Build: #5 failed

Job: Python 3.8 failed

Stages & jobs

  1. Default Stage

  2. Test

  3. Publish wheels

Build log

The build generated 506 lines of output. Download or view full build log.

28-Jul-2021 10:33:05 Build CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5) started building on agent cbt-el7-10.cv.nrao.edu
28-Jul-2021 10:33:05 Remote agent on host cbt-el7-10.cv.nrao.edu
28-Jul-2021 10:33:05 Build working directory is /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:33:05 Executing build CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)
28-Jul-2021 10:33:05 Starting task 'Clean working directory task' of type 'com.atlassian.bamboo.plugins.bamboo-artifact-downloader-plugin:cleanWorkingDirectoryTask'
28-Jul-2021 10:33:05 Cleaning working directory '/export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38'
28-Jul-2021 10:33:05 Finished task 'Clean working directory task' with result: Success
28-Jul-2021 10:33:05 Running pre-build action: VCS Version Collector
28-Jul-2021 10:33:05
Substituting variable: ${bamboo.planRepository.branchName} with CAS-13478
28-Jul-2021 10:33:05 Starting task 'Clone casa6, shell and casa-build-utils' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:33:05
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-5-ScriptBuildTask-1731007607519653293.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 10:33:05 branch: CAS-13478
28-Jul-2021 10:33:05 Cloning into 'casa-build-utils'...
28-Jul-2021 10:33:05 Switched to a new branch 'CAS-13478'
28-Jul-2021 10:33:05 Branch CAS-13478 set up to track remote branch CAS-13478 from origin.
28-Jul-2021 10:33:05 /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 10:33:24 Checking out files: 100% (10892/10892), done.
28-Jul-2021 10:33:24 Submodule 'casatools/casacore' (https://github.com/casacore/casacore.git) registered for path 'casatools/casacore'
28-Jul-2021 10:33:24 Submodule 'casatools/grpc-source' (https://github.com/grpc/grpc) registered for path 'casatools/grpc-source'
28-Jul-2021 10:33:24 Cloning into 'casatools/casacore'...
28-Jul-2021 10:33:50 Submodule path 'casatools/casacore': checked out 'dc540dcbada16af64d2c00e3e211e10e691dc260'
28-Jul-2021 10:33:50 Cloning into 'casatools/grpc-source'...
28-Jul-2021 10:34:37 Submodule path 'casatools/grpc-source': checked out 'cca868ac8f3641df4003a82b7fc54c921e14f765'
28-Jul-2021 10:34:37 Submodule 'third_party/abseil-cpp' (https://github.com/abseil/abseil-cpp) registered for path 'third_party/abseil-cpp'
28-Jul-2021 10:34:37 Submodule 'third_party/benchmark' (https://github.com/google/benchmark) registered for path 'third_party/benchmark'
28-Jul-2021 10:34:37 Submodule 'third_party/bloaty' (https://github.com/google/bloaty.git) registered for path 'third_party/bloaty'
28-Jul-2021 10:34:37 Submodule 'third_party/boringssl' (https://github.com/google/boringssl.git) registered for path 'third_party/boringssl'
28-Jul-2021 10:34:37 Submodule 'third_party/boringssl-with-bazel' (https://github.com/google/boringssl.git) registered for path 'third_party/boringssl-with-bazel'
28-Jul-2021 10:34:38 Submodule 'third_party/cares/cares' (https://github.com/c-ares/c-ares.git) registered for path 'third_party/cares/cares'
28-Jul-2021 10:34:38 Submodule 'third_party/gflags' (https://github.com/gflags/gflags.git) registered for path 'third_party/gflags'
28-Jul-2021 10:34:38 Submodule 'third_party/googletest' (https://github.com/google/googletest.git) registered for path 'third_party/googletest'
28-Jul-2021 10:34:38 Submodule 'third_party/protobuf' (https://github.com/google/protobuf.git) registered for path 'third_party/protobuf'
28-Jul-2021 10:34:38 Submodule 'third_party/zlib' (https://github.com/madler/zlib) registered for path 'third_party/zlib'
28-Jul-2021 10:34:38 Cloning into 'third_party/abseil-cpp'...
28-Jul-2021 10:34:41 Submodule path 'casatools/grpc-source/third_party/abseil-cpp': checked out 'cc4bed2d74f7c8717e31f9579214ab52a9c9c610'
28-Jul-2021 10:34:41 Cloning into 'third_party/benchmark'...
28-Jul-2021 10:34:43 Submodule path 'casatools/grpc-source/third_party/benchmark': checked out '5b7683f49e1e9223cf9927b24f6fd3d6bd82e3f8'
28-Jul-2021 10:34:43 Cloning into 'third_party/bloaty'...
