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sjackman/# abyss - 2018-11-12_09-29-18.txt

Created November 12, 2018 17:31
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abyss on macOS 10.13.6 - Homebrew build logs
Raw
# abyss - 2018-11-12_09-29-18.txt
Homebrew build logs for abyss on macOS 10.13.6
Build date: 2018-11-12 09:29:18
Raw
00.config.out
HOMEBREW_VERSION: 1.8.2-48-ga8aed38
ORIGIN: https://github.com/Homebrew/brew
HEAD: a8aed381ca4ab271775c3f3682445c4fa2cbbbee
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 50f3ef60bce2bc1d29e23f6266a3c16021ea2df9
Core tap last commit: 3 days ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_BINTRAY_KEY: set
HOMEBREW_BINTRAY_USER: sjackman
HOMEBREW_DEVELOPER: 1
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_VISUAL: gvim
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.2 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 9.0.4, 1.8.0_181
macOS: 10.13.6-x86_64
CLT: 10.1.0.0.1.1539992718
Xcode: 10.1
XQuartz: 2.7.11 => /opt/X11
Raw
00.doctor.out
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: Homebrew/homebrew-core is not on the master branch
Check out the master branch by running:
git -C "$(brew --repo homebrew/core)" checkout master
Warning: The following directories do not exist:
/usr/local/sbin
You should create these directories and change their ownership to your account.
sudo mkdir -p /usr/local/sbin
sudo chown -R $(whoami) /usr/local/sbin
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/libtcl8.6.dylib
/usr/local/lib/libtk8.6.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/fakemysql.h
/usr/local/include/fakepq.h
/usr/local/include/fakesql.h
/usr/local/include/itcl.h
/usr/local/include/itcl2TclOO.h
/usr/local/include/itclDecls.h
/usr/local/include/itclInt.h
/usr/local/include/itclIntDecls.h
/usr/local/include/itclMigrate2TclCore.h
/usr/local/include/itclTclIntStubsFcn.h
/usr/local/include/mysqlStubs.h
/usr/local/include/odbcStubs.h
/usr/local/include/pqStubs.h
/usr/local/include/tcl.h
/usr/local/include/tclDecls.h
/usr/local/include/tclOO.h
/usr/local/include/tclOODecls.h
/usr/local/include/tclPlatDecls.h
/usr/local/include/tclThread.h
/usr/local/include/tclTomMath.h
/usr/local/include/tclTomMathDecls.h
/usr/local/include/tdbc.h
/usr/local/include/tdbcDecls.h
/usr/local/include/tdbcInt.h
/usr/local/include/tk.h
/usr/local/include/tkDecls.h
/usr/local/include/tkPlatDecls.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/tcl.pc
/usr/local/lib/pkgconfig/tk.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/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
util-linux
tigmint
matplotlib
Warning: Broken symlinks were found. Remove them with `brew prune`:
/usr/local/bin/bundle
/usr/local/bin/bundler
/usr/local/bin/docker-compose.backup
/usr/local/bin/docker-credential-osxkeychain.backup
/usr/local/bin/docker-machine.backup
/usr/local/bin/docker.backup
/usr/local/bin/hyperkit.backup
/usr/local/bin/notary.backup
/usr/local/bin/vpnkit.backup
Warning: Use htslib instead of deprecated homebrew/science/htslib
Warning: Use samtools instead of deprecated homebrew/science/samtools
Raw
01.configure
2018-11-12 09:27:59 -0800
./configure
--enable-maxk=128
--prefix=/usr/local/Cellar/abyss/2.1.4
--with-boost=/usr/local/opt/boost/include
--with-mpi=/usr/local/opt/open-mpi
--with-sparsehash=/usr/local/opt/google-sparsehash
--disable-dependency-tracking
--disable-silent-rules
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) awk
checking for gcc... gcc-8
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-8 accepts -g... yes
checking for gcc-8 option to accept ISO C89... none needed
checking whether gcc-8 understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc-8... none
checking how to run the C preprocessor... gcc-8 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++-8 accepts -g... yes
checking dependency style of g++-8... none
checking for ranlib... ranlib
checking for ghc... no
./configure: line 5229: : command not found
checking for pandoc... no
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for std::hash<int>... yes
checking for std::tr1::hash<int>... yes
checking for std::tr1::tuple<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... no
checking build system type... x86_64-apple-darwin17.7.0
checking host system type... x86_64-apple-darwin17.7.0
checking if compiler needs -Werror to reject unknown flags... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking for MPI_Init in -lmpi... yes
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... g++-8 -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... yes
checking tr1/functional presence... yes
checking for tr1/functional... yes
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... yes
checking google/sparse_hash_map presence... yes
checking for google/sparse_hash_map... yes
checking unordered_map usability... yes
checking unordered_map presence... yes
checking for unordered_map... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for g++-8 option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Misc/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating lib/gtest-1.7.0/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating lib/bloomfilter/Makefile
config.status: creating lib/nthash/Makefile
config.status: creating config.h
config.status: executing depfiles commands
Raw
01.configure.cc
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o a.out -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccRnmGKI.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o a.out -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccRnmGKI.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccRCOCk1.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccRCOCk1.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccHcKFtg.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccHcKFtg.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccqZdJ3I.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccqZdJ3I.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cc7kSnmX.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cc7kSnmX.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccc628DS.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccc628DS.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cchSMzsi.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cchSMzsi.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccPfCq4w.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccPfCq4w.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cc9XQRkO.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cc9XQRkO.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccgyDOJL.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccgyDOJL.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccBdf0gr.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccBdf0gr.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccOMGiKR.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccOMGiKR.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cczhCzD6.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cczhCzD6.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccuP95zs.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccuP95zs.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cccqb5lY.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cccqb5lY.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccr8BD2V.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccr8BD2V.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccE1OTbD.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccE1OTbD.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccU3yFBv.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccU3yFBv.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccEIvqRO.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccEIvqRO.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccumqYBE.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccumqYBE.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccYetPW2.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccYetPW2.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cc9da9ul.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cc9da9ul.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccWgDROH.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccWgDROH.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccKUL96y.o -lmpi -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccKUL96y.o -lmpi -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccz2oTg9.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccz2oTg9.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccJ4Wo7K.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccJ4Wo7K.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccj3hqIc.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccj3hqIc.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccKGm3Em.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccKGm3Em.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cczPS8Sm.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cczPS8Sm.o -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cci0usbz.o -lsqlite3 -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/cci0usbz.o -lsqlite3 -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccToFXRG.o -lstdc++ -lgomp -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o conftest -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. /private/tmp/ccToFXRG.o -lstdc++ -lgomp -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
Raw
02.make
2018-11-12 09:28:24 -0800
make
install
Making install in bin
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in doc
make[2]: Nothing to be done for `install-exec-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/share/doc/abyss'
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/share/man/man1'
mkdir: /usr/local/Cellar/abyss/2.1.4/share: File exists
/usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/usr/local/Cellar/abyss/2.1.4/share/doc/abyss'
/usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/usr/local/Cellar/abyss/2.1.4/share/man/man1'
Making install in Common
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
rm -f libcommon.a
ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o
ranlib libcommon.a
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in Graph
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
g++-8 -Wall -Wextra -Werror -g -O2 -L. -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c abyss-gc abyss-todot '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in DataLayer
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
ranlib libdatalayer.a
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c abyss-fac abyss-tofastq '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in DataBase
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
ranlib libdb.a
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c abyss-db-txt '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c abyss-db-csv '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in FMIndex
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
rm -f libfmindex.a
ar cru libfmindex.a libfmindex_a-bit_array.o
ranlib libfmindex.a
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in Assembly
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
rm -f libassembly.a
ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a
ranlib libassembly.a
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in dialign
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o museq.o museq.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o alig.o alig.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o assemble.o assemble.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o diag.o diag.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o io.o io.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o orf.o orf.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o parameters.o parameters.c
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o prob.o prob.c
assemble.c:40:20: warning: inline function 'align_diag' declared but never defined
extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
^~~~~~~~~~
assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined
extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
^~~~~~~~
assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined
extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
^~~~~~~~~~~~~~~~~
assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
^~~~~~~~~~~~~~
assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined
extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
^~~~~~~~~~~
alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
^~~~~~~~~~~
museq.c: In function 'main':
museq.c:168:2: warning: implicit declaration of function 'free_diag'; did you mean 'free_diag_col'? [-Wimplicit-function-declaration]
free_diag(adcol.diags[i]);
^~~~~~~~~
free_diag_col
museq.c:278:27: warning: implicit declaration of function 'free_alignment' [-Wimplicit-function-declaration]
if(! para->FAST_MODE) free_alignment(algn);
^~~~~~~~~~~~~~
diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
^~~~~~~~~~~~~~~~
gcc-8 -DHAVE_CONFIG_H -I. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -g -O2 -c -o translate.o translate.c
rm -f libdialign.a
ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
ranlib libdialign.a
gcc-8 -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o dialign museq.o libdialign.a -ldl -lm
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in Align
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
rm -f libalign.a
ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
ranlib libalign.a
g++-8 -Wall -Wextra -Werror -fopenmp -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
g++-8 -Wall -Wextra -Werror -fopenmp -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c abyss-align abyss-mergepairs '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in ABYSS
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c ABYSS '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in Parallel
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
g++-8 -Wall -Wextra -Werror -g -O2 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
make[2]: Nothing to be done for `install-data-am'.
