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GCC installation fails on Azure Pipelines #15832

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sylee957 opened this issue Jan 23, 2019 · 22 comments
Closed

GCC installation fails on Azure Pipelines #15832

sylee957 opened this issue Jan 23, 2019 · 22 comments
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Travis Related to the Travis CI setup. Do not use for test failures unless they are Travis specific.

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@sylee957
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I think azure had also started to fail on installing gcc, and it had gotten worse than #15671 as no optional dependency tests are getting run right now.

It had started failing after this commit
https://dev.azure.com/SymPy/SymPy/_build/results?buildId=1091

2019-01-17T00:33:49.1071875Z Preparing transaction: ...working... done
2019-01-17T00:34:04.0495709Z Verifying transaction: ...working... done
2019-01-17T00:34:08.7432693Z Executing transaction: ...working... failed
2019-01-17T00:34:08.7436317Z ERROR conda.core.link:_execute(502): An error occurred while installing package 'defaults::gcc-4.8.5-7'.
2019-01-17T00:34:08.7436642Z LinkError: post-link script failed for package defaults::gcc-4.8.5-7
2019-01-17T00:34:08.7436877Z running your command again with `-v` will provide additional information
2019-01-17T00:34:08.7437261Z location of failed script: /usr/envs/optional-dependencies/bin/.gcc-post-link.sh
2019-01-17T00:34:08.7437316Z ==> script messages <==
2019-01-17T00:34:08.7437478Z <None>
2019-01-17T00:34:08.7437880Z 
2019-01-17T00:34:08.7437934Z Attempting to roll back.
2019-01-17T00:34:08.7437991Z 
2019-01-17T00:34:09.2786714Z Rolling back transaction: ...working... done
2019-01-17T00:34:09.3103253Z 
2019-01-17T00:34:09.3104036Z LinkError: post-link script failed for package defaults::gcc-4.8.5-7
2019-01-17T00:34:09.3104266Z running your command again with `-v` will provide additional information
2019-01-17T00:34:09.3104498Z location of failed script: /usr/envs/optional-dependencies/bin/.gcc-post-link.sh
2019-01-17T00:34:09.3104750Z ==> script messages <==
2019-01-17T00:34:09.3104794Z <None>
2019-01-17T00:34:09.3104841Z 
2019-01-17T00:34:09.3104866Z 
2019-01-17T00:34:09.3104889Z 
2019-01-17T00:34:10.4683799Z ##[error]Failed to create Conda environment /usr/envs/optional-dependencies: Error: /usr/bin/conda failed with return code: 1
2019-01-17T00:34:10.4694586Z ##[error]Failed to create Conda environment /usr/envs/optional-dependencies: Error: /usr/bin/conda failed with return code: 1
2019-01-17T00:34:10.4721384Z ##[section]Finishing: Create conda environment

As long as my findings, I think I could reproduce the failing while installing gcc with anaconda in my local Windows Subsystem for Linux (ubuntu), but I may post some experiment PRs to see what really happens with verbose logs,

as this line suggests

2019-01-17T00:34:09.3104266Z running your command again with `-v` will provide additional information
@sylee957 sylee957 mentioned this issue Jan 23, 2019
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@sylee957
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An example of verbose log:
https://dev.azure.com/SymPy/SymPy/_build/results?buildId=1222&view=logs&jobId=ae3035cf-29c3-5ed9-f0ce-f4976257ba11&taskId=58b30f76-ea06-5178-fcd4-036671e4d1d3&lineStart=816&lineEnd=908&colStart=1&colEnd=70