28-Jul-2021 10:34:45 Submodule path 'casatools/grpc-source/third_party/bloaty': checked out '73594cde8c9a52a102c4341c244c833aa61b9c06'
28-Jul-2021 10:34:45 Submodule 'third_party/googletest' (https://github.com/google/googletest.git) registered for path 'third_party/googletest'
28-Jul-2021 10:34:45 Submodule 'third_party/libFuzzer' (https://chromium.googlesource.com/chromium/llvm-project/llvm/lib/Fuzzer) registered for path 'third_party/libFuzzer'
28-Jul-2021 10:34:45 Submodule 'third_party/re2' (https://github.com/google/re2) registered for path 'third_party/re2'
28-Jul-2021 10:34:45 Cloning into 'third_party/googletest'...
28-Jul-2021 10:34:47 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/googletest': checked out 'a2b8a8e07628e5fd60644b6dd99c1b5e7d7f1f47'
28-Jul-2021 10:34:48 Cloning into 'third_party/libFuzzer'...
28-Jul-2021 10:34:49 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/libFuzzer': checked out '1b543d6e5073b56be214394890c9193979a3d7e1'
28-Jul-2021 10:34:49 Cloning into 'third_party/re2'...
28-Jul-2021 10:34:50 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/re2': checked out 'c964d9b07816f9b52ca692e23b8b3dba33beec54'
28-Jul-2021 10:34:50 Cloning into 'third_party/boringssl'...
28-Jul-2021 10:35:16 Submodule path 'casatools/grpc-source/third_party/boringssl': checked out 'be2ee342d3781ddb954f91f8a7e660c6f59e87e5'
28-Jul-2021 10:35:17 Cloning into 'third_party/boringssl-with-bazel'...
28-Jul-2021 10:35:42 Submodule path 'casatools/grpc-source/third_party/boringssl-with-bazel': checked out '886e7d75368e3f4fab3f4d0d3584e4abfc557755'
28-Jul-2021 10:35:43 Cloning into 'third_party/cares/cares'...
28-Jul-2021 10:35:45 Submodule path 'casatools/grpc-source/third_party/cares/cares': checked out '3be1924221e1326df520f8498d704a5c4c8d0cce'
28-Jul-2021 10:35:45 Cloning into 'third_party/gflags'...
28-Jul-2021 10:35:46 Submodule path 'casatools/grpc-source/third_party/gflags': checked out '30dbc81fb5ffdc98ea9b14b1918bfe4e8779b26e'
28-Jul-2021 10:35:46 Submodule 'doc' (https://github.com/gflags/gflags.git) registered for path 'doc'
28-Jul-2021 10:35:46 Cloning into 'doc'...
28-Jul-2021 10:35:49 Submodule path 'casatools/grpc-source/third_party/gflags/doc': checked out '971dd2a4fadac9cdab174c523c22df79efd63aa5'
28-Jul-2021 10:35:49 Cloning into 'third_party/googletest'...
28-Jul-2021 10:35:53 Submodule path 'casatools/grpc-source/third_party/googletest': checked out 'ec44c6c1675c25b9827aacd08c02433cccde7780'
28-Jul-2021 10:35:53 Cloning into 'third_party/protobuf'...
28-Jul-2021 10:35:55 fatal: reference is not a tree: 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 10:35:55 Cloning into 'third_party/zlib'...
28-Jul-2021 10:35:56 Submodule path 'casatools/grpc-source/third_party/zlib': checked out 'cacf7f1d4e3d44d871b605da3b647f07d718623f'
28-Jul-2021 10:35:56 Unable to checkout '2761122b810fe8861004ae785cc3ab39f384d342' in submodule path 'casatools/grpc-source/third_party/protobuf'
28-Jul-2021 10:35:56 Failed to recurse into submodule path 'casatools/grpc-source'
28-Jul-2021 10:35:58 M        casatools/grpc-source
28-Jul-2021 10:35:58 Branch CAS-13478 set up to track remote branch CAS-13478 from origin.
28-Jul-2021 10:35:58 Switched to a new branch 'CAS-13478'
28-Jul-2021 10:35:58 /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source
28-Jul-2021 10:35:58 Cloning into 'casashell'...
28-Jul-2021 10:35:59 error: pathspec 'CAS-13478' did not match any file(s) known to git.
28-Jul-2021 10:35:59 /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source
28-Jul-2021 10:35:59 Finished task 'Clone casa6, shell and casa-build-utils' with result: Success
28-Jul-2021 10:35:59
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:35:59
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:35:59 Starting task 'Docker' of type 'com.atlassian.bamboo.plugins.bamboo-docker-plugin:task.docker.cli'
28-Jul-2021 10:35:59 Running image name (casa-docker.nrao.edu:5000/casatools-manylinux2010-py38:2)
28-Jul-2021 10:35:59
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/bin/docker run --volume /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/../ccache:/ccache --volume /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source:/source --detach --name build_container -v /opt/casa/data/master:/opt/casa/data:ro -v /opt/casa/data/casa-data-req:/opt/casa/data-req:ro casa-docker.nrao.edu:5000/casatools-manylinux2010-py38:2 tail -f /dev/null
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
... using extra environment variables:
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bamboo_repository_name=casa-build-utils
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28-Jul-2021 10:36:04 d7213fde29d5aedb330ef6e883ff3a30a64d458bbb26aeb9402bc10770fe3419
28-Jul-2021 10:36:06 Finished task 'Docker' with result: Success
28-Jul-2021 10:36:06 Starting task 'Update casatestdata' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:36:06
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-5-ScriptBuildTask-916762872985882422.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
... using extra environment variables:
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bamboo_repository_50463083_revision_number=7e25456701d599a4eee9c4af8d1c69c34f0b0062
28-Jul-2021 10:36:13 Already on 'master'
28-Jul-2021 10:36:21 Already up-to-date.