.././install-sh -c -d '/usr/local/Cellar/abyss/2.1.4/bin'
/usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/usr/local/Cellar/abyss/2.1.4/bin'
Making install in Bloom
g++-8 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
In file included from bloom.cc:24:
../BloomDBG/HashAgnosticCascadingBloom.h: In member function 'bool HashAgnosticCascadingBloom::contains(const std::vector<long unsigned int>&) const':
../BloomDBG/HashAgnosticCascadingBloom.h:103:40: error: no matching function for call to 'BloomFilter::contains(const std::vector<long unsigned int>&)'
return m_data.back()->contains(hashes);
^
In file included from ../BloomDBG/BloomIO.h:6,
from bloom.cc:23:
../lib/bloomfilter/BloomFilter.hpp:206:7: note: candidate: 'bool BloomFilter::contains(const std::vector<long long unsigned int>&) const'
bool contains(vector<uint64_t> const &precomputed) const {
^~~~~~~~
../lib/bloomfilter/BloomFilter.hpp:206:7: note: no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'const std::vector<long long unsigned int>&'
../lib/bloomfilter/BloomFilter.hpp:220:7: note: candidate: 'bool BloomFilter::contains(const uint64_t*) const'
bool contains(const uint64_t precomputed[]) const {
^~~~~~~~
../lib/bloomfilter/BloomFilter.hpp:220:7: note: no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'const uint64_t*' {aka 'const long long unsigned int*'}
In file included from bloom.cc:24:
../BloomDBG/HashAgnosticCascadingBloom.h: In member function 'bool HashAgnosticCascadingBloom::contains(const size_t*) const':
../BloomDBG/HashAgnosticCascadingBloom.h:113:34: error: invalid conversion from 'const size_t*' {aka 'const long unsigned int*'} to 'const uint64_t*' {aka 'const long long unsigned int*'} [-fpermissive]
return m_data.back()->contains(hashes);
^~~~~~
In file included from ../BloomDBG/BloomIO.h:6,
from bloom.cc:23:
../lib/bloomfilter/BloomFilter.hpp:220:31: note: initializing argument 1 of 'bool BloomFilter::contains(const uint64_t*) const'
bool contains(const uint64_t precomputed[]) const {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from bloom.cc:24:
../BloomDBG/HashAgnosticCascadingBloom.h: In member function 'void HashAgnosticCascadingBloom::insert(const std::vector<long unsigned int>&)':
../BloomDBG/HashAgnosticCascadingBloom.h:121:37: error: no matching function for call to 'BloomFilter::contains(const std::vector<long unsigned int>&)'
if (!(*m_data[i]).contains(hashes)) {
^
In file included from ../BloomDBG/BloomIO.h:6,
from bloom.cc:23:
../lib/bloomfilter/BloomFilter.hpp:206:7: note: candidate: 'bool BloomFilter::contains(const std::vector<long long unsigned int>&) const'
bool contains(vector<uint64_t> const &precomputed) const {
^~~~~~~~
../lib/bloomfilter/BloomFilter.hpp:206:7: note: no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'const std::vector<long long unsigned int>&'
../lib/bloomfilter/BloomFilter.hpp:220:7: note: candidate: 'bool BloomFilter::contains(const uint64_t*) const'
bool contains(const uint64_t precomputed[]) const {
^~~~~~~~
../lib/bloomfilter/BloomFilter.hpp:220:7: note: no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'const uint64_t*' {aka 'const long long unsigned int*'}
In file included from bloom.cc:24:
../BloomDBG/HashAgnosticCascadingBloom.h:122:29: error: no matching function for call to 'BloomFilter::insert(const std::vector<long unsigned int>&)'
m_data[i]->insert(hashes);
^
In file included from ../BloomDBG/BloomIO.h:6,
from bloom.cc:23:
../lib/bloomfilter/BloomFilter.hpp:146:7: note: candidate: 'void BloomFilter::insert(const std::vector<long long unsigned int>&)'
void insert(vector<uint64_t> const &precomputed) {
^~~~~~
../lib/bloomfilter/BloomFilter.hpp:146:7: note: no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'const std::vector<long long unsigned int>&'
../lib/bloomfilter/BloomFilter.hpp:159:7: note: candidate: 'void BloomFilter::insert(const uint64_t*)'
void insert(const uint64_t precomputed[]) {
^~~~~~
../lib/bloomfilter/BloomFilter.hpp:159:7: note: no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'const uint64_t*' {aka 'const long long unsigned int*'}
In file included from bloom.cc:24:
../BloomDBG/HashAgnosticCascadingBloom.h: In member function 'void HashAgnosticCascadingBloom::insert(const size_t*)':
../BloomDBG/HashAgnosticCascadingBloom.h:133:31: error: invalid conversion from 'const size_t*' {aka 'const long unsigned int*'} to 'const uint64_t*' {aka 'const long long unsigned int*'} [-fpermissive]
if (!(*m_data[i]).contains(hashes)) {
^~~~~~
In file included from ../BloomDBG/BloomIO.h:6,
from bloom.cc:23:
../lib/bloomfilter/BloomFilter.hpp:220:31: note: initializing argument 1 of 'bool BloomFilter::contains(const uint64_t*) const'
bool contains(const uint64_t precomputed[]) const {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from bloom.cc:24:
../BloomDBG/HashAgnosticCascadingBloom.h:134:23: error: invalid conversion from 'const size_t*' {aka 'const long unsigned int*'} to 'const uint64_t*' {aka 'const long long unsigned int*'} [-fpermissive]
m_data[i]->insert(hashes);
^~~~~~
In file included from ../BloomDBG/BloomIO.h:6,
from bloom.cc:23:
../lib/bloomfilter/BloomFilter.hpp:159:29: note: initializing argument 1 of 'void BloomFilter::insert(const uint64_t*)'
void insert(const uint64_t precomputed[]) {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~
make[1]: *** [abyss_bloom-bloom.o] Error 1
make: *** [install-recursive] Error 1
HOMEBREW_VERSION: 1.8.2-48-ga8aed38
ORIGIN: https://github.com/Homebrew/brew
HEAD: a8aed381ca4ab271775c3f3682445c4fa2cbbbee
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 50f3ef60bce2bc1d29e23f6266a3c16021ea2df9
Core tap last commit: 3 days ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CACHE: /Users/sjackman/Library/Caches/Homebrew
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.2 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 9.0.4, 1.8.0_181
macOS: 10.13.6-x86_64
CLT: 10.1.0.0.1.1539992718
Xcode: 10.1
XQuartz: 2.7.11 => /opt/X11
HOMEBREW_CC: gcc-8
HOMEBREW_CXX: g++-8
MAKEFLAGS: -j8
CMAKE_PREFIX_PATH: /usr/local/opt/openssl:/usr/local
CMAKE_INCLUDE_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/libxml2:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH: /usr/local/opt/google-sparsehash/lib/pkgconfig:/usr/local/opt/isl/lib/pkgconfig:/usr/local/opt/mpfr/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/libevent/lib/pkgconfig:/usr/local/opt/open-mpi/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/10.13
HOMEBREW_GIT: git