2019-01-23T07:27:13.8703161Z ===> LINKING PACKAGE: defaults::gcc-4.8.5-7 <===
2019-01-23T07:27:13.8703442Z   prefix=/usr/envs/optional-dependencies
2019-01-23T07:27:13.8703685Z   source=/home/vsts/.conda/pkgs/gcc-4.8.5-7
2019-01-23T07:27:13.8703754Z 
2019-01-23T07:27:13.8703785Z 
2019-01-23T07:27:14.1858720Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libasan.so'
2019-01-23T07:27:14.1859421Z 
2019-01-23T07:27:14.1861480Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libatomic.so'
2019-01-23T07:27:14.1861840Z 
2019-01-23T07:27:14.1863185Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libatomic.so.1'
2019-01-23T07:27:14.1863499Z 
2019-01-23T07:27:14.1864960Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libgcc_s.so'
2019-01-23T07:27:14.1865274Z 
2019-01-23T07:27:14.1866711Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libgcc_s.so.1'
2019-01-23T07:27:14.1866985Z 
2019-01-23T07:27:14.1872567Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libgfortran.so'
2019-01-23T07:27:14.1872975Z 
2019-01-23T07:27:14.1877226Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libgomp.so'
2019-01-23T07:27:14.1877551Z 
2019-01-23T07:27:14.1878884Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libgomp.so.1'
2019-01-23T07:27:14.1879164Z 
2019-01-23T07:27:14.1881001Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libgomp.so.1.0.0'
2019-01-23T07:27:14.1881341Z 
2019-01-23T07:27:14.1883546Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libitm.so'
2019-01-23T07:27:14.1883883Z 
2019-01-23T07:27:14.1885269Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libitm.so.1'
2019-01-23T07:27:14.1885553Z 
2019-01-23T07:27:14.1886615Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libitm.so.1.0.0'
2019-01-23T07:27:14.1886872Z 
2019-01-23T07:27:14.1893123Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libquadmath.so'
2019-01-23T07:27:14.1894426Z 
2019-01-23T07:27:14.1895059Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libquadmath.so.0'
2019-01-23T07:27:14.1896002Z 
2019-01-23T07:27:14.1896593Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libquadmath.so.0.0.0'
2019-01-23T07:27:14.1896826Z 
2019-01-23T07:27:14.1899221Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libstdc++.so'
2019-01-23T07:27:14.1899555Z 
2019-01-23T07:27:14.1903830Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libstdc++.so.6'
2019-01-23T07:27:14.1904841Z 
2019-01-23T07:27:14.1906232Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libtsan.so'
2019-01-23T07:27:14.1906523Z 
2019-01-23T07:27:14.1946948Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libtsan.so.0'
2019-01-23T07:27:14.1947474Z 
2019-01-23T07:27:14.1948030Z file exists, but clobbering: '/usr/envs/optional-dependencies/lib/libtsan.so.0.0.0'
2019-01-23T07:27:14.1948272Z 
2019-01-23T07:27:14.1948742Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/cpp.info'
2019-01-23T07:27:14.1948980Z 
2019-01-23T07:27:14.1949396Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/cppinternals.info'
2019-01-23T07:27:14.1949617Z 
2019-01-23T07:27:14.1950050Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/gcc.info'
2019-01-23T07:27:14.1950264Z 
2019-01-23T07:27:14.1951101Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/gccinstall.info'
2019-01-23T07:27:14.1952114Z 
2019-01-23T07:27:14.1952744Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/gccint.info'
2019-01-23T07:27:14.1953023Z 
2019-01-23T07:27:14.1954327Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/gfortran.info'
2019-01-23T07:27:14.1955987Z 
2019-01-23T07:27:14.1957137Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/libgomp.info'
2019-01-23T07:27:14.1957976Z 
2019-01-23T07:27:14.1959070Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/info/libquadmath.info'
2019-01-23T07:27:14.1959289Z 
2019-01-23T07:27:14.1959804Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/man/man7/fsf-funding.7'
2019-01-23T07:27:14.1959956Z 
2019-01-23T07:27:14.1960781Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/man/man7/gfdl.7'
2019-01-23T07:27:14.1960987Z 
2019-01-23T07:27:14.1961370Z file exists, but clobbering: '/usr/envs/optional-dependencies/share/man/man7/gpl.7'
2019-01-23T07:27:14.1961534Z 
2019-01-23T07:27:15.1214015Z $ bash -x /usr/envs/optional-dependencies/bin/.gcc-post-link.sh
2019-01-23T07:27:15.1215360Z ==> cwd: /usr/envs/optional-dependencies/bin <==
2019-01-23T07:27:15.1215705Z ==> exit code: 1 <==
2019-01-23T07:27:15.1215903Z ==> stdout <==
2019-01-23T07:27:15.1216338Z b"Installation failed: gcc is not able to compile a simple 'Hello, World' program.\n"
2019-01-23T07:27:15.1216587Z ==> stderr <==
2019-01-23T07:27:15.1260514Z b'++ uname\n+ \'[\' Linux == Darwin \']\'\n+ build_os_md5=($(md5sum "${PREFIX}/share/conda-gcc-build-machine-os-details"))\n++ md5sum /usr/envs/optional-dependencies/share/conda-gcc-build-machine-os-details\n+ target_os_md5=($(lsb_release -a | md5sum))\n++ lsb_release -a\n++ md5sum\nNo LSB modules are available.\n+ [[ 3a1ea953f62ce0736a77dca2afccb825 == \\5\\b\\9\\d\\e\\6\\9\\9\\a\\1\\5\\6\\a\\9\\e\\9\\d\\1\\d\\f\\d\\9\\7\\9\\2\\c\\1\\f\\9\\b\\6\\b ]]\n+ read -r x\n++ find /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/ /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed/ /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/ -name \'*.h\'\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/bmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/popcntintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/ia32intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/x86intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avxintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/wmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stddef.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/fxsrintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xsavecintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/ammintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/lzcntintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/cross-stdarg.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/quadmath.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512vldqintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/openacc.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdfix.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512dqintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/cpuid.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdarg.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/bmiintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/sanitizer/asan_interface.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/sanitizer/lsan_interface.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/sanitizer/common_interface_defs.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/clwbintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/mm_malloc.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx5124vnniwintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/lwpintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/rdseedintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/omp.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512vlintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdint-gcc.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512erintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/pmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/smmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/fma4intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/tbmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx2intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdint.