vcflib (brewsci/bio/vcflib) on macOS 12 - Homebrew build logs

# 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

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

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
  [email protected]

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

00.options.out

brewsci/bio/vcflib

00.tap.out

Formula: vcflib
    Tap: brewsci/bio
   Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/vcflib.rb

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/[email protected]:/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/[email protected]/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/[email protected]/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/[email protected]/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/[email protected]/bin:/opt/homebrew/opt/sqlite/bin:/opt/homebrew/opt/xz/bin:/opt/homebrew/opt/[email protected]/bin:/usr/bin:/bin:/usr/sbin:/sbin

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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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