HOMEBREW_SDKROOT: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Homebrew/Library/Homebrew/shims/mac/super:/usr/local/opt/gcc/bin:/usr/local/opt/openssl/bin:/usr/local/opt/libevent/bin:/usr/local/opt/open-mpi/bin:/usr/bin:/bin:/usr/sbin:/sbin
Raw
02.make.cc
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-gc -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_gc-gc.o ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-gc -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_gc-gc.o ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-todot -L. -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_todot-todot.o ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-todot -L. -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_todot-todot.o ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-tofastq -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-tofastq -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-fac -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-fac -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-db-csv -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-db-csv -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-count -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_count-count.o libfmindex.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-count -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_count-count.o libfmindex.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-dawg -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-dawg -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o dialign -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. museq.o libdialign.a -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o dialign -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. museq.o libdialign.a -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-align -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -lstdc++ -lgomp -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-align -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -lstdc++ -lgomp -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-mergepairs -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -lstdc++ -lgomp -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-mergepairs -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -lstdc++ -lgomp -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o ABYSS -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o ABYSS -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o ABYSS-P -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -lmpi -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o ABYSS-P -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -lmpi -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ld called with: -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-paired-dbg-mpi -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -lmpi -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv added: -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
superenv executed: ld -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.13.0 -weak_reference_mismatches non-weak -o abyss-paired-dbg-mpi -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -lmpi -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
Raw
config.log
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by ABySS configure 2.1.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --enable-maxk=128 --prefix=/usr/local/Cellar/abyss/2.1.4 --with-boost=/usr/local/opt/boost/include --with-mpi=/usr/local/opt/open-mpi --with-sparsehash=/usr/local/opt/google-sparsehash --disable-dependency-tracking --disable-silent-rules
## --------- ##
## Platform. ##
## --------- ##
hostname = Shauns-MacBook-Pro.local
uname -m = x86_64
uname -r = 17.7.0
uname -s = Darwin
uname -v = Darwin Kernel Version 17.7.0: Wed Oct 10 23:06:14 PDT 2018; root:xnu-4570.71.13~1/RELEASE_X86_64
/usr/bin/uname -p = i386
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = Mach kernel version:
Darwin Kernel Version 17.7.0: Wed Oct 10 23:06:14 PDT 2018; root:xnu-4570.71.13~1/RELEASE_X86_64
Kernel configured for up to 8 processors.
4 processors are physically available.
8 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3 4 5 6 7
Primary memory available: 16.00 gigabytes
Default processor set: 335 tasks, 1569 threads, 8 processors
Load average: 2.42, Mach factor: 5.56
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/Homebrew/Library/Homebrew/shims/mac/super
PATH: /usr/local/opt/gcc/bin
PATH: /usr/local/opt/openssl/bin
PATH: /usr/local/opt/libevent/bin
PATH: /usr/local/opt/open-mpi/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2873: checking for a BSD-compatible install
configure:2941: result: /usr/bin/install -c
configure:2952: checking whether build environment is sane
configure:3007: result: yes
configure:3158: checking for a thread-safe mkdir -p
configure:3197: result: ./install-sh -c -d
configure:3204: checking for gawk
configure:3234: result: no
configure:3204: checking for mawk
configure:3234: result: no
configure:3204: checking for nawk
configure:3234: result: no
configure:3204: checking for awk
configure:3220: found /usr/bin/awk
configure:3231: result: awk
configure:3242: checking whether make sets $(MAKE)
configure:3264: result: yes
configure:3293: checking whether make supports nested variables
configure:3310: result: yes
configure:3445: checking for gawk
configure:3472: result: awk
configure:3531: checking for gcc
configure:3558: result: gcc-8
configure:3787: checking for C compiler version
configure:3796: gcc-8 --version >&5
gcc-8 (Homebrew GCC 8.2.0) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3807: $? = 0
configure:3796: gcc-8 -v >&5
Using built-in specs.
COLLECT_GCC=gcc-8
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/8.2.0/libexec/gcc/x86_64-apple-darwin17.7.0/8.2.0/lto-wrapper
Target: x86_64-apple-darwin17.7.0
Configured with: ../configure --build=x86_64-apple-darwin17.7.0 --prefix=/usr/local/Cellar/gcc/8.2.0 --libdir=/usr/local/Cellar/gcc/8.2.0/lib/gcc/8 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-8 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-checking=release --with-pkgversion='Homebrew GCC 8.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-nls
Thread model: posix
gcc version 8.2.0 (Homebrew GCC 8.2.0)
configure:3807: $? = 0
configure:3796: gcc-8 -V >&5
gcc-8: error: unrecognized command line option '-V'
gcc-8: fatal error: no input files
compilation terminated.
configure:3807: $? = 1
configure:3796: gcc-8 -qversion >&5
gcc-8: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc-8: fatal error: no input files
compilation terminated.