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdalign.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/clzerointrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/fmaintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdatomic.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/gcov.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/emmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/sgxintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xtestintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512vbmivlintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xsaveoptintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/iso646.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/float.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/immintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/adxintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/nmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512vpopcntdqintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdbool.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512pfintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xsaveintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/quadmath_weak.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/mmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/clflushoptintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512ifmaintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/bmi2intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512fintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/f16cintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/stdnoreturn.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xsavesintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/rtmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/tmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/prfchwintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/mwaitxintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx5124fmapsintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512vbmiintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/pkuintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/varargs.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512bwintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/unwind.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512vlbwintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512ifmavlintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/shaintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/xopintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/mm3dnow.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include/avx512cdintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed/limits.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed/linux/a.out.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed/linux/a.out.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed/syslimits.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/bmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/popcntintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ia32intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/x86intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/avxintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/wmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stddef.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/fxsrintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ammintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/lzcntintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/cross-stdarg.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/quadmath.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdfix.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/cpuid.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdarg.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/bmiintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/gcj/libgcj-config.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/mm_malloc.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/lwpintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/rdseedintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/omp.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdint-gcc.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/pmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/smmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/jni.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/fma4intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/tbmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/avx2intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdint.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdalign.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/jni_md.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/fmaintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/xmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/emmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/xtestintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/xsaveoptintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/iso646.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/float.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/immintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/jawt.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/adxintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/nmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdbool.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/jvmpi.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/xsaveintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/quadmath_weak.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/mmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/bmi2intrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/f16cintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stdnoreturn.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/rtmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/tmmintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/prfchwintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/varargs.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/unwind.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/xopintrin.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ssp/unistd.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ssp/stdio.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ssp/ssp.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/ssp/string.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/jawt_md.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/mf-runtime.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/mm3dnow.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/wchar.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/wchar.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/sys/sysmacros.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/sys/sysmacros.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/sys/stat.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/sys/stat.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/features.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/features.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/limits.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/tgmath.