28-Jul-2021 10:36:21 Finished task 'Update casatestdata' with result: Success
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:36:21 Starting task 'Build casa' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:36:21
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-5-ScriptBuildTask-3043803027523429039.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
... using extra environment variables:
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bamboo_capability_system_jdk_JDK_1_8_0_252=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64
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28-Jul-2021 10:37:38 Executing: docker exec build_container /bin/bash -c "useradd -u 9285 casaci"
28-Jul-2021 10:37:38 Executing: docker exec build_container /bin/bash -c "pip install auditwheel numpy==1.18.4 scipy==1.4.1 matplotlib==3.2.1 "
28-Jul-2021 10:37:38 Collecting auditwheel
28-Jul-2021 10:37:38 Downloading auditwheel-4.0.0-py3-none-any.whl (48 kB)
28-Jul-2021 10:37:38 Collecting numpy==1.18.4
28-Jul-2021 10:37:38 Downloading numpy-1.18.4-cp38-cp38-manylinux1_x86_64.whl (20.7 MB)
28-Jul-2021 10:37:38 Collecting scipy==1.4.1
28-Jul-2021 10:37:38 Downloading scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl (26.0 MB)
28-Jul-2021 10:37:38 Collecting matplotlib==3.2.1
28-Jul-2021 10:37:38 Downloading matplotlib-3.2.1-cp38-cp38-manylinux1_x86_64.whl (12.4 MB)
28-Jul-2021 10:37:38 Collecting pyelftools>=0.24
28-Jul-2021 10:37:38 Downloading pyelftools-0.27-py2.py3-none-any.whl (151 kB)
28-Jul-2021 10:37:38 Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
28-Jul-2021 10:37:38 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
28-Jul-2021 10:37:38 Collecting cycler>=0.10
28-Jul-2021 10:37:38 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
28-Jul-2021 10:37:38 Collecting kiwisolver>=1.0.1
28-Jul-2021 10:37:38 Downloading kiwisolver-1.3.1-cp38-cp38-manylinux1_x86_64.whl (1.2 MB)
28-Jul-2021 10:37:38 Collecting python-dateutil>=2.1
28-Jul-2021 10:37:38 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
28-Jul-2021 10:37:38 Collecting six
28-Jul-2021 10:37:38 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
28-Jul-2021 10:37:38 Installing collected packages: pyelftools, auditwheel, numpy, scipy, pyparsing, six, cycler, kiwisolver, python-dateutil, matplotlib
28-Jul-2021 10:37:38 Attempting uninstall: numpy
28-Jul-2021 10:37:38 Found existing installation: numpy 1.18.0
28-Jul-2021 10:37:38 Uninstalling numpy-1.18.0:
28-Jul-2021 10:37:38 Successfully uninstalled numpy-1.18.0
28-Jul-2021 10:37:38 Successfully installed auditwheel-4.0.0 cycler-0.10.0 kiwisolver-1.3.1 matplotlib-3.2.1 numpy-1.18.4 pyelftools-0.27 pyparsing-2.4.7 python-dateutil-2.8.2 scipy-1.4.1 six-1.16.0
28-Jul-2021 10:37:38 WARNING: You are using pip version 20.2.3; however, version 21.2.1 is available.
28-Jul-2021 10:37:38 You should consider upgrading via the '/opt/_internal/cpython-3.8.6/bin/python3.8 -m pip install --upgrade pip' command.
28-Jul-2021 10:37:38 Executing: docker exec -u casaci build_container /bin/bash -c "mkdir ~/.casa && mkdir -p ~/.config/pip"
28-Jul-2021 10:37:38 Executing: docker cp /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/casa-build-utils/devbuild/config/config.py build_container:/home/casaci/.casa/config.py
28-Jul-2021 10:37:38 Executing: docker cp /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/casa-build-utils/devbuild/config/pip.conf build_container:/home/casaci/.config/pip/pip.conf
28-Jul-2021 10:37:38 Executing: docker exec -u casaci build_container /bin/bash -c "ccache -M 50G"
28-Jul-2021 10:37:38 Set cache size limit to 50.0 Gbytes
28-Jul-2021 10:37:38 Executing: docker exec -u casaci build_container /bin/bash -c "export CCACHE_DIR=/ccache && cd /source/casa6/casatools/ && scripts/gcw-pick && autoconf && ./configure && python setup.py  --relwithdebinfo --stripsyms bdist_wheel"
28-Jul-2021 10:37:38 found java version 1.8
28-Jul-2021 10:37:38 configuring CASAtools... this may take a little while...