configure:3807: $? = 1
configure:3827: checking whether the C compiler works
configure:3849: gcc-8 conftest.c >&5
configure:3853: $? = 0
configure:3901: result: yes
configure:3904: checking for C compiler default output file name
configure:3906: result: a.out
configure:3912: checking for suffix of executables
configure:3919: gcc-8 -o conftest conftest.c >&5
configure:3923: $? = 0
configure:3945: result:
configure:3967: checking whether we are cross compiling
configure:3975: gcc-8 -o conftest conftest.c >&5
configure:3979: $? = 0
configure:3986: ./conftest
configure:3990: $? = 0
configure:4005: result: no
configure:4010: checking for suffix of object files
configure:4032: gcc-8 -c conftest.c >&5
configure:4036: $? = 0
configure:4057: result: o
configure:4061: checking whether we are using the GNU C compiler
configure:4080: gcc-8 -c conftest.c >&5
configure:4080: $? = 0
configure:4089: result: yes
configure:4098: checking whether gcc-8 accepts -g
configure:4118: gcc-8 -c -g conftest.c >&5
configure:4118: $? = 0
configure:4159: result: yes
configure:4176: checking for gcc-8 option to accept ISO C89
configure:4239: gcc-8 -c -g -O2 conftest.c >&5
configure:4239: $? = 0
configure:4252: result: none needed
configure:4277: checking whether gcc-8 understands -c and -o together
configure:4299: gcc-8 -c conftest.c -o conftest2.o
configure:4302: $? = 0
configure:4299: gcc-8 -c conftest.c -o conftest2.o
configure:4302: $? = 0
configure:4314: result: yes
configure:4334: checking whether make supports the include directive
configure:4349: make -f confmf.GNU && cat confinc.out
this is the am__doit target
configure:4352: $? = 0
configure:4371: result: yes (GNU style)
configure:4396: checking dependency style of gcc-8
configure:4507: result: none
configure:4527: checking how to run the C preprocessor
configure:4558: gcc-8 -E conftest.c
configure:4558: $? = 0
configure:4572: gcc-8 -E conftest.c
conftest.c:11:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:4572: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4597: result: gcc-8 -E
configure:4617: gcc-8 -E conftest.c
configure:4617: $? = 0
configure:4631: gcc-8 -E conftest.c
conftest.c:11:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:4631: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4771: checking for C++ compiler version
configure:4780: g++-8 --version >&5
g++-8 (Homebrew GCC 8.2.0) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:4791: $? = 0
configure:4780: g++-8 -v >&5
Using built-in specs.
COLLECT_GCC=g++-8
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/8.2.0/libexec/gcc/x86_64-apple-darwin17.7.0/8.2.0/lto-wrapper
Target: x86_64-apple-darwin17.7.0
Configured with: ../configure --build=x86_64-apple-darwin17.7.0 --prefix=/usr/local/Cellar/gcc/8.2.0 --libdir=/usr/local/Cellar/gcc/8.2.0/lib/gcc/8 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-8 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-checking=release --with-pkgversion='Homebrew GCC 8.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-nls
Thread model: posix
gcc version 8.2.0 (Homebrew GCC 8.2.0)
configure:4791: $? = 0
configure:4780: g++-8 -V >&5
g++-8: error: unrecognized command line option '-V'
g++-8: fatal error: no input files
compilation terminated.
configure:4791: $? = 1
configure:4780: g++-8 -qversion >&5
g++-8: error: unrecognized command line option '-qversion'; did you mean '--version'?
g++-8: fatal error: no input files
compilation terminated.
configure:4791: $? = 1
configure:4795: checking whether we are using the GNU C++ compiler
configure:4814: g++-8 -c conftest.cpp >&5
configure:4814: $? = 0
configure:4823: result: yes
configure:4832: checking whether g++-8 accepts -g
configure:4852: g++-8 -c -g conftest.cpp >&5
configure:4852: $? = 0
configure:4893: result: yes
configure:4918: checking dependency style of g++-8
configure:5029: result: none
configure:5088: checking for ranlib
configure:5104: found /usr/bin/ranlib
configure:5115: result: ranlib
configure:5180: checking for ghc
configure:5210: result: no
configure:5239: checking for pandoc
configure:5269: result: no
configure:5286: checking for grep that handles long lines and -e
configure:5344: result: /usr/bin/grep
configure:5349: checking for egrep
configure:5411: result: /usr/bin/grep -E
configure:5416: checking for ANSI C header files
configure:5436: gcc-8 -c -g -O2 conftest.c >&5
configure:5436: $? = 0
configure:5509: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:5509: $? = 0
configure:5509: ./conftest
configure:5509: $? = 0
configure:5520: result: yes
configure:5533: checking for sys/types.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for sys/stat.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for stdlib.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for string.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for memory.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for strings.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for inttypes.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for stdint.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for unistd.h
configure:5533: gcc-8 -c -g -O2 conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5549: checking dlfcn.h usability
configure:5549: gcc-8 -c -g -O2 conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking dlfcn.h presence
configure:5549: gcc-8 -E conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for dlfcn.h
configure:5549: result: yes
configure:5549: checking fcntl.h usability
configure:5549: gcc-8 -c -g -O2 conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking fcntl.h presence
configure:5549: gcc-8 -E conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for fcntl.h
configure:5549: result: yes
configure:5549: checking float.h usability
configure:5549: gcc-8 -c -g -O2 conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking float.h presence
configure:5549: gcc-8 -E conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for float.h
configure:5549: result: yes
configure:5549: checking limits.h usability
configure:5549: gcc-8 -c -g -O2 conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking limits.h presence
configure:5549: gcc-8 -E conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for limits.h
configure:5549: result: yes
configure:5549: checking stddef.h usability
configure:5549: gcc-8 -c -g -O2 conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking stddef.h presence
configure:5549: gcc-8 -E conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for stddef.h
configure:5549: result: yes
configure:5549: checking for stdint.h
configure:5549: result: yes
configure:5549: checking for stdlib.h
configure:5549: result: yes
configure:5549: checking sys/param.h usability
configure:5549: gcc-8 -c -g -O2 conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking sys/param.h presence
configure:5549: gcc-8 -E conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for sys/param.h
configure:5549: result: yes
configure:5559: checking for stdbool.h that conforms to C99
configure:5626: gcc-8 -c -g -O2 conftest.c >&5
configure:5626: $? = 0
configure:5633: result: yes
configure:5635: checking for _Bool
configure:5635: gcc-8 -c -g -O2 conftest.c >&5
configure:5635: $? = 0
configure:5635: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:65:20: error: expected expression before ')' token
if (sizeof ((_Bool)))
^
configure:5635: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((_Bool)))
| return 0;
| ;
| return 0;
| }
configure:5635: result: yes
configure:5652: checking for ANSI C header files
configure:5756: result: yes
configure:5766: checking whether byte ordering is bigendian
configure:5781: gcc-8 -c -g -O2 conftest.c >&5
configure:5781: $? = 0
configure:5826: gcc-8 -c -g -O2 conftest.c >&5
configure:5826: $? = 0
configure:5844: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:39:4: error: unknown type name 'not'; did you mean 'ino_t'?