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/tgmath.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/zutil.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/zutil.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/bits/string2.h\n+ rm -f /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/bits/string2.h\n+ read -r x\n+ grep -q \'It has been auto-edited by fixincludes from\' /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include-fixed/syslimits.h\n+ read -r x\n+ C_RUNTIME_OBJ_FILES=\'crt0.o crt1.o crt2.o crt3.o crti.o crtn.o\'\n+ c_runtime_obj_files_found=0\n++ ld --verbose\n++ grep SEARCH_DIR\n++ sed -r \'s/SEARCH_DIR\\("=?([^"]*)"\\);/ \\1/g\'\n+ for library_path in \'$(ld --verbose | grep SEARCH_DIR | sed -r \'\\\'\'s/SEARCH_DIR\\("=?([^"]*)"\\);/ \\1/g\'\\\'\')\'\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/local/lib/x86_64-linux-gnu/crt0.o\n+ [[ -e /usr/local/lib/x86_64-linux-gnu/crt0.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/local/lib/x86_64-linux-gnu/crt1.o\n+ [[ -e /usr/local/lib/x86_64-linux-gnu/crt1.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/local/lib/x86_64-linux-gnu/crt2.o\n+ [[ -e /usr/local/lib/x86_64-linux-gnu/crt2.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/local/lib/x86_64-linux-gnu/crt3.o\n+ [[ -e /usr/local/lib/x86_64-linux-gnu/crt3.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/local/lib/x86_64-linux-gnu/crti.o\n+ [[ -e /usr/local/lib/x86_64-linux-gnu/crti.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/local/lib/x86_64-linux-gnu/crtn.o\n+ [[ -e /usr/local/lib/x86_64-linux-gnu/crtn.o ]]\n+ \'[\' 0 -eq 1 \']\'\n+ for library_path in \'$(ld --verbose | grep SEARCH_DIR | sed -r \'\\\'\'s/SEARCH_DIR\\("=?([^"]*)"\\);/ \\1/g\'\\\'\')\'\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/lib/x86_64-linux-gnu/crt0.o\n+ [[ -e /lib/x86_64-linux-gnu/crt0.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/lib/x86_64-linux-gnu/crt1.o\n+ [[ -e /lib/x86_64-linux-gnu/crt1.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/lib/x86_64-linux-gnu/crt2.o\n+ [[ -e /lib/x86_64-linux-gnu/crt2.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/lib/x86_64-linux-gnu/crt3.o\n+ [[ -e /lib/x86_64-linux-gnu/crt3.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/lib/x86_64-linux-gnu/crti.o\n+ [[ -e /lib/x86_64-linux-gnu/crti.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/lib/x86_64-linux-gnu/crtn.o\n+ [[ -e /lib/x86_64-linux-gnu/crtn.o ]]\n+ \'[\' 0 -eq 1 \']\'\n+ for library_path in \'$(ld --verbose | grep SEARCH_DIR | sed -r \'\\\'\'s/SEARCH_DIR\\("=?([^"]*)"\\);/ \\1/g\'\\\'\')\'\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/lib/x86_64-linux-gnu/crt0.o\n+ [[ -e /usr/lib/x86_64-linux-gnu/crt0.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/lib/x86_64-linux-gnu/crt1.o\n+ [[ -e /usr/lib/x86_64-linux-gnu/crt1.o ]]\n+ ln -s /usr/lib/x86_64-linux-gnu/crt1.o /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/ /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/\n+ c_runtime_obj_files_found=1\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/lib/x86_64-linux-gnu/crt2.o\n+ [[ -e /usr/lib/x86_64-linux-gnu/crt2.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/lib/x86_64-linux-gnu/crt3.o\n+ [[ -e /usr/lib/x86_64-linux-gnu/crt3.o ]]\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/lib/x86_64-linux-gnu/crti.o\n+ [[ -e /usr/lib/x86_64-linux-gnu/crti.o ]]\n+ ln -s /usr/lib/x86_64-linux-gnu/crti.o /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/ /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/\nln: failed to create symbolic link \'/usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/7.3.0\': File exists\n+ c_runtime_obj_files_found=1\n+ for obj_file in \'$C_RUNTIME_OBJ_FILES\'\n+ obj_file_full_path=/usr/lib/x86_64-linux-gnu/crtn.o\n+ [[ -e /usr/lib/x86_64-linux-gnu/crtn.o ]]\n+ ln -s /usr/lib/x86_64-linux-gnu/crtn.o /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/ /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/\nln: failed to create symbolic link \'/usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/7.3.0\': File exists\n+ c_runtime_obj_files_found=1\n+ \'[\' 1 -eq 1 \']\'\n+ break\n+ \'[\' 1 -ne 1 \']\'\n+ \'[\' 1 -ne 1 \']\'\n++ echo /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5\n+ SPECS_DIR=\'/usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5\'\n+ SPECS_FILE=\'/usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs\'\n+ /usr/envs/optional-dependencies/bin/gcc -dumpspecs\n/usr/envs/optional-dependencies/bin/.gcc-post-link.sh: line 98: /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs: No such file or directory\n+ EXTRA_SYSTEM_INCLUDE_DIRS=\'/usr/include/x86_64-linux-gnu /usr/include/i686-linux-gnu /usr/include/i386-linux-gnu\'\n+ for INCDIR in \'${EXTRA_SYSTEM_INCLUDE_DIRS}\'\n+ sed -i \':a;N;$!ba;s|\\(*cpp:\\n[^\\n]*\\)|\\1 -isystem /usr/include/x86_64-linux-gnu|g\' \'/usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs\'\nsed: can\'t read /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs: No such file or directory\n+ for INCDIR in \'${EXTRA_SYSTEM_INCLUDE_DIRS}\'\n+ sed -i \':a;N;$!ba;s|\\(*cpp:\\n[^\\n]*\\)|\\1 -isystem /usr/include/i686-linux-gnu|g\' \'/usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs\'\nsed: can\'t read /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs: No such file or directory\n+ for INCDIR in \'${EXTRA_SYSTEM_INCLUDE_DIRS}\'\n+ sed -i \':a;N;$!ba;s|\\(*cpp:\\n[^\\n]*\\)|\\1 -isystem /usr/include/i386-linux-gnu|g\' \'/usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs\'\nsed: can\'t read /usr/envs/optional-dependencies/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 /usr/envs/optional-dependencies/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs: No such file or directory\n++ mktemp -d XXXXXXXXXX\n+ workdir=Mai5iCY0fY\n+ cd Mai5iCY0fY\n+ cat\n+ cat\n+ set +e\n+ set -e\n+ /usr/envs/optional-dependencies/bin/gcc -o hello_c.out hello.c\nIn file included from /usr/include/stdio.h:27:0,\n                 from hello.c:1:\n/usr/include/features.h:367:25: fatal error: sys/cdefs.h: No such file or directory\n #  include <sys/cdefs.h>\n                         ^\ncompilation terminated.\n+ SUCCESS=1\n+ \'[\' 1 -ne 0 \']\'\n+ echo \'Installation failed: gcc is not able to compile a simple \'\\\'\'Hello, World\'\\\'\' program.\'\n+ cd ..\n+ rm -r Mai5iCY0fY\n+ exit 1\n'
2019-01-23T07:27:15.1269857Z 
2019-01-23T07:27:15.1269907Z 
2019-01-23T07:27:15.1270872Z ===> REVERSING PACKAGE LINK: defaults::gcc-4.8.5-7 <===
2019-01-23T07:27:15.1271116Z   prefix=/usr/envs/optional-dependencies
2019-01-23T07:27:15.1271179Z 
2019-01-23T07:27:15.1271207Z 
2019-01-23T07:27:15.3545095Z failed
2019-01-23T07:27:15.3546181Z An error occurred while installing package 'defaults::gcc-4.8.5-7'.
2019-01-23T07:27:15.3546450Z LinkError: post-link script failed for package defaults::gcc-4.8.5-7
2019-01-23T07:27:15.3546937Z running your command again with `-v` will provide additional information
2019-01-23T07:27:15.3547190Z location of failed script: /usr/envs/optional-dependencies/bin/.gcc-post-link.sh
2019-01-23T07:27:15.3547241Z ==> script messages <==
2019-01-23T07:27:15.3547280Z <None>
2019-01-23T07:27:15.3547319Z 
2019-01-23T07:27:15.3547378Z Attempting to roll back.
2019-01-23T07:27:15.3547406Z 
2019-01-23T07:27:15.3547429Z 
2019-01-23T07:27:15.3547693Z Rolling back transaction: ...working... ===> REVERSING PACKAGE LINK: conda-forge::fontconfig-2.13.1-h2176d3f_1000 <===
2019-01-23T07:27:15.3547919Z   prefix=/usr/envs/optional-dependencies