28-Jul-2021 10:37:38 configure: host os is linux
28-Jul-2021 10:37:38 checking for g++... g++
28-Jul-2021 10:37:38 checking whether the C++ compiler works... yes
28-Jul-2021 10:37:38 checking for C++ compiler default output file name... a.out
28-Jul-2021 10:37:38 checking for suffix of executables...
28-Jul-2021 10:37:38 checking whether we are cross compiling... no
28-Jul-2021 10:37:38 checking for suffix of object files... o
28-Jul-2021 10:37:38 checking whether we are using the GNU C++ compiler... yes
28-Jul-2021 10:37:38 checking whether g++ accepts -g... yes
28-Jul-2021 10:37:38 checking for OpenMP flag of C++ compiler... -fopenmp
28-Jul-2021 10:37:38 checking whether we are using the GNU C++ compiler... yes
28-Jul-2021 10:37:38 checking whether g++ accepts -g... yes
28-Jul-2021 10:37:38 checking whether g++ supports C++11 features by default... no
28-Jul-2021 10:37:38 checking whether g++ supports C++11 features with -std=c++11... yes
28-Jul-2021 10:37:38 checking for OpenMP flag of C++ compiler... -fopenmp
28-Jul-2021 10:37:38 configure: C++11 compiler /opt/rh/devtoolset-4/root/usr/bin/g++
28-Jul-2021 10:37:38 checking for std::defaultfloat... yes
28-Jul-2021 10:37:38 configure: Looking for MPI compiler wrappers in extended path: /opt/python/cp38-cp38/bin:/opt/rh/devtoolset-4/root/usr/bin:/opt/rh/devtoolset-8/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/casa/03/bin/
28-Jul-2021 10:37:38 checking for mpiCC,... no
28-Jul-2021 10:37:38 checking for mpicxx,... no
28-Jul-2021 10:37:38 checking for mpic++... /opt/casa/03/bin//mpic++
28-Jul-2021 10:37:38 configure: After looking for an MPI wrapper, the C++ compiler is: /opt/casa/03/bin//mpic++
28-Jul-2021 10:37:38 checking for mpicc... /opt/casa/03/bin//mpicc
28-Jul-2021 10:37:38 configure: After looking for an MPI wrapper, the C compiler is: /opt/casa/03/bin//mpicc
28-Jul-2021 10:37:38 checking whether to compile using MPI... yes
28-Jul-2021 10:37:44 checking whether we are using the GNU C++ compiler... (cached) yes
28-Jul-2021 10:37:44 checking whether /opt/casa/03/bin//mpic++ accepts -g... (cached) yes
28-Jul-2021 10:37:44 checking for function MPI_Init... yes
28-Jul-2021 10:37:44 checking for mpi.h... yes
28-Jul-2021 10:37:44 checking whether C++ compiler accepts -fcx-fortran-rules... yes
28-Jul-2021 10:37:44 checking for flags to support C++11 libc++... no
28-Jul-2021 10:37:44 configure: c++ compiler is /opt/casa/03/bin//mpic++
28-Jul-2021 10:37:44 configure:  temporary directory /tmp/casatools-config-869
28-Jul-2021 10:37:44 configure: creating /tmp/casatools-config-869
28-Jul-2021 10:37:44 checking whether we are using the GNU C compiler... no
28-Jul-2021 10:37:44 checking whether /opt/casa/03/bin//mpicc accepts -g... no
28-Jul-2021 10:37:44 checking for /opt/casa/03/bin//mpicc option to accept ISO C89... unsupported
28-Jul-2021 10:37:44 configure: C compiler /opt/casa/03/bin//mpicc
28-Jul-2021 10:37:44 checking whether C compiler accepts -fcx-fortran-rules... no
28-Jul-2021 10:37:44 checking for gfortran-mp-9... no
28-Jul-2021 10:37:44 checking for gfortran-mp-8... no
28-Jul-2021 10:37:44 checking for gfortran-mp-5... no
28-Jul-2021 10:37:44 checking for gfortran-mp-4.9... no
28-Jul-2021 10:37:44 checking for gfortran-mp-4.8... no
28-Jul-2021 10:37:44 checking for gfortran... no
28-Jul-2021 10:37:44 checking whether we are using the GNU Fortran compiler... no
28-Jul-2021 10:37:44 checking whether  accepts -g... no
28-Jul-2021 10:37:44 checking for gfortran-mp-9... no
28-Jul-2021 10:37:44 checking for gfortran-mp-8... no
28-Jul-2021 10:37:44 checking for gfortran-mp-5... no
28-Jul-2021 10:37:44 checking for gfortran-mp-4.9... no
28-Jul-2021 10:37:44 checking for gfortran-mp-4.8... no
28-Jul-2021 10:37:44 checking for gfortran... gfortran
28-Jul-2021 10:37:44 checking whether we are using the GNU Fortran compiler... (cached) no
28-Jul-2021 10:37:44 checking whether gfortran accepts -g... (cached) no
28-Jul-2021 10:37:44 configure: Fortran compiler /opt/rh/devtoolset-4/root/usr/bin/gfortran
28-Jul-2021 10:37:44 checking for ccache... /usr/bin/ccache
28-Jul-2021 10:37:44 checking for pread... yes
28-Jul-2021 10:37:44 checking for pwrite... yes
28-Jul-2021 10:37:44 checking for boostlib >= 1.41... configure: We could not detect the boost libraries (version 1.41 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
28-Jul-2021 10:37:44 checking for python... /opt/python/cp38-cp38/bin/python
28-Jul-2021 10:37:44 checking for a version of Python >= '2.1.0'... yes
28-Jul-2021 10:37:44 checking for a version of Python >= '2.7.0'... yes
28-Jul-2021 10:37:44 checking for the distutils Python package... yes
28-Jul-2021 10:37:44 checking for Python include path... /opt/python/cp38-cp38/include/python3.8
28-Jul-2021 10:37:44 checking for Python library path... ls: cannot access /opt/_internal/cpython-3.8.6/lib/libpython3.8.*: No such file or directory
28-Jul-2021 10:37:44
28-Jul-2021 10:37:44 checking for Python site-packages path... /opt/python/cp38-cp38/lib/python3.8/site-packages
28-Jul-2021 10:37:44 checking python extra libraries... -lcrypt -lpthread -ldl  -lutil -lrt -lm -lm
28-Jul-2021 10:37:44 checking python extra linking flags... -Xlinker -export-dynamic
28-Jul-2021 10:37:44 checking consistency of all components of python development environment... hmmm...