not big endian
^~~
ino_t
conftest.c:39:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian'
not big endian
^~~~~~
configure:5844: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| /* end confdefs.h. */
| #include <sys/types.h>
| #include <sys/param.h>
|
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| not big endian
| #endif
|
| ;
| return 0;
| }
configure:5972: result: no
configure:5990: checking for an ANSI C-conforming const
configure:6056: gcc-8 -c -g -O2 conftest.c >&5
configure:6056: $? = 0
configure:6063: result: yes
configure:6071: checking for inline
configure:6087: gcc-8 -c -g -O2 conftest.c >&5
configure:6087: $? = 0
configure:6095: result: inline
configure:6113: checking for ptrdiff_t
configure:6113: gcc-8 -c -g -O2 conftest.c >&5
configure:6113: $? = 0
configure:6113: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:68:24: error: expected expression before ')' token
if (sizeof ((ptrdiff_t)))
^
configure:6113: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((ptrdiff_t)))
| return 0;
| ;
| return 0;
| }
configure:6113: result: yes
configure:6123: checking for mode_t
configure:6123: gcc-8 -c -g -O2 conftest.c >&5
configure:6123: $? = 0
configure:6123: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:21: error: expected expression before ')' token
if (sizeof ((mode_t)))
^
configure:6123: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((mode_t)))
| return 0;
| ;
| return 0;
| }
configure:6123: result: yes
configure:6134: checking for pid_t
configure:6134: gcc-8 -c -g -O2 conftest.c >&5
configure:6134: $? = 0
configure:6134: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:20: error: expected expression before ')' token
if (sizeof ((pid_t)))
^
configure:6134: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((pid_t)))
| return 0;
| ;
| return 0;
| }
configure:6134: result: yes
configure:6145: checking for size_t
configure:6145: gcc-8 -c -g -O2 conftest.c >&5
configure:6145: $? = 0
configure:6145: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:21: error: expected expression before ')' token
if (sizeof ((size_t)))
^
configure:6145: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:6145: result: yes
configure:6156: checking for ssize_t
configure:6156: gcc-8 -c -g -O2 conftest.c >&5
configure:6156: $? = 0
configure:6156: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:22: error: expected expression before ')' token
if (sizeof ((ssize_t)))
^
configure:6156: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((ssize_t)))
| return 0;
| ;
| return 0;
| }
configure:6156: result: yes
configure:6167: checking for int64_t
configure:6167: gcc-8 -c -g -O2 conftest.c >&5
configure:6167: $? = 0
configure:6167: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:71:53: warning: integer overflow in expression of type 'long long int' results in '-9223372036854775808' [-Woverflow]
< (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))];
^
conftest.c:70:12: error: storage size of 'test_array' isn't constant
static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1)
^~~~~~~~~~
configure:6167: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| enum { N = 64 / 2 - 1 };
| int
| main ()
| {
| static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1)
| < (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))];
| test_array [0] = 0;
| return test_array [0];
|
| ;
| return 0;
| }
configure:6167: result: yes
configure:6178: checking for uint8_t
configure:6178: gcc-8 -c -g -O2 conftest.c >&5
configure:6178: $? = 0
configure:6178: result: yes
configure:6192: checking for uint16_t
configure:6192: gcc-8 -c -g -O2 conftest.c >&5
configure:6192: $? = 0
configure:6192: result: yes
configure:6204: checking for uint32_t
configure:6204: gcc-8 -c -g -O2 conftest.c >&5
configure:6204: $? = 0
configure:6204: result: yes
configure:6218: checking for uint64_t
configure:6218: gcc-8 -c -g -O2 conftest.c >&5
configure:6218: $? = 0
configure:6218: result: yes
configure:6242: checking for std::hash<int>
configure:6242: g++-8 -c -g -O2 conftest.cpp >&5
configure:6242: $? = 0
configure:6242: g++-8 -c -g -O2 conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:43:28: error: expected primary-expression before ')' token
if (sizeof ((std::hash<int>)))
^
configure:6242: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
|
| #ifdef __FUJITSU
| #include <string>
| #else
| #include <functional>
| #endif
|
| int
| main ()
| {
| if (sizeof ((std::hash<int>)))
| return 0;
| ;
| return 0;
| }
configure:6242: result: yes
configure:6256: checking for std::tr1::hash<int>
configure:6256: g++-8 -c -g -O2 conftest.cpp >&5
configure:6256: $? = 0
configure:6256: g++-8 -c -g -O2 conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:39:33: error: expected primary-expression before ')' token
if (sizeof ((std::tr1::hash<int>)))
^
configure:6256: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| /* end confdefs.h. */
| #include <tr1/functional>
|
| int
| main ()
| {
| if (sizeof ((std::tr1::hash<int>)))
| return 0;
| ;
| return 0;
| }
configure:6256: result: yes
configure:6265: checking for std::tr1::tuple<int>
configure:6265: g++-8 -c -g -O2 conftest.cpp >&5
configure:6265: $? = 0
configure:6265: g++-8 -c -g -O2 conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:40:34: error: expected primary-expression before ')' token
if (sizeof ((std::tr1::tuple<int>)))
^
configure:6265: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| /* end confdefs.h. */
| #include <tr1/tuple>
|
| int
| main ()
| {
| if (sizeof ((std::tr1::tuple<int>)))
| return 0;
| ;
| return 0;
| }
configure:6265: result: yes
configure:6301: checking for dup2
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for gethostname
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for getopt_long
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for getpagesize
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for memset
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
conftest.c:64:6: warning: conflicting types for built-in function 'memset' [-Wbuiltin-declaration-mismatch]
char memset ();
^~~~~~
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for strdup
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
conftest.c:65:6: warning: conflicting types for built-in function 'strdup' [-Wbuiltin-declaration-mismatch]
char strdup ();
^~~~~~
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for strerror
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for strtoul
configure:6301: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6312: checking vfork.h usability
configure:6312: gcc-8 -c -g -O2 conftest.c >&5
conftest.c:78:10: fatal error: vfork.h: No such file or directory
#include <vfork.h>
^~~~~~~~~
compilation terminated.
configure:6312: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <vfork.h>
configure:6312: result: no
configure:6312: checking vfork.h presence
configure:6312: gcc-8 -E conftest.c
conftest.c:45:10: fatal error: vfork.h: No such file or directory
#include <vfork.h>
^~~~~~~~~
compilation terminated.
configure:6312: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| /* end confdefs.h. */
| #include <vfork.h>
configure:6312: result: no
configure:6312: checking for vfork.h
configure:6312: result: no
configure:6325: checking for fork
configure:6325: gcc-8 -o conftest -g -O2 conftest.c >&5
conftest.c:68:6: warning: conflicting types for built-in function 'fork' [-Wbuiltin-declaration-mismatch]
char fork ();
^~~~
configure:6325: $? = 0
configure:6325: result: yes
configure:6325: checking for vfork
configure:6325: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6325: $? = 0
configure:6325: result: yes
configure:6335: checking for working fork
configure:6357: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6357: $? = 0
configure:6357: ./conftest
configure:6357: $? = 0
configure:6367: result: yes
configure:6388: checking for working vfork
configure:6498: result: yes
configure:6525: checking for stdlib.h
configure:6525: result: yes
configure:6535: checking for GNU libc compatible malloc
configure:6559: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6559: $? = 0
configure:6559: ./conftest
configure:6559: $? = 0
configure:6569: result: yes
configure:6590: checking for working memcmp
configure:6633: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6633: $? = 0
configure:6633: ./conftest
configure:6633: $? = 0
configure:6643: result: yes
configure:6654: checking for stdlib.h
configure:6654: result: yes
configure:6664: checking for GNU libc compatible realloc
configure:6688: gcc-8 -o conftest -g -O2 conftest.c >&5
configure:6688: $? = 0
configure:6688: ./conftest
configure:6688: $? = 0
configure:6698: result: yes
configure:6728: checking for vprintf
configure:6728: gcc-8 -o conftest -g -O2 conftest.c >&5
conftest.c:76:6: warning: conflicting types for built-in function 'vprintf' [-Wbuiltin-declaration-mismatch]
char vprintf ();
^~~~~~~
configure:6728: $? = 0
configure:6728: result: yes
configure:6734: checking for _doprnt
configure:6734: gcc-8 -o conftest -g -O2 conftest.c >&5
Undefined symbols for architecture x86_64:
"__doprnt", referenced from:
_main in ccumqYBE.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
configure:6734: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| /* end confdefs.h. */
| /* Define _doprnt to an innocuous variant, in case <limits.h> declares _doprnt.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define _doprnt innocuous__doprnt
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char _doprnt (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef _doprnt
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char _doprnt ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub__doprnt || defined __stub____doprnt
| choke me
| #endif
|
| int
| main ()
| {
| return _doprnt ();
| ;
| return 0;
| }
configure:6734: result: no
configure:6747: checking whether HOST_NAME_MAX is declared
configure:6747: gcc-8 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:63:10: error: 'HOST_NAME_MAX' undeclared (first use in this function); did you mean 'NAME_MAX'?
