaltree && /Applications/Xcode.app/Contents/Developer/usr/bin/make && cp -f *.h* /private/tmp/vcflib-20211226-94802-xp20zo/include/
g++-11 -O3 -c -o disorder.o disorder.cpp -I.
g++-11 multichoose.cpp -o multichoose
g++-11 -O3 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I.
g++-11 multipermute.cpp -o multipermute
g++-11 -Wall interval_tree_test.cpp -std=c++0x -o interval_tree_test
g++ -O3 -D_FILE_OFFSET_BITS=64 -c Fasta.cpp
gcc -c filevercmp.c
g++-11 -g -Wall -O2 -fPIC -c tabix.cpp -I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib
src/ssw.cpp:38:10: fatal error: emmintrin.h: No such file or directory
38 | #include <emmintrin.h>
| ^~~~~~~~~~~~~
compilation terminated.
make: *** [src/ssw.o] Error 1
make: *** Waiting for unfinished jobs....
g++-11 -O3 -c -o LeftAlign.o LeftAlign.cpp -I.
In file included from src/ssw_cpp.cpp:2:
src/ssw.hpp:17:10: fatal error: emmintrin.h: No such file or directory
17 | #include <emmintrin.h>
| ^~~~~~~~~~~~~
compilation terminated.
make: *** [src/ssw_cpp.o] Error 1
g++ -O3 -D_FILE_OFFSET_BITS=64 -c split.cpp
gcc -o filevercmp main.c filevercmp.o
g++-11 -O3 -c -o Repeats.o Repeats.cpp -I.
cd htslib && /Applications/Xcode.app/Contents/Developer/usr/bin/make lib-static
g++ -O3 -D_FILE_OFFSET_BITS=64 -c disorder.c
g++-11 -O3 -c -o IndelAllele.o IndelAllele.cpp -I.
g++-11 -O3 -c -o smithwaterman.o smithwaterman.cpp -I.
g++-11 -O3 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I.
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HTS_VERSION "1.5"' > version.h
gcc-11 -g -Wall -O2 -I. -c -o md5.o md5.c
gcc-11 -g -Wall -O2 -I. -c -o multipart.o multipart.c
gcc-11 -g -Wall -O2 -I. -c -o probaln.o probaln.c
gcc-11 -g -Wall -O2 -I. -c -o realn.o realn.c
gcc-11 -g -Wall -O2 -I. -c -o regidx.o regidx.c
gcc-11 -g -Wall -O2 -I. -c -o sam.o sam.c
g++ -O3 -D_FILE_OFFSET_BITS=64 Fasta.o FastaHack.cpp split.o disorder.o -o fastahack
gcc-11 -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc-11 -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc-11 -g -Wall -O2 -I. -c -o tbx.o tbx.c
gcc-11 -g -Wall -O2 -I. -c -o textutils.o textutils.c
gcc-11 -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
gcc-11 -g -Wall -O2 -I. -c -o vcf.o vcf.c
gcc-11 -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
g++-11 -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman
ld -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L.
#g++-11 -O3 -c -o smithwaterman.cpp disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -I.