@sylee957 sylee957 mentioned this issue Jan 23, 2019
Merged
@bjodah
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bjodah commented Jan 23, 2019

I think the gcc package is called gcc_linux-64 nowadays, but I haven't kept up with the latest developments in anaconda/conda-forge.

@sylee957
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I think the test runs without gcc installation, can 0880f73e5f8343b3006fa2adb6d9bb09b3df8b55 be a workaround?
https://dev.azure.com/SymPy/SymPy/_build/results?buildId=1224

As far as I had inspected the issue, I think there is a conflict of theano and gcc
I think theano already gets shipped with gcc_linux-64

(base) sylee957@DESKTOP-F7U88QO:~/anaconda3/envs$ conda create -n test -c conda-forge python=3.6 theano
Solving environment: done

## Package Plan ##

  environment location: /home/sylee957/anaconda3/envs/test

  added / updated specs:
    - python=3.6
    - theano


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    gcc_impl_linux-64-7.3.0    |       habb00fd_1        73.2 MB  conda-forge
    setuptools-40.6.3          |           py36_0         631 KB  conda-forge
    mkl_fft-1.0.10             |   py36h470a237_1         640 KB  conda-forge
    mkl_random-1.0.2           |           py36_0         1.3 MB  conda-forge
    binutils_impl_linux-64-2.31.1|       h6176602_1        16.5 MB  conda-forge
    wheel-0.32.3               |           py36_0          34 KB  conda-forge
    gxx_impl_linux-64-7.3.0    |       hdf63c60_1        18.7 MB  conda-forge
    ------------------------------------------------------------
                                           Total:       111.0 MB

The following NEW packages will be INSTALLED:

    binutils_impl_linux-64: 2.31.1-h6176602_1       conda-forge
    binutils_linux-64:      2.31.1-h6176602_3       conda-forge
    blas:                   1.0-mkl
    ca-certificates:        2018.11.29-ha4d7672_0   conda-forge
    certifi:                2018.11.29-py36_1000    conda-forge
    gcc_impl_linux-64:      7.3.0-habb00fd_1        conda-forge
    gcc_linux-64:           7.3.0-h553295d_3        conda-forge
    gxx_impl_linux-64:      7.3.0-hdf63c60_1        conda-forge
    gxx_linux-64:           7.3.0-h553295d_3        conda-forge
    intel-openmp:           2019.1-144
    libffi:                 3.2.1-hf484d3e_1005     conda-forge
    libgcc-ng:              7.3.0-hdf63c60_0        conda-forge
    libgfortran-ng:         7.2.0-hdf63c60_3        conda-forge
    libgpuarray:            0.7.6-h14c3975_1003     conda-forge
    libstdcxx-ng:           7.3.0-hdf63c60_0        conda-forge
    mako:                   1.0.7-py_1              conda-forge
    markupsafe:             1.1.0-py36h14c3975_1000 conda-forge
    mkl:                    2019.1-144
    mkl_fft:                1.0.10-py36h470a237_1   conda-forge
    mkl_random:             1.0.2-py36_0            conda-forge
    ncurses:                6.1-hf484d3e_1002       conda-forge
    numpy:                  1.15.4-py36h7e9f1db_0
    numpy-base:             1.15.4-py36hde5b4d6_0
    openssl:                1.0.2p-h14c3975_1002    conda-forge
    pip:                    18.1-py36_1000          conda-forge
    pygpu:                  0.7.6-py36h3010b51_1000 conda-forge
    python:                 3.6.7-hd21baee_1001     conda-forge
    readline:               7.0-hf8c457e_1001       conda-forge
    scipy:                  1.1.0-py36h7c811a0_2
    setuptools:             40.6.3-py36_0           conda-forge
    six:                    1.12.0-py36_1000        conda-forge
    sqlite:                 3.26.0-h67949de_1000    conda-forge
    theano:                 1.0.4-py36hf484d3e_1000 conda-forge
    tk:                     8.6.9-h84994c4_1000     conda-forge
    wheel:                  0.32.3-py36_0           conda-forge
    xz:                     5.2.4-h14c3975_1001     conda-forge
    zlib:                   1.2.11-h14c3975_1004    conda-forge