28-Jul-2021 10:37:44 configure: looking harder for shared library flags...
28-Jul-2021 10:37:44 checking for python-config... no
28-Jul-2021 10:37:44 configure: WARNING:
28-Jul-2021 10:37:44 Could not link test program to Python. Maybe the main Python library has been
28-Jul-2021 10:37:44 installed in some non-standard library path. If so, pass it to configure,
28-Jul-2021 10:37:44 via the LIBS environment variable.
28-Jul-2021 10:37:44 Example: ./configure LIBS="-L/usr/non-standard-path/python/lib"
28-Jul-2021 10:37:44 ============================================================================
28-Jul-2021 10:37:44 ERROR!
28-Jul-2021 10:37:44 You probably have to install the development version of the Python package
28-Jul-2021 10:37:44 for your distribution.  The exact name of this package varies among them.
28-Jul-2021 10:37:44 ============================================================================
28-Jul-2021 10:37:44
28-Jul-2021 10:37:44 checking for python... /opt/python/cp38-cp38/bin/python
28-Jul-2021 10:37:44 checking for numpy includedir... /opt/python/cp38-cp38/lib/python3.8/site-packages/numpy/core/include
28-Jul-2021 10:37:44 checking whether linking to numpy library works... yes
28-Jul-2021 10:37:44 checking for readline in -lreadline... yes
28-Jul-2021 10:37:44 checking for flex... flex
28-Jul-2021 10:37:44 checking lex output file root... lex.yy
28-Jul-2021 10:37:44 checking lex library... none needed
28-Jul-2021 10:37:44 checking whether yytext is a pointer... no
28-Jul-2021 10:37:44 checking for bison... bison -y
28-Jul-2021 10:37:44 checking if compiler needs -Werror to reject unknown flags... no
28-Jul-2021 10:37:44 checking for the pthreads library -lpthreads... no
28-Jul-2021 10:37:44 checking whether pthreads work without any flags... yes
28-Jul-2021 10:37:44 checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
28-Jul-2021 10:37:44 checking if more special flags are required for pthreads... no
28-Jul-2021 10:38:31 checking for PTHREAD_PRIO_INHERIT... no
28-Jul-2021 10:38:31 checking for pkg-config... /usr/bin/pkg-config
28-Jul-2021 10:38:31 checking pkg-config is at least version 0.9.0... yes
28-Jul-2021 10:38:31 checking how to run the C++ preprocessor... /opt/casa/03/bin//mpic++ -E
28-Jul-2021 10:38:31 checking for grep that handles long lines and -e... /bin/grep
28-Jul-2021 10:38:31 checking for egrep... /bin/grep -E
28-Jul-2021 10:38:31 checking for ANSI C header files... yes
28-Jul-2021 10:38:31 checking for sys/types.h... yes
28-Jul-2021 10:38:31 checking for sys/stat.h... yes
28-Jul-2021 10:38:31 checking for stdlib.h... yes
28-Jul-2021 10:38:31 checking for string.h... yes
28-Jul-2021 10:38:31 checking for memory.h... yes
28-Jul-2021 10:38:31 checking for strings.h... yes
28-Jul-2021 10:38:31 checking for inttypes.h... yes
28-Jul-2021 10:38:31 checking for stdint.h... yes
28-Jul-2021 10:38:31 checking for unistd.h... yes
28-Jul-2021 10:38:31 checking for CFITSIO... yes
28-Jul-2021 10:38:31 checking for WCSLIB... yes
28-Jul-2021 10:38:31 checking for rpfitsin_ in -lrpfits... yes
28-Jul-2021 10:38:31 checking for gsl-config... /usr/local/bin/gsl-config
28-Jul-2021 10:38:31 checking requested gsl version (2.0)... yes
28-Jul-2021 10:38:31 checking for swig3... no
28-Jul-2021 10:38:31 checking for swig... /usr/local/bin/swig
28-Jul-2021 10:38:31 checking swig version... 3.0.12
28-Jul-2021 10:38:31 checking requested swig version (3.0.0)... yes
28-Jul-2021 10:38:31 checking for libxml2 library... checking for xml2-config... /usr/bin/xml2-config
28-Jul-2021 10:38:31 yes
28-Jul-2021 10:38:31 checking for EIGEN... yes
28-Jul-2021 10:38:31 configure: removing /tmp/casatools-config-869
28-Jul-2021 10:38:31 configure: creating ./config.status
28-Jul-2021 10:38:31 config.status: creating build.properties
28-Jul-2021 10:38:31 config.status: creating setup.py
28-Jul-2021 10:38:31 conflicts: 8 shift/reduce
28-Jul-2021 10:38:31 _debug_build_: False
28-Jul-2021 10:38:31 _rel_with_deb_info_: True
28-Jul-2021 10:38:31 _strip_syms_: True
28-Jul-2021 10:38:31 Using /opt/casa/03 for third party libraries
28-Jul-2021 10:38:31 6.3.0.23 dirty
28-Jul-2021 10:38:31
28-Jul-2021 10:38:31
28-Jul-2021 10:38:31 Latest commit doesn't have a tag. Adding -dirty flag to version string.