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc-11 -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc-11 -g -Wall -O2 -I. -c -o cram/files.o cram/files.c
gcc-11 -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc-11 -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc-11 -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc-11 -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc-11 -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc-11 -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc-11 -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc-11 -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
gcc-11 -g -Wall -O2 -I. -c -o kstring.o kstring.c
gcc-11 -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc-11 -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
gcc-11 -g -Wall -O2 -I. -c -o errmod.o errmod.c
gcc-11 -g -Wall -O2 -I. -c -o faidx.o faidx.c
gcc-11 -g -Wall -O2 -I. -c -o hfile.o hfile.c
gcc-11 -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
gcc-11 -g -Wall -O2 -I. -c -o hts.o hts.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
g++-11 -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o -I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -L. -L/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread \
-lhts -lpthread -lm -lbz2 -llzma -lz
HOMEBREW_VERSION: 3.3.9
ORIGIN: https://github.com/Homebrew/brew
HEAD: 96137bc19e68398ebbb7033379df288cd8b9a3f9
Last commit: 9 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 37b1ec5189d5d75b439837bc3547d5134ba0d935
Core tap last commit: 4 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_BROWSER: open -a Firefox.app
HOMEBREW_CASK_OPTS: []
HOMEBREW_CORE_GIT_REMOTE: https://github.com/Homebrew/homebrew-core
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.tFZwW8Plls/org.xquartz:0
HOMEBREW_EDITOR: mate_wait
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_NO_BOOTSNAP: set
Homebrew Ruby: 2.6.8 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: 10-core 64-bit arm_firestorm_icestorm
Clang: 13.0.0 build 1300
Git: 2.34.1 => /opt/homebrew/bin/git
Curl: 7.77.0 => /usr/bin/curl
macOS: 12.1-arm64
CLT: 13.2.0.0.1.1638488800
Xcode: 13.2.1
Rosetta 2: false
HOMEBREW_CC: gcc-11
HOMEBREW_CXX: g++-11
MAKEFLAGS: -j10
CMAKE_PREFIX_PATH: /opt/homebrew/opt/openssl@1.1:/opt/homebrew/opt/readline:/opt/homebrew/opt/sqlite:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /opt/homebrew/opt/python@3.9/Frameworks
PKG_CONFIG_PATH: /opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/openssl@1.1/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/python@3.9/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/12
HOMEBREW_GIT: git
HOMEBREW_SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
ACLOCAL_PATH: /opt/homebrew/share/aclocal
PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew/opt/zstd/bin:/opt/homebrew/opt/gcc/bin:/opt/homebrew/opt/gdbm/bin:/opt/homebrew/opt/openssl@1.1/bin:/opt/homebrew/opt/sqlite/bin:/opt/homebrew/opt/xz/bin:/opt/homebrew/opt/python@3.9/bin:/usr/bin:/bin:/usr/sbin:/sbin
Raw
01.make.cc
g++-11 called with: -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw.o src/ssw.cpp
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw.o src/ssw.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw_cpp.o src/ssw_cpp.cpp
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw_cpp.o src/ssw_cpp.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: multichoose.cpp -o multichoose
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-11 -pipe -w -Os multichoose.cpp -o multichoose -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++-11 called with: -Wall interval_tree_test.cpp -std=c++0x -o interval_tree_test
superenv removed: -Wall
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-11 -pipe -w -Os interval_tree_test.cpp -std=c++0x -o interval_tree_test -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++-11 called with: -O3 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -O3 -c -o disorder.o disorder.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o disorder.o disorder.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: multipermute.cpp -o multipermute
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-11 -pipe -w -Os multipermute.cpp -o multipermute -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++ called with: -O3 -D_FILE_OFFSET_BITS=64 -c Fasta.cpp
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -D_FILE_OFFSET_BITS=64 -c Fasta.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc called with: -c filevercmp.c
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -c filevercmp.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -g -Wall -O2 -fPIC -c tabix.cpp -I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -fPIC -c tabix.cpp -I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -O3 -c -o LeftAlign.o LeftAlign.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o LeftAlign.o LeftAlign.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++ called with: -O3 -D_FILE_OFFSET_BITS=64 -c split.cpp
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -D_FILE_OFFSET_BITS=64 -c split.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc called with: -o filevercmp main.c filevercmp.o
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-11 -pipe -w -Os -o filevercmp main.c filevercmp.o -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++-11 called with: -O3 -c -o Repeats.o Repeats.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o Repeats.o Repeats.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o filevercmp -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccOlH27u.o filevercmp.o -headerpad_max_install_names -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o filevercmp -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccOlH27u.o filevercmp.o -headerpad_max_install_names -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
g++ called with: -O3 -D_FILE_OFFSET_BITS=64 -c disorder.c
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -D_FILE_OFFSET_BITS=64 -c disorder.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -O3 -c -o IndelAllele.o IndelAllele.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o IndelAllele.o IndelAllele.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o multichoose -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccXfWOkJ.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o multichoose -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccXfWOkJ.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
g++-11 called with: -O3 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -O3 -c -o smithwaterman.o smithwaterman.cpp -I.