But if I try to install gcc package on top of theano installation, it fails like below

(base) sylee957@DESKTOP-F7U88QO:~/anaconda3/envs$ conda activate test
(test) sylee957@DESKTOP-F7U88QO:~/anaconda3/envs$ conda install -c conda-forge gcc
Solving environment: done

## Package Plan ##

  environment location: /home/sylee957/anaconda3/envs/test

  added / updated specs:
    - gcc


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    isl-0.12.2                 |                0         1.1 MB
    cloog-0.18.0               |                0         617 KB
    gcc-4.8.5                  |                7        66.6 MB
    ------------------------------------------------------------
                                           Total:        68.3 MB

The following NEW packages will be INSTALLED:

    cloog: 0.18.0-0
    gcc:   4.8.5-7
    gmp:   6.1.2-hf484d3e_1000 conda-forge
    isl:   0.12.2-0
    mpc:   1.1.0-4             conda-forge
    mpfr:  3.1.5-0             conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
isl-0.12.2           | 1.1 MB    | ############################################################################################################################################################################################################################################################################################################### | 100%
cloog-0.18.0         | 617 KB    | ############################################################################################################################################################################################################################################################################################################### | 100%
gcc-4.8.5            | 66.6 MB   | ############################################################################################################################################################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(507): An error occurred while installing package 'defaults::gcc-4.8.5-7'.
LinkError: post-link script failed for package defaults::gcc-4.8.5-7
running your command again with `-v` will provide additional information
location of failed script: /home/sylee957/anaconda3/envs/test/bin/.gcc-post-link.sh
==> script messages <==
<None>

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package defaults::gcc-4.8.5-7
running your command again with `-v` will provide additional information
location of failed script: /home/sylee957/anaconda3/envs/test/bin/.gcc-post-link.sh
==> script messages <==
<None>

@bjodah
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bjodah commented Jan 23, 2019 •
edited

gcc-4.8.5 is old. It looks like related issue(s)(?) are currently being discussed on gitter:
https://gitter.im/conda-forge/conda-forge.github.io

EDIT: I don't we think we should give up on having a C-compiler for at least some test environments.

@sylee957
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sylee957 commented Jan 23, 2019 •
edited

I think it was after theano 1.0.3 which had introduced gcc_linux-64 and gxx_linux-64.
I still don't know how the gcc package is getting maintained on anaconda
Do anyone know where is the upstream for conda-forge gcc package?

@oscarbenjamin oscarbenjamin added the Travis Related to the Travis CI setup. Do not use for test failures unless they are Travis specific. label Jan 23, 2019
@asmeurer
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I think gcc has to be built manually because it cannot be built on CI (it takes too long). I guess someone built it manually and uploaded it. You would have to ask on the conda-forge gitter for details.

@sylee957
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sylee957 commented Jan 23, 2019 •
edited

From the log in https://dev.azure.com/SymPy/SymPy/_build/results?buildId=1224,
I think c compiler test from test_algorithm(test 2 and 5) gets passed without gcc installation.

2019-01-23T09:54:46.0541565Z sympy/codegen/tests/test_algorithms.py[5] ./usr/envs/optional-dependencies/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/tmpgpESA0/_newton.pyx
2019-01-23T09:54:46.0541897Z   tree = Parsing.p_module(s, pxd, full_module_name)
2019-01-23T09:54:46.4913196Z .E./usr/envs/optional-dependencies/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/tmpDDHho_/_newton_par.pyx
2019-01-23T09:54:46.4913520Z   tree = Parsing.p_module(s, pxd, full_module_name)
2019-01-23T09:54:46.6607647Z .                           [FAIL]

It can imply that either gcc installed with theano can work, or gcc gets shopped with azure's ubuntu agent, or other c compiler could have been installed.

But I don't know if it is a right claim that dropping gcc from azure installation can be a workaround.

@sylee957
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From one of my trials in https://dev.azure.com/SymPy/SymPy/_build/results?buildId=1235

GCC may had already been shipped with agent, so there may have not been any need to install gcc from the conda-forge from the first.

2019-01-23T23:39:10.6823182Z whereis gcc
2019-01-23T23:39:10.6854193Z [command]/bin/bash --noprofile --norc /home/vsts/work/_temp/3a689d8d-f9f8-41bb-8183-8b35fd497180.sh
2019-01-23T23:39:11.0501217Z gcc: /usr/bin/gcc /usr/lib/gcc /usr/share/man/man1/gcc.1.gz
2019-01-23T23:39:11.0699177Z ##[section]Finishing: Locate gcc

Possibly, there can be two ways to fix this issue.