(void) HOST_NAME_MAX;
^~~~~~~~~~~~~
NAME_MAX
conftest.c:63:10: note: each undeclared identifier is reported only once for each function it appears in
configure:6747: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| /* end confdefs.h. */
| #include <limits.h>
|
| int
| main ()
| {
| #ifndef HOST_NAME_MAX
| #ifdef __cplusplus
| (void) HOST_NAME_MAX;
| #else
| (void) HOST_NAME_MAX;
| #endif
| #endif
|
| ;
| return 0;
| }
configure:6747: result: no
configure:6881: checking build system type
configure:6895: result: x86_64-apple-darwin17.7.0
configure:6915: checking host system type
configure:6928: result: x86_64-apple-darwin17.7.0
configure:7060: checking if compiler needs -Werror to reject unknown flags
configure:7076: gcc-8 -c -g -O2 -Werror -Wunknown-warning-option -Wsizeof-array-argument -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.c >&5
gcc-8: error: unrecognized command line option '-Wunknown-warning-option'
configure:7076: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| #define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
| #define FMBITS 64
| #define MAX_KMER 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| int foo(void);
| int
| main ()
| {
| foo()
| ;
| return 0;
| }
configure:7081: result: no
configure:7097: checking whether pthreads work with -pthread
configure:7185: gcc-8 -o conftest -g -O2 -pthread -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c >&5
configure:7185: $? = 0
configure:7194: result: yes
configure:7213: checking for joinable pthread attribute
configure:7228: gcc-8 -o conftest -g -O2 -pthread -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c >&5
configure:7228: $? = 0
configure:7234: result: PTHREAD_CREATE_JOINABLE
configure:7244: checking if more special flags are required for pthreads
configure:7259: result: -D_THREAD_SAFE
configure:7265: checking for PTHREAD_PRIO_INHERIT
configure:7282: gcc-8 -o conftest -g -O2 -pthread -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c >&5
configure:7282: $? = 0
configure:7291: result: yes
configure:7407: checking mpi.h usability
configure:7407: gcc-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.c >&5
configure:7407: $? = 0
configure:7407: result: yes
configure:7407: checking mpi.h presence
configure:7407: gcc-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.c
configure:7407: $? = 0
configure:7407: result: yes
configure:7407: checking for mpi.h
configure:7407: result: yes
configure:7787: checking for MPI_Init in -lmpi
configure:7812: gcc-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c -lmpi >&5
configure:7812: $? = 0
configure:7821: result: yes
configure:7846: checking for sqrt in -lm
configure:7871: gcc-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c -lm >&5
conftest.c:70:6: warning: conflicting types for built-in function 'sqrt' [-Wbuiltin-declaration-mismatch]
char sqrt ();
^~~~
configure:7871: $? = 0
configure:7880: result: yes
configure:7894: checking for pow
configure:7894: gcc-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c -lm >&5
conftest.c:87:6: warning: conflicting types for built-in function 'pow' [-Wbuiltin-declaration-mismatch]
char pow ();
^~~
configure:7894: $? = 0
configure:7894: result: yes
configure:7894: checking for sqrt
configure:7894: gcc-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c -lm >&5
conftest.c:88:6: warning: conflicting types for built-in function 'sqrt' [-Wbuiltin-declaration-mismatch]
char sqrt ();
^~~~
configure:7894: $? = 0
configure:7894: result: yes
configure:7903: checking for ceilf
configure:7903: gcc-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c -lm >&5
conftest.c:89:6: warning: conflicting types for built-in function 'ceilf' [-Wbuiltin-declaration-mismatch]
char ceilf ();
^~~~~
configure:7903: $? = 0
configure:7903: result: yes
configure:7914: checking for dlsym in -ldl
configure:7939: gcc-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.c -ldl -lm >&5
configure:7939: $? = 0
configure:7948: result: yes
configure:7973: gcc-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.c >&5
conftest.c:67:20: warning: extra tokens at end of #include directive
#include <stdint.h>,
^
configure:7973: $? = 0
configure:7996: checking how to run the C++ preprocessor
configure:8023: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8023: $? = 0
configure:8037: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
conftest.cpp:68:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:8037: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| #define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
| #define FMBITS 64
| #define MAX_KMER 128
| #define MAX_HASHES 32
| #define HAVE_PTHREAD_PRIO_INHERIT 1
| #define MPICH_SKIP_MPICXX 1
| #define OMPI_SKIP_MPICXX 1
| #define HAVE_MPI_H 1
| #define HAVE_LIBMPI 1
| #define HAVE_LIBM 1
| #define HAVE_POW 1
| #define HAVE_SQRT 1
| #define HAVE_LIBDL 1
| #define HAVE_POPCNT 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8062: result: g++-8 -E
configure:8082: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8082: $? = 0
configure:8096: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
conftest.cpp:68:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:8096: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| #define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
| #define FMBITS 64
| #define MAX_KMER 128
| #define MAX_HASHES 32
| #define HAVE_PTHREAD_PRIO_INHERIT 1
| #define MPICH_SKIP_MPICXX 1
| #define OMPI_SKIP_MPICXX 1
| #define HAVE_MPI_H 1
| #define HAVE_LIBMPI 1
| #define HAVE_LIBM 1
| #define HAVE_POW 1
| #define HAVE_SQRT 1
| #define HAVE_LIBDL 1
| #define HAVE_POPCNT 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8137: checking functional usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking functional presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for functional
configure:8137: result: yes
configure:8137: checking tr1/functional usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking tr1/functional presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for tr1/functional
configure:8137: result: yes
configure:8137: checking boost/functional/hash.hpp usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking boost/functional/hash.hpp presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for boost/functional/hash.hpp
configure:8137: result: yes
configure:8137: checking boost/property_map/property_map.hpp usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking boost/property_map/property_map.hpp presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for boost/property_map/property_map.hpp
configure:8137: result: yes
configure:8137: checking google/sparse_hash_map usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking google/sparse_hash_map presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for google/sparse_hash_map
configure:8137: result: yes
configure:8137: checking unordered_map usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking unordered_map presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for unordered_map
configure:8137: result: yes
configure:8137: checking tr1/unordered_map usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking tr1/unordered_map presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for tr1/unordered_map
configure:8137: result: yes
configure:8137: checking unordered_set usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking unordered_set presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for unordered_set
configure:8137: result: yes
configure:8137: checking tr1/unordered_set usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking tr1/unordered_set presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for tr1/unordered_set
configure:8137: result: yes
configure:8137: checking boost/unordered_set.hpp usability
configure:8137: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking boost/unordered_set.hpp presence
configure:8137: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for boost/unordered_set.hpp
configure:8137: result: yes