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: g++-11 -pipe -w -Os -c -o smithwaterman.o smithwaterman.cpp -I. -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o md5.o md5.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o md5.o md5.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o multipermute -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/cc5EKVYu.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o multipermute -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/cc5EKVYu.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
gcc-11 called with: -g -Wall -O2 -I. -c -o multipart.o multipart.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o multipart.o multipart.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o probaln.o probaln.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o probaln.o probaln.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o realn.o realn.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o realn.o realn.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o regidx.o regidx.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o regidx.o regidx.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o sam.o sam.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o sam.o sam.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++ called with: -O3 -D_FILE_OFFSET_BITS=64 Fasta.o FastaHack.cpp split.o disorder.o -o fastahack
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-11 -pipe -w -Os -D_FILE_OFFSET_BITS=64 Fasta.o FastaHack.cpp split.o disorder.o -o fastahack -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
gcc-11 called with: -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o synced_bcf_reader.o synced_bcf_reader.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o vcf_sweep.o vcf_sweep.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o tbx.o tbx.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o tbx.o tbx.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o textutils.o textutils.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o textutils.o textutils.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o thread_pool.o thread_pool.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o vcf.o vcf.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o vcf.o vcf.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o vcfutils.o vcfutils.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_decode.o cram/cram_decode.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_codecs.o cram/cram_codecs.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_encode.o cram/cram_encode.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_external.o cram/cram_external.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_index.o cram/cram_index.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o fastahack -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. Fasta.o /private/tmp/ccQiaXx8.o split.o disorder.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o fastahack -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. Fasta.o /private/tmp/ccQiaXx8.o split.o disorder.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_io.o cram/cram_io.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman
superenv removed: -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-11 -pipe -w -Os smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
ld called with: -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L.
superenv added: -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_samtools.o cram/cram_samtools.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o smithwaterman -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o smithwaterman -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/cram_stats.o cram/cram_stats.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/files.o cram/files.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/files.o cram/files.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/mFILE.o cram/mFILE.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/open_trace_file.o cram/open_trace_file.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/rANS_static.o cram/rANS_static.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/sam_header.o cram/sam_header.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o cram/string_alloc.o cram/string_alloc.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o kfunc.o kfunc.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o knetfile.o knetfile.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o kstring.o kstring.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o kstring.o kstring.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o bcf_sr_sort.o bcf_sr_sort.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o bgzf.o bgzf.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o errmod.o errmod.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o errmod.o errmod.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o faidx.o faidx.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o faidx.o faidx.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o hfile.o hfile.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o hfile.o hfile.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o hfile_net.o hfile_net.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
gcc-11 called with: -g -Wall -O2 -I. -c -o hts.o hts.c
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
superenv executed: gcc-11 -pipe -w -Os -I. -c -o hts.o hts.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include
g++-11 called with: -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o -I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -L. -L/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread -lhts -lpthread -lm -lbz2 -llzma -lz
superenv removed: -g -Wall -O2
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-11 -pipe -w -Os -fPIC -o tabix++ main.cpp tabix.o -I/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -L. -L/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread -lhts -lpthread -lm -lbz2 -llzma -lz -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -I/opt/homebrew/opt/openssl@1.1/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/sqlite/include -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o tabix++ -L. -L/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccGGndUn.o tabix.o -lhts -lbz2 -lz -llzma -lhts -lbz2 -llzma -lz -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o tabix++ -L. -L/private/tmp/vcflib-20211226-94802-xp20zo/tabixpp/htslib -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccGGndUn.o tabix.o -lhts -lbz2 -lz -llzma -lhts -lbz2 -llzma -lz -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
ld called with: -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o interval_tree_test -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccR4mnyf.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../..
superenv executed: ld -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch arm64 -macosx_version_min 12.1.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -weak_reference_mismatches non-weak -w -o interval_tree_test -L/opt/homebrew/opt/gcc/lib/gcc/11 -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/sqlite/lib -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -L/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. /private/tmp/ccR4mnyf.o -headerpad_max_install_names -lstdc++ -lgcc_s.1.1 -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11 -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc -rpath /opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/aarch64-apple-darwin21/11/../../.. -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
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