First way would be using the gcc shipped with azure, so the sympy's compilation utilities would use gcc shipped with OS, while the theano may run on gcc_linux-64 installed with conda.

Other way would be making sympy's compilation utilities to make use of gcc_linux-64 with environment variable $CC, as suggested by @bjodah in #15818

I see that the gcc package is indeed listed in azure-pipelines, what's the executable name for it then? (I seem to recall conda compilers having longer explicit names). We should probably inspect $CC etc. using e.g. os.environ.get('CC', ''), and make sure we support the conda names of the compilers.

@asmeurer
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Is @bjodah's suggestion about library code or just test code?

@bjodah
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bjodah commented Jan 24, 2019

My comment was regarding the _compilation submodule which is only used internally by our test suite.

@bjodah
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bjodah commented Jan 24, 2019

Okay, so @sylee957 got a good answer on gitter:

Jonathan J. Helmus:

The gcc compiler in the gcc_linux-64 package names the binary x86_64-conda_cos6-linux-gnu-gcc to prevent it from shadowing a system installed version. In an activated environment the $CC variable will be set appropriately to this compiler.

We should install gcc_linux-64 instead of "gcc" under conda.
Are we using an activated environment on azure?

  • If yes: inspecting $CC should do the trick.
  • If no: we should add x86_64-conda_cos6-linux-gnu-gcc as a binary name to look for.

those changes need to be made to:
https://github.com/sympy/sympy/blob/master/sympy/utilities/_compilation/runners.py

@asmeurer
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So this is related to this issue microsoft/azure-pipelines-tasks#8504. We should set $CC on Azure manually.

@isuruf
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isuruf commented Jan 24, 2019

If yes: inspecting $CC should do the trick.
If no: we should add x86_64-conda_cos6-linux-gnu-gcc as a binary name to look for.

I'd go with the first one.

@asmeurer
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I also think we should go with the first one, in case that wasn't clear.

@sylee957
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Even for the first one, I think that environment variable should be manually set to the binaries like x86_64-conda_cos6-linux-gnu-gcc, as I have confirmed that azure does not actually 'activate' conda for now.

So this is related to this issue microsoft/azure-pipelines-tasks#8504. We should set $CC on Azure manually.

I have a plan for fixing this in #15833 like adding environment variable manually
https://github.com/sympy/sympy/blob/4422f2d69a9b387894c93a0641b8f27e3928f68a/azure-pipelines.yml#L181-L186
and modifying some library code to lookup those variables, hopefully it may also be used to fix gfortran issues as well

@bjodah
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bjodah commented Jan 25, 2019

yes, you can use $FC for the fortran compiler

@asmeurer
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You have to set the environment variables in the same script that the tests are run in. Unlike Travis, environment variables are not shared across scripts in Azure. See how the Sage environment variables work (they work around the same conda activate problem).

@sylee957
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sylee957 commented Jan 26, 2019 •
edited

I think manually setting environment variable to the compiler binaries are causing some issues.

For example, looking up for $FC in travis (where previously it had worked fine without gfortran_linux-64 installed) now looks up for /usr/bin/gfortran, but it is now giving linking errors like below

Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/compilation.py", line 528, in compile_link_import_py_ext
    mod = import_module_from_file(os.path.join(build_dir, extname), sources)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/util.py", line 266, in import_module_from_file
    raise ImportError("Failed to import: '%s'" % filename)
ImportError: Failed to import: '/tmp/tmp5lula42s/_rms'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/runtests.py", line 1306, in _timeout
    function()
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/codegen/tests/test_fnodes.py", line 207, in test_bind_C
    ], build_dir=folder)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/compilation.py", line 584, in compile_link_import_strings
    mod = compile_link_import_py_ext(source_files, build_dir=build_dir, **kwargs)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/compilation.py", line 533, in compile_link_import_py_ext
    cplus=any_cplus_src(sources), **link_kwargs)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/compilation.py", line 254, in link_py_so
    libraries=libraries, library_dirs=library_dirs, **kwargs)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/compilation.py", line 188, in link
    runner.run()
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/sympy-1.4.dev0-py3.6.egg/sympy/utilities/_compilation/runners.py", line 222, in run
    raise CompileError(msg)
distutils.errors.CompileError: Error executing '/usr/bin/gfortran -pthread -shared -o /tmp/tmp5lula42s/_rms.cpython-36m-x86_64-linux-gnu.so ./rms.o ./_rms.o' in /tmp/tmp5lula42s (exited status 1):
 /usr/bin/ld: ./_rms.o: unrecognized relocation (0x2a) in section `.text'
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status

Though it is somewhat getting solved after installing gfortran_linux-64 manually on conda and setting environment variable to the binary.