configure:8165: checking sqlite3.h usability
configure:8165: g++-8 -c -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp >&5
configure:8165: $? = 0
configure:8165: result: yes
configure:8165: checking sqlite3.h presence
configure:8165: g++-8 -E -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 conftest.cpp
configure:8165: $? = 0
configure:8165: result: yes
configure:8165: checking for sqlite3.h
configure:8165: result: yes
configure:8175: checking for main in -lsqlite3
configure:8194: g++-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.cpp -lsqlite3 -ldl -lm >&5
configure:8194: $? = 0
configure:8203: result: yes
configure:8241: checking for g++-8 option to support OpenMP
configure:8256: g++-8 -o conftest -g -O2 -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.cpp -ldl -lm >&5
conftest.cpp:83:2: error: 'choke' does not name a type
choke me
^~~~~
In file included from conftest.cpp:85:
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:39:3: error: 'omp_lock_t' does not name a type
} omp_lock_t;
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:95:28: error: variable or field 'omp_init_lock' declared void
extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:95:28: error: 'omp_lock_t' was not declared in this scope
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:95:28: note: suggested alternative: 'omp_lock_hint_t'
extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
omp_lock_hint_t
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:95:40: error: expected primary-expression before ')' token
extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW;
^
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:96:38: error: variable or field 'omp_init_lock_with_hint' declared void
extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t)
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:96:38: error: 'omp_lock_t' was not declared in this scope
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:96:38: note: suggested alternative: 'omp_lock_hint_t'
extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t)
^~~~~~~~~~
omp_lock_hint_t
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:96:50: error: expected primary-expression before ',' token
extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t)
^
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:96:67: error: expected primary-expression before ')' token
extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t)
^
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:98:31: error: variable or field 'omp_destroy_lock' declared void
extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:98:31: error: 'omp_lock_t' was not declared in this scope
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:98:31: note: suggested alternative: 'omp_lock_hint_t'
extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
omp_lock_hint_t
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:98:43: error: expected primary-expression before ')' token
extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW;
^
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:99:27: error: variable or field 'omp_set_lock' declared void
extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:99:27: error: 'omp_lock_t' was not declared in this scope
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:99:27: note: suggested alternative: 'omp_lock_hint_t'
extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
omp_lock_hint_t
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:99:39: error: expected primary-expression before ')' token
extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW;
^
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:100:29: error: variable or field 'omp_unset_lock' declared void
extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:100:29: error: 'omp_lock_t' was not declared in this scope
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:100:29: note: suggested alternative: 'omp_lock_hint_t'
extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
omp_lock_hint_t
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:100:41: error: expected primary-expression before ')' token
extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW;
^
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:101:27: error: 'omp_lock_t' was not declared in this scope
extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:101:27: note: suggested alternative: 'omp_lock_hint_t'
extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW;
^~~~~~~~~~
omp_lock_hint_t
/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/include/omp.h:101:39: error: expected primary-expression before ')' token
extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW;
^
configure:8256: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| #define HAVE_STD_TR1_TUPLE 1
| #define BOOST_HAS_TR1_TUPLE 1
| #define HAVE_DUP2 1
| #define HAVE_GETHOSTNAME 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MEMSET 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| #define HAVE_STRTOUL 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| #define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
| #define FMBITS 64
| #define MAX_KMER 128
| #define MAX_HASHES 32
| #define HAVE_PTHREAD_PRIO_INHERIT 1
| #define MPICH_SKIP_MPICXX 1
| #define OMPI_SKIP_MPICXX 1
| #define HAVE_MPI_H 1
| #define HAVE_LIBMPI 1
| #define HAVE_LIBM 1
| #define HAVE_POW 1
| #define HAVE_SQRT 1
| #define HAVE_LIBDL 1
| #define HAVE_POPCNT 1
| #define HAVE_FUNCTIONAL 1
| #define HAVE_TR1_FUNCTIONAL 1
| #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1
| #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1
| #define HAVE_GOOGLE_SPARSE_HASH_MAP 1
| #define HAVE_UNORDERED_MAP 1
| #define HAVE_TR1_UNORDERED_MAP 1
| #define HAVE_UNORDERED_SET 1
| #define HAVE_TR1_UNORDERED_SET 1
| #define HAVE_BOOST_UNORDERED_SET_HPP 1
| #define HAVE_SQLITE3_H 1
| #define HAVE_LIBSQLITE3 1
| #define _SQL 1
| /* end confdefs.h. */
|
| #ifndef _OPENMP
| choke me
| #endif
| #include <omp.h>
| int main () { return omp_get_num_threads (); }
|
configure:8274: g++-8 -o conftest -g -O2 -fopenmp -I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0 -L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib conftest.cpp -ldl -lm >&5
configure:8274: $? = 0
configure:8288: result: -fopenmp
configure:8460: checking that generated files are newer than configure
configure:8466: result: done
configure:8522: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by ABySS config.status 2.1.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on Shauns-MacBook-Pro.local
config.status:995: creating Makefile
config.status:995: creating ABYSS/Makefile
config.status:995: creating Align/Makefile
config.status:995: creating Assembly/Makefile
config.status:995: creating Common/Makefile
config.status:995: creating DataLayer/Makefile
config.status:995: creating FMIndex/Makefile
config.status:995: creating Graph/Makefile
config.status:995: creating Parallel/Makefile
config.status:995: creating bin/Makefile
config.status:995: creating doc/Makefile
config.status:995: creating dialign/Makefile
config.status:995: creating kmerprint/Makefile
config.status:995: creating AdjList/Makefile
config.status:995: creating Konnector/Makefile
config.status:995: creating DAssembler/Makefile
config.status:995: creating DistanceEst/Makefile
config.status:995: creating Layout/Makefile
config.status:995: creating Map/Makefile
config.status:995: creating Misc/Makefile
config.status:995: creating Overlap/Makefile
config.status:995: creating PopBubbles/Makefile
config.status:995: creating Scaffold/Makefile
config.status:995: creating SimpleGraph/Makefile
config.status:995: creating MergePaths/Makefile
config.status:995: creating KAligner/Makefile
config.status:995: creating PairedDBG/Makefile
config.status:995: creating ParseAligns/Makefile
config.status:995: creating PathOverlap/Makefile
config.status:995: creating Consensus/Makefile
config.status:995: creating FilterGraph/Makefile
config.status:995: creating GapFiller/Makefile