28-Jul-2021 10:38:31 6.3.0.23
28-Jul-2021 10:38:31 6 3 0 23 100  +dirty
28-Jul-2021 10:38:31 6.3.0.23a100.dev+dirty
28-Jul-2021 10:38:31 generating version header...
28-Jul-2021 10:38:31 <inc> coordsys, image, synthesisimstore, componentlist, msmetadata, table
28-Jul-2021 10:38:31 <tgt> libmsmetadata < msmetadata
28-Jul-2021 10:38:31 <tgt> libtable < table
28-Jul-2021 10:38:31 <tgt> libcomponentlistcoordsysimage < componentlist coordsys image
28-Jul-2021 10:38:31 <tgt> libsynthesisimstore < synthesisimstore
28-Jul-2021 10:38:31 <tgt> synthesismaskhandler : synthesismaskhandler
28-Jul-2021 10:38:31 <tgt> utils : utils
28-Jul-2021 10:38:31 <tgt> miriadfiller : miriadfiller
28-Jul-2021 10:38:31 <tgt> coordsys : libcomponentlistcoordsysimage
28-Jul-2021 10:38:31 <tgt> mstransformer : mstransformer
28-Jul-2021 10:38:31 <tgt> vpmanager : vpmanager
28-Jul-2021 10:38:31 <tgt> image : libcomponentlistcoordsysimage
28-Jul-2021 10:38:31 <tgt> sidebandseparator : sidebandseparator
28-Jul-2021 10:38:31 <tgt> measures : measures
28-Jul-2021 10:38:31 <tgt> sakura : sakura
28-Jul-2021 10:38:31 <tgt> atmosphere : atmosphere
28-Jul-2021 10:38:31 <tgt> quanta : quanta
28-Jul-2021 10:38:31 <tgt> vlafiller : vlafiller
28-Jul-2021 10:38:31 <tgt> synthesisdeconvolver : synthesisdeconvolver
28-Jul-2021 10:38:31 <tgt> synthesisimstore : libsynthesisimstore
28-Jul-2021 10:38:31 <tgt> synthesisnormalizer : libsynthesisimstore synthesisnormalizer
28-Jul-2021 10:38:31 <tgt> regionmanager : regionmanager
28-Jul-2021 10:38:31 <tgt> calanalysis : calanalysis
28-Jul-2021 10:38:31 <tgt> iterbotsink : iterbotsink
28-Jul-2021 10:38:31 <tgt> singledishms : singledishms
28-Jul-2021 10:38:31 <tgt> synthesisimager : libsynthesisimstore synthesisimager
28-Jul-2021 10:38:31 <tgt> linearmosaic : linearmosaic
28-Jul-2021 10:38:31 <tgt> imager : imager
28-Jul-2021 10:38:31 <tgt> simulator : simulator
28-Jul-2021 10:38:31 <tgt> componentlist : libcomponentlistcoordsysimage
28-Jul-2021 10:38:31 <tgt> spectralline : spectralline
28-Jul-2021 10:38:31 <tgt> msmetadata : libmsmetadata
28-Jul-2021 10:38:31 <tgt> imagepol : imagepol libcomponentlistcoordsysimage
28-Jul-2021 10:38:31 <tgt> agentflagger : agentflagger
28-Jul-2021 10:38:31 <tgt> sdm : sdm
28-Jul-2021 10:38:31 <tgt> atcafiller : atcafiller
28-Jul-2021 10:38:31 <tgt> imagemetadata : imagemetadata
28-Jul-2021 10:38:31 <tgt> calibrater : calibrater
28-Jul-2021 10:38:31 <tgt> logsink : logsink
28-Jul-2021 10:38:31 <tgt> functional : functional
28-Jul-2021 10:38:31 <tgt> ms : libmsmetadata libtable ms
28-Jul-2021 10:38:31 <tgt> synthesisutils : libsynthesisimstore synthesisutils
28-Jul-2021 10:38:31 <tgt> table : libtable
28-Jul-2021 10:38:31
28-Jul-2021 10:38:31 Casacore version 3.4.0
28-Jul-2021 10:38:31 copying the grpc source directory...