And using x86_64-conda_cos6-linux-gnu-cc as gcc, is now giving errors in python 2.7 test, which seems like it fails while locating python libraries with the command -lpython2.7 .

2019-01-26T02:08:31.8347672Z ________________________________________________________________________________
2019-01-26T02:08:31.8347735Z  sympy/utilities/_compilation/tests/test_compilation.py:test_compile_link_import_strings 
2019-01-26T02:08:31.8347777Z Traceback (most recent call last):
2019-01-26T02:08:31.8348533Z   File "/usr/envs/optional-dependencies/lib/python2.7/site-packages/sympy-1.4.dev0-py2.7.egg/sympy/utilities/_compilation/tests/test_compilation.py", line 54, in test_compile_link_import_strings
2019-01-26T02:08:31.8348614Z     mod, info = compile_link_import_strings(_sources1, compile_kwargs=compile_kw)
2019-01-26T02:08:31.8348912Z   File "/usr/envs/optional-dependencies/lib/python2.7/site-packages/sympy-1.4.dev0-py2.7.egg/sympy/utilities/_compilation/compilation.py", line 584, in compile_link_import_strings
2019-01-26T02:08:31.8348995Z     mod = compile_link_import_py_ext(source_files, build_dir=build_dir, **kwargs)
2019-01-26T02:08:31.8349290Z   File "/usr/envs/optional-dependencies/lib/python2.7/site-packages/sympy-1.4.dev0-py2.7.egg/sympy/utilities/_compilation/compilation.py", line 533, in compile_link_import_py_ext
2019-01-26T02:08:31.8349358Z     cplus=any_cplus_src(sources), **link_kwargs)
2019-01-26T02:08:31.8349812Z   File "/usr/envs/optional-dependencies/lib/python2.7/site-packages/sympy-1.4.dev0-py2.7.egg/sympy/utilities/_compilation/compilation.py", line 254, in link_py_so
2019-01-26T02:08:31.8349872Z     libraries=libraries, library_dirs=library_dirs, **kwargs)
2019-01-26T02:08:31.8350173Z   File "/usr/envs/optional-dependencies/lib/python2.7/site-packages/sympy-1.4.dev0-py2.7.egg/sympy/utilities/_compilation/compilation.py", line 188, in link
2019-01-26T02:08:31.8350230Z     runner.run()
2019-01-26T02:08:31.8350506Z   File "/usr/envs/optional-dependencies/lib/python2.7/site-packages/sympy-1.4.dev0-py2.7.egg/sympy/utilities/_compilation/runners.py", line 222, in run
2019-01-26T02:08:31.8350571Z     raise CompileError(msg)
2019-01-26T02:08:31.8350918Z CompileError: Error executing '/usr/envs/optional-dependencies/bin/x86_64-conda_cos6-linux-gnu-cc -pthread -shared -std=c89 -o /tmp/tmpPbRtNs/_sigmoid.so ./sigmoid.o ./_sigmoid.o -lpython2.7' in /tmp/tmpPbRtNs (exited status 1):
2019-01-26T02:08:31.8351230Z  /usr/envs/optional-dependencies/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lpython2.7
2019-01-26T02:08:31.8351291Z collect2: error: ld returned 1 exit status

I think that there can be more complicated things going on the system while installing compiler package, or activating conda environment with compilers, and it may have to touch other environment variables or PATH variable.
I also don't know that it is safe way to access the compilers, or if it is free of any false-positives.

One of the newer posts in the thread
microsoft/azure-pipelines-tasks#8504 suggests that there can be a way to manually activate conda environment in the shell script,

@bjodah
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bjodah commented Jan 26, 2019

When setting $CC and $FC to conda compilers we should also set:

export CPATH=$CONDA_PREFIX/include
export LIBRARY_PATH=$CONDA_PREFIX/lib
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib

if we have activated a conda environment the $CONDA_PREFIX variable is already set, if not: we would need to specify the absolute path.

@sylee957 sylee957 mentioned this issue Jan 27, 2019
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@sylee957
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sylee957 commented Jan 27, 2019 •
edited

Anyway, I think workaround with using apt-get package installer goes fine.

I think it may get more complicated to use gcc_linux-64, gfortran_linux-64 right now. As it may need a lot of work to make sympy's compilation utilities to support those compilers properly, as well as having to deal with Microsoft's "simulated" conda activation in tests.

I think it would be a better idea to open another matrix which would exclusively test compilers installed with conda, while the default optional dependency test would remain same to test the compilers installed directly with apt-get, as before.

Right now, I have made a patch in #15857, which may solve current problems we are facing at least.

@asmeurer
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I'd appreciate if you could give your opinion on Azure Pipelines in general https://groups.google.com/forum/#!msg/sympy/jyYrYz8ys9o/OrVSL4NeAQAJ.

@asmeurer
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Azure pipelines was removed. #15998

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@asmeurer @bjodah @oscarbenjamin @isuruf @sylee957