config.status:995: creating Sealer/Makefile
config.status:995: creating lib/gtest-1.7.0/Makefile
config.status:995: creating Unittest/Makefile
config.status:995: creating LogKmerCount/Makefile
config.status:995: creating Bloom/Makefile
config.status:995: creating BloomDBG/Makefile
config.status:995: creating DataBase/Makefile
config.status:995: creating lib/bloomfilter/Makefile
config.status:995: creating lib/nthash/Makefile
config.status:995: creating config.h
config.status:1224: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-apple-darwin17.7.0
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_inline=inline
ac_cv_c_int64_t=yes
ac_cv_c_uint16_t=yes
ac_cv_c_uint32_t=yes
ac_cv_c_uint64_t=yes
ac_cv_c_uint8_t=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=gcc-8
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=g++-8
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func__doprnt=no
ac_cv_func_ceilf=yes
ac_cv_func_dup2=yes
ac_cv_func_fork=yes
ac_cv_func_fork_works=yes
ac_cv_func_gethostname=yes
ac_cv_func_getopt_long=yes
ac_cv_func_getpagesize=yes
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_memcmp_working=yes
ac_cv_func_memset=yes
ac_cv_func_pow=yes
ac_cv_func_realloc_0_nonnull=yes
ac_cv_func_setvbuf_reversed=no
ac_cv_func_sqrt=yes
ac_cv_func_strdup=yes
ac_cv_func_strerror=yes
ac_cv_func_strtoul=yes
ac_cv_func_vfork=yes
ac_cv_func_vfork_works=yes
ac_cv_func_vprintf=yes
ac_cv_have_decl_HOST_NAME_MAX=no
ac_cv_header_boost_functional_hash_hpp=yes
ac_cv_header_boost_property_map_property_map_hpp=yes
ac_cv_header_boost_unordered_set_hpp=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_fcntl_h=yes
ac_cv_header_float_h=yes
ac_cv_header_functional=yes
ac_cv_header_google_sparse_hash_map=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_limits_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_mpi_h=yes
ac_cv_header_sqlite3_h=yes
ac_cv_header_stdbool_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stddef_h=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_param_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_tr1_functional=yes
ac_cv_header_tr1_unordered_map=yes
ac_cv_header_tr1_unordered_set=yes
ac_cv_header_unistd_h=yes
ac_cv_header_unordered_map=yes
ac_cv_header_unordered_set=yes
ac_cv_header_vfork_h=no
ac_cv_host=x86_64-apple-darwin17.7.0
ac_cv_lib_dl_dlsym=yes
ac_cv_lib_m_sqrt=yes
ac_cv_lib_mpi_MPI_Init=yes
ac_cv_lib_sqlite3_main=yes
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=awk
ac_cv_prog_CPP='gcc-8 -E'
ac_cv_prog_CXXCPP='g++-8 -E'
ac_cv_prog_ac_ct_CC=gcc-8
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_cxx_openmp=-fopenmp
ac_cv_prog_make_make_set=yes
ac_cv_type__Bool=yes
ac_cv_type_mode_t=yes
ac_cv_type_pid_t=yes
ac_cv_type_ptrdiff_t=yes
ac_cv_type_size_t=yes
ac_cv_type_ssize_t=yes
ac_cv_type_std__hash_int_=yes
ac_cv_type_std__tr1__hash_int_=yes
ac_cv_type_std__tr1__tuple_int_=yes
am_cv_CC_dependencies_compiler_type=none
am_cv_CXX_dependencies_compiler_type=none
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
ax_cv_PTHREAD_PRIO_INHERIT=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/missing aclocal-1.16'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE='#'
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_CXXFLAGS='-Wall -Wextra -Werror'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AUTOCONF='${SHELL} /private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/missing autoconf'
AUTOHEADER='${SHELL} /private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/missing autoheader'
AUTOMAKE='${SHELL} /private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/missing automake-1.16'
AWK='awk'
CC='gcc-8'
CCDEPMODE='depmode=none'
CFLAGS='-g -O2'
CPP='gcc-8 -E'
CPPFLAGS='-I/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4 -isystem/usr/local/opt/boost/include -isystem/usr/local/opt/boost/include/include -isystem/usr/local/opt/open-mpi/include -isystem/usr/local/opt/google-sparsehash/include -isystem/private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/boost_1_56_0'
CXX='g++-8'
CXXCPP='g++-8 -E'
CXXDEPMODE='depmode=none'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
GHC=''
GREP='/usr/bin/grep'
HAVE_GHC_FALSE=''
HAVE_GHC_TRUE='#'
HAVE_LIBMPI_FALSE='#'
HAVE_LIBMPI_TRUE=''
HAVE_PANDOC_FALSE=''
HAVE_PANDOC_TRUE='#'
HAVE_PTHREAD_FALSE='#'
HAVE_PTHREAD_TRUE=''
HAVE_SQLITE3_FALSE='#'
HAVE_SQLITE3_TRUE=''
HAVE_TR1_TUPLE_FALSE='#'
HAVE_TR1_TUPLE_TRUE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS='-L/usr/local/opt/open-mpi/lib -L/usr/local/opt/google-sparsehash/lib '
LIBOBJS=''
LIBS='-ldl -lm '
LTLIBOBJS=''
MAKEINFO='${SHELL} /private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/missing makeinfo'
MKDIR_P='./install-sh -c -d'
MPI_LIBS='-lmpi '
OBJEXT='o'
OPENMP_CXXFLAGS='-fopenmp'
PACKAGE='abyss'
PACKAGE_BUGREPORT='abyss-users@bcgsc.ca'
PACKAGE_NAME='ABySS'
PACKAGE_STRING='ABySS 2.1.4'
PACKAGE_TARNAME='abyss'
PACKAGE_URL='http://www.bcgsc.ca/platform/bioinfo/software/abyss'
PACKAGE_VERSION='2.1.4'
PAIRED_DBG_FALSE='#'
PAIRED_DBG_TRUE=''
PANDOC=''
PATH_SEPARATOR=':'
PTHREAD_CC='gcc-8'
PTHREAD_CFLAGS='-D_THREAD_SAFE -pthread'
PTHREAD_LIBS=''
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/sh'
SQLITE_LIBS='-lsqlite3 -ldl -lm '
STRIP=''
VERSION='2.1.4'
ac_ct_CC='gcc-8'
ac_ct_CXX=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE='#'
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE='#'
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep=''
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
ax_pthread_config=''
bindir='${exec_prefix}/bin'
build='x86_64-apple-darwin17.7.0'
build_alias=''
build_cpu='x86_64'
build_os='darwin17.7.0'
build_vendor='apple'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-apple-darwin17.7.0'
host_alias=''
host_cpu='x86_64'
host_os='darwin17.7.0'
host_vendor='apple'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /private/tmp/abyss-20181112-25614-1pqmx43/abyss-2.1.4/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local/Cellar/abyss/2.1.4'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "ABySS"
#define PACKAGE_TARNAME "abyss"
#define PACKAGE_VERSION "2.1.4"
#define PACKAGE_STRING "ABySS 2.1.4"
#define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
#define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
#define PACKAGE "abyss"
#define VERSION "2.1.4"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define HAVE_FCNTL_H 1
#define HAVE_FLOAT_H 1
#define HAVE_LIMITS_H 1
#define HAVE_STDDEF_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_SYS_PARAM_H 1
#define HAVE__BOOL 1
#define HAVE_STDBOOL_H 1
#define STDC_HEADERS 1
#define HAVE_PTRDIFF_T 1
#define HAVE_STD_HASH 1
#define HAVE_STD_TR1_HASH 1
#define HAVE_STD_TR1_TUPLE 1
#define BOOST_HAS_TR1_TUPLE 1
#define HAVE_DUP2 1
#define HAVE_GETHOSTNAME 1
#define HAVE_GETOPT_LONG 1
#define HAVE_GETPAGESIZE 1
#define HAVE_MEMSET 1
#define HAVE_STRDUP 1
#define HAVE_STRERROR 1
#define HAVE_STRTOUL 1
#define HAVE_FORK 1
#define HAVE_VFORK 1
#define HAVE_WORKING_VFORK 1
#define HAVE_WORKING_FORK 1
#define HAVE_STDLIB_H 1
#define HAVE_MALLOC 1
#define HAVE_STDLIB_H 1
#define HAVE_REALLOC 1
#define HAVE_VPRINTF 1
#define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
#define FMBITS 64
#define MAX_KMER 128
#define MAX_HASHES 32
#define HAVE_PTHREAD_PRIO_INHERIT 1
#define MPICH_SKIP_MPICXX 1
#define OMPI_SKIP_MPICXX 1
#define HAVE_MPI_H 1
#define HAVE_LIBMPI 1
#define HAVE_LIBM 1
#define HAVE_POW 1
#define HAVE_SQRT 1
#define HAVE_LIBDL 1
#define HAVE_POPCNT 1
#define HAVE_FUNCTIONAL 1
#define HAVE_TR1_FUNCTIONAL 1
#define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1
#define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1
#define HAVE_GOOGLE_SPARSE_HASH_MAP 1
#define HAVE_UNORDERED_MAP 1
#define HAVE_TR1_UNORDERED_MAP 1
#define HAVE_UNORDERED_SET 1
#define HAVE_TR1_UNORDERED_SET 1
#define HAVE_BOOST_UNORDERED_SET_HPP 1
#define HAVE_SQLITE3_H 1
#define HAVE_LIBSQLITE3 1
#define _SQL 1
configure: exit 0
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