28-Jul-2021 10:38:31 ]=> ['rsync', '-aq', 'grpc-source/', 'build/grpc.linux-x86_64-3.8'] (cwd: /source/casa6/casatools)
28-Jul-2021 10:38:31
28-Jul-2021 10:38:31 checking out google protobuf...
28-Jul-2021 10:38:31 ]=> ['git', 'submodule', 'update', '--init', '--recursive', 'grpc-source'] (cwd: /source/casa6/casatools)
28-Jul-2021 10:38:31 failure...
28-Jul-2021 10:38:31 fatal: remote error: upload-pack: not our ref 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 10:38:31 fatal: the remote end hung up unexpectedly
28-Jul-2021 10:38:31 Fetched in submodule path 'grpc-source/third_party/protobuf', but it did not contain 2761122b810fe8861004ae785cc3ab39f384d342. Direct fetching of that commit failed.
28-Jul-2021 10:38:31 Failed to recurse into submodule path 'grpc-source'
28-Jul-2021 10:38:31
28-Jul-2021 10:38:31 fatal: remote error: upload-pack: not our ref 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 10:38:31 fatal: the remote end hung up unexpectedly
28-Jul-2021 10:38:31 Fetched in submodule path 'grpc-source/third_party/protobuf', but it did not contain 2761122b810fe8861004ae785cc3ab39f384d342. Direct fetching of that commit failed.
28-Jul-2021 10:39:02 Failed to recurse into submodule path 'grpc-source'
28-Jul-2021 10:39:02
28-Jul-2021 10:39:02 Executing: docker exec -u casaci build_container /bin/bash -c 'cd /source/casa6/casatools/dist && auditwheel repair `ls -t *.whl | head -1`'
28-Jul-2021 10:39:02 /bin/bash: line 0: cd: /source/casa6/casatools/dist: No such file or directory
28-Jul-2021 10:39:02 Executing: docker exec -u casaci build_container /bin/bash -c "export PYTHONPATH=/source/casa6/casatools/build/lib.linux-x86_64-3.8/ && cd /source/casa6/casatasks/ && python setup.py bdist_wheel"
28-Jul-2021 10:39:02 Executing: docker exec -u casaci build_container /bin/bash -c "export PYTHONPATH=/source/casa6/casatools/build/lib.linux-x86_64-3.8/:/source/casa6/casatasks/build/lib.linux-x86_64-3.8/ && cd /source/casashell/ && python setup.py bdist_wheel"
28-Jul-2021 10:39:02 cannot find CASAtasks (https://open-bitbucket.nrao.edu/projects/CASA/repos/casatasks/browse) in PYTHONPATH
28-Jul-2021 10:39:02 Executing: docker exec -u casaci build_container /bin/bash -c "mkdir /source/extralibs"
28-Jul-2021 10:39:02 Executing: docker exec -u casaci build_container /bin/bash -c "cp /usr/lib64/libgfortran.so.3 /source/extralibs"
28-Jul-2021 10:39:02 Executing: docker exec -u casaci build_container /bin/bash -c "export PYTHONPATH=/source/casa6/casatools/build/lib.linux-x86_64-3.8:/source/casa6/casatasks/build/lib.linux-x86_64-3.8/ && cd /source/casa6/casatestutils && python setup.py build"
28-Jul-2021 10:39:02 6.3.0.23 dirty
28-Jul-2021 10:39:02
28-Jul-2021 10:39:02
28-Jul-2021 10:39:02 Latest commit doesn't have a tag. Adding -dirty flag to version string.
