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September 3, 2019 22:33
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| No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11 | |
| WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11 | |
| Adding in variants from internal_defaults | |
| INFO:conda_build.variants:Adding in variants from internal_defaults | |
| Attempting to finalize metadata for solexaqa | |
| INFO:conda_build.metadata:Attempting to finalize metadata for solexaqa | |
| Collecting package metadata (repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| Collecting package metadata (repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| Collecting package metadata (repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| BUILD START: ['solexaqa-3.1.7.1-h04f5b5a_0.tar.bz2'] | |
| Collecting package metadata (repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho | |
| The following NEW packages will be INSTALLED: | |
| blas: 1.0-mkl | |
| boost: 1.67.0-py37_4 | |
| bzip2: 1.0.8-h1de35cc_0 | |
| ca-certificates: 2019.5.15-1 | |
| certifi: 2019.6.16-py37_1 | |
| icu: 58.2-h4b95b61_1 | |
| intel-openmp: 2019.4-233 | |
| libboost: 1.67.0-hebc422b_4 | |
| libcxx: 4.0.1-hcfea43d_1 | |
| libcxxabi: 4.0.1-hcfea43d_1 | |
| libedit: 3.1.20181209-hb402a30_0 | |
| libffi: 3.2.1-h475c297_4 | |
| libgfortran: 3.0.1-h93005f0_2 | |
| libiconv: 1.15-hdd342a3_7 | |
| mkl: 2019.4-233 | |
| mkl-service: 2.0.2-py37h1de35cc_0 | |
| mkl_fft: 1.0.14-py37h5e564d8_0 | |
| mkl_random: 1.0.2-py37h27c97d8_0 | |
| ncurses: 6.1-h0a44026_1 | |
| numpy: 1.16.4-py37hacdab7b_0 | |
| numpy-base: 1.16.4-py37h6575580_0 | |
| openssl: 1.1.1c-h1de35cc_1 | |
| pip: 19.2.2-py37_0 | |
| py-boost: 1.67.0-py37h6440ff4_4 | |
| python: 3.7.4-h359304d_1 | |
| readline: 7.0-h1de35cc_5 | |
| setuptools: 41.0.1-py37_0 | |
| six: 1.12.0-py37_0 | |
| sqlite: 3.29.0-ha441bb4_0 | |
| tk: 8.6.8-ha441bb4_0 | |
| wheel: 0.33.4-py37_0 | |
| xz: 5.2.4-h1de35cc_4 | |
| zlib: 1.2.11-h1de35cc_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Collecting package metadata (repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| Collecting package metadata (repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/_build_env | |
| The following NEW packages will be INSTALLED: | |
| cctools: 895-1 | |
| clang: 4.0.1-1 | |
| clang_osx-64: 4.0.1-h1ce6c1d_18 | |
| clangxx: 4.0.1-1 | |
| clangxx_osx-64: 4.0.1-h22b1bf0_18 | |
| compiler-rt: 4.0.1-hcfea43d_1 | |
| ld64: 274.2-1 | |
| libcxx: 4.0.1-hcfea43d_1 | |
| libcxxabi: 4.0.1-hcfea43d_1 | |
| llvm: 4.0.1-1 | |
| llvm-lto-tapi: 4.0.1-1 | |
| make: 4.2.1-h3efe00b_1 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Source cache directory is: /usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/src_cache | |
| INFO:conda_build.source:Source cache directory is: /usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/src_cache | |
| INFO conda_build.source:download_to_cache(43): Source cache directory is: /usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/src_cache | |
| Found source in cache: SolexaQA++_v3.1.7.1_b3bdabf955.zip | |
| INFO:conda_build.source:Found source in cache: SolexaQA++_v3.1.7.1_b3bdabf955.zip | |
| INFO conda_build.source:download_to_cache(63): Found source in cache: SolexaQA++_v3.1.7.1_b3bdabf955.zip | |
| Extracting download | |
| source tree in: /usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/work | |
| export PREFIX=/usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho | |
| export BUILD_PREFIX=/usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/_build_env | |
| export SRC_DIR=/usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/work | |
| INFO: activate_clang_osx-64.sh made the following environmental changes: | |
| +AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar | |
| +AS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-as | |
| +CC=x86_64-apple-darwin13.4.0-clang | |
| +CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I$PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/solexaqa-3.1.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix | |
| +CHECKSYMS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-checksyms | |
| +CLANG=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang | |
| +CMAKE_PREFIX_PATH=:$PREFIX | |
| +CODESIGN_ALLOCATE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-codesign_allocate | |
| +CONDA_BUILD_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk | |
| +CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I$PREFIX/include | |
| +DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -I$PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/solexaqa-3.1.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix | |
| +HOST=x86_64-apple-darwin13.4.0 | |
| +INDR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-indr | |
| +INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool | |
| +LD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld | |
| +LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib | |
| +LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib | |
| +LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool | |
| +LIPO=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-lipo | |
| +NM=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nm | |
| +NMEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nmedit | |
| +OTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-otool | |
| +PAGESTUFF=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-pagestuff | |
| +RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib | |
| +REDO_PREBINDING=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-redo_prebinding | |
| +SEGEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-segedit | |
| +SEG_ADDR_TABLE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_addr_table | |
| +SEG_HACK=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_hack | |
| +SIZE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-size | |
| +STRINGS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strings | |
| +STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip | |
| +_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 | |
| INFO: activate_clangxx_osx-64.sh made the following environmental changes: | |
| +CLANGXX=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang++ | |
| +CXX=x86_64-apple-darwin13.4.0-clang++ | |
| +CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -I$PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/solexaqa-3.1.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix | |
| +DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -I$PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/solexaqa-3.1.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix | |
| + cd source | |
| + sed -i.bak -e 's/\$(CC)/$(CXX)/' -e '/CFLAGS=/s/$/ -D_GLIBCXX_USE_CXX11_ABI=0/' -e '/LIBS=/s/-lpthread/-licutu -licui18n -licuuc -licudata -ldl -lpthread/' makefile | |
| + BOOST_PATH=/usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho | |
| + make | |
| x86_64-apple-darwin13.4.0-clang++ main.cpp -o SolexaQA++ -I. -I/usr/local/include/boost -I/usr/local/include/ -L/usr/local/lib -lm -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.11 -lz -licutu -licui18n -licuuc -licudata -ldl -lpthread | |
| ld: library not found for -licutu | |
| clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation) | |
| make: *** [makefile:73: SolexaQA++] Error 1 | |
| Traceback (most recent call last): | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/bin/conda-build", line 11, in <module> | |
| sys.exit(main()) | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 445, in main | |
| execute(sys.argv[1:]) | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 436, in execute | |
| verify=args.verify, variants=args.variants) | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/api.py", line 209, in build | |
| notest=notest, need_source_download=need_source_download, variants=variants) | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2343, in build_tree | |
| notest=notest, | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 1491, in build | |
| cwd=src_dir, stats=build_stats) | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/utils.py", line 397, in check_call_env | |
| return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs) | |
| File "/usr/local/Caskroom/miniconda/base/envs/testenv/lib/python3.7/site-packages/conda_build/utils.py", line 377, in _func_defaulting_env_to_os_environ | |
| raise subprocess.CalledProcessError(proc.returncode, _args) | |
| subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/usr/local/Caskroom/miniconda/base/envs/testenv/conda-bld/solexaqa_1567549192865/work/conda_build.sh']' returned non-zero exit status 2. |
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