28-Jul-2021 10:39:02 6.3.0.23
28-Jul-2021 10:39:02 6 3 0 23 100  +dirty
28-Jul-2021 10:39:02 6.3.0.23a100.dev+dirty
28-Jul-2021 10:39:02 running build
28-Jul-2021 10:39:02 running build_py
28-Jul-2021 10:39:02 creating build
28-Jul-2021 10:39:02 creating build/lib
28-Jul-2021 10:39:02 creating build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/testhelper.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/weblog.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/xmlhelper.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/runtest.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/extractcasascript.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/compare.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/__init__.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/filltsys.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/selection_syntax.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/listing.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/check.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 copying casatestutils/restfreqtool.py -> build/lib/casatestutils
28-Jul-2021 10:39:02 creating build/lib/casatestutils/datahelpers
28-Jul-2021 10:39:02 copying casatestutils/datahelpers/getTelescope.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 10:39:02 copying casatestutils/datahelpers/selectTaql.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 10:39:02 copying casatestutils/datahelpers/__init__.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 10:39:02 creating build/lib/casatestutils/imagerhelpers
28-Jul-2021 10:39:02 copying casatestutils/imagerhelpers/imagetesthelpers.py -> build/lib/casatestutils/imagerhelpers
28-Jul-2021 10:39:02 copying casatestutils/imagerhelpers/__init__.py -> build/lib/casatestutils/imagerhelpers
28-Jul-2021 10:39:02 copying casatestutils/component_to_test_map.json -> build/lib/casatestutils
28-Jul-2021 10:39:02 /opt/python/cp38-cp38/lib/python3.8/site-packages/setuptools/dist.py:452: UserWarning: Normalizing '6.3.0.23a100.dev+dirty' to '6.3.0.23a100.dev0+dirty'
28-Jul-2021 10:39:02 warnings.warn(tmpl.format(**locals()))
28-Jul-2021 10:39:02 cp: cannot stat ‘/export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source/casashell/dist/*.whl’: No such file or directory
28-Jul-2021 10:39:02 cp: cannot stat ‘/export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatools/dist/wheelhouse/*.whl’: No such file or directory
28-Jul-2021 10:39:02 cp: cannot stat ‘/export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatasks/dist/*.whl’: No such file or directory
28-Jul-2021 10:39:02 Failing task since return code of [/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-5-ScriptBuildTask-3043803027523429039.sh] was 1 while expected 0
28-Jul-2021 10:39:02 Finished task 'Build casa' with result: Failed
28-Jul-2021 10:39:02 Starting task 'Stop casalith-container' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:39:02
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-5-ScriptBuildTask-7028385187156836133.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 10:39:02 Error response from daemon: No such container: casalith-container
28-Jul-2021 10:39:02 Error: No such container: casalith-container
28-Jul-2021 10:39:02 Removed casalith-container
28-Jul-2021 10:39:02 Finished task 'Stop casalith-container' with result: Success
28-Jul-2021 10:39:02 Starting task 'Stop build_container' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:39:02
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-5-ScriptBuildTask-4271451366820738349.sh
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28-Jul-2021 10:39:02 Error response from daemon: No such container: build-container
28-Jul-2021 10:39:02 Error: No such container: build-container
28-Jul-2021 10:39:02 Removed casalith-container
28-Jul-2021 10:39:02 Finished task 'Stop build_container' with result: Success
28-Jul-2021 10:39:02 Running post build plugin 'Docker Container Cleanup'
28-Jul-2021 10:39:02
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #5 (CASA-CPY380-P38-5)'
... running command line:
/bin/docker rm -f build_container
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:39:04 build_container
28-Jul-2021 10:39:04 Running post build plugin 'NCover Results Collector'
28-Jul-2021 10:39:04 Running post build plugin 'Clover Results Collector'
28-Jul-2021 10:39:04 Running post build plugin 'npm Cache Cleanup'
28-Jul-2021 10:39:04 Running post build plugin 'Artifact Copier'
28-Jul-2021 10:39:04 Publishing an artifact: casatools python 3.8
28-Jul-2021 10:39:04 Unable to publish artifact [casatools python 3.8]: the source directory /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatools/dist/wheelhouse does not exist.
28-Jul-2021 10:39:04 The artifact is required, build will now fail.
28-Jul-2021 10:39:04 The artifact hasn't been successfully published after 1.792 ms
28-Jul-2021 10:39:04 Publishing an artifact: casatasks
28-Jul-2021 10:39:04 Unable to publish artifact [casatasks]: the source directory /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatools/dist does not exist.
28-Jul-2021 10:39:04 The artifact is required, build will now fail.
28-Jul-2021 10:39:04 The artifact hasn't been successfully published after 212.0 μs
28-Jul-2021 10:39:04 Publishing an artifact: casashell
28-Jul-2021 10:39:04 Unable to publish artifact [casashell]: the source directory /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/casashell/dist does not exist.
28-Jul-2021 10:39:04 The artifact is required, build will now fail.
28-Jul-2021 10:39:04 The artifact hasn't been successfully published after 196.0 μs
28-Jul-2021 10:39:04 Finalising the build...
28-Jul-2021 10:39:04 Stopping timer.
28-Jul-2021 10:39:04 Build CASA-CPY380-P38-5 completed.
28-Jul-2021 10:39:04 Running on server: post build plugin 'NCover Results Collector'
28-Jul-2021 10:39:04 Running on server: post build plugin 'Build Hanging Detection Configuration'
28-Jul-2021 10:39:04 Running on server: post build plugin 'Clover Delta Calculator'
28-Jul-2021 10:39:04 Running on server: post build plugin 'Maven Dependencies Postprocessor'
28-Jul-2021 10:39:04 All post build plugins have finished
28-Jul-2021 10:39:04 Generating build results summary...
28-Jul-2021 10:39:04 Saving build results to disk...
28-Jul-2021 10:39:05 Logging substituted variables...
28-Jul-2021 10:39:05 Indexing build results...
28-Jul-2021 10:39:05 Finished building CASA-CPY380-P38-5.