Build: #6 failed

Job: Python 3.8 failed

Stages & jobs

  1. Build Casatestutils

  2. Default Stage

  3. Test

  4. Publish wheels

Build log

The build generated 1,010 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log.

28-Jul-2021 10:51:13
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-1/bamboo-home/temp/CASA-CPY380-P38-6-ScriptBuildTask-8461832805123387755.sh
... in: /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 10:51:13 branch: CAS-13478
28-Jul-2021 10:51:14 Cloning into 'casa-build-utils'...
28-Jul-2021 10:51:15 Switched to a new branch 'CAS-13478'
28-Jul-2021 10:51:15 Branch CAS-13478 set up to track remote branch CAS-13478 from origin.
28-Jul-2021 10:51:15 /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:51:15 Cloning into 'casa6'...
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28-Jul-2021 10:51:29 Checking out files: 100% (10892/10892), done.
28-Jul-2021 10:51:29 Submodule 'casatools/casacore' (https://github.com/casacore/casacore.git) registered for path 'casatools/casacore'
28-Jul-2021 10:51:29 Submodule 'casatools/grpc-source' (https://github.com/grpc/grpc) registered for path 'casatools/grpc-source'
28-Jul-2021 10:51:30 Cloning into 'casatools/casacore'...
28-Jul-2021 10:51:48 Submodule path 'casatools/casacore': checked out 'dc540dcbada16af64d2c00e3e211e10e691dc260'
28-Jul-2021 10:51:49 Cloning into 'casatools/grpc-source'...
28-Jul-2021 10:52:20 Submodule path 'casatools/grpc-source': checked out 'cca868ac8f3641df4003a82b7fc54c921e14f765'
28-Jul-2021 10:52:20 Submodule 'third_party/abseil-cpp' (https://github.com/abseil/abseil-cpp) registered for path 'third_party/abseil-cpp'
28-Jul-2021 10:52:20 Submodule 'third_party/benchmark' (https://github.com/google/benchmark) registered for path 'third_party/benchmark'
28-Jul-2021 10:52:20 Submodule 'third_party/bloaty' (https://github.com/google/bloaty.git) registered for path 'third_party/bloaty'
28-Jul-2021 10:52:20 Submodule 'third_party/boringssl' (https://github.com/google/boringssl.git) registered for path 'third_party/boringssl'
28-Jul-2021 10:52:20 Submodule 'third_party/boringssl-with-bazel' (https://github.com/google/boringssl.git) registered for path 'third_party/boringssl-with-bazel'
28-Jul-2021 10:52:20 Submodule 'third_party/cares/cares' (https://github.com/c-ares/c-ares.git) registered for path 'third_party/cares/cares'
28-Jul-2021 10:52:20 Submodule 'third_party/gflags' (https://github.com/gflags/gflags.git) registered for path 'third_party/gflags'
28-Jul-2021 10:52:20 Submodule 'third_party/googletest' (https://github.com/google/googletest.git) registered for path 'third_party/googletest'
28-Jul-2021 10:52:21 Submodule 'third_party/protobuf' (https://github.com/google/protobuf.git) registered for path 'third_party/protobuf'
28-Jul-2021 10:52:21 Submodule 'third_party/zlib' (https://github.com/madler/zlib) registered for path 'third_party/zlib'
28-Jul-2021 10:52:21 Cloning into 'third_party/abseil-cpp'...
28-Jul-2021 10:52:24 Submodule path 'casatools/grpc-source/third_party/abseil-cpp': checked out 'cc4bed2d74f7c8717e31f9579214ab52a9c9c610'
28-Jul-2021 10:52:24 Cloning into 'third_party/benchmark'...
28-Jul-2021 10:52:25 Submodule path 'casatools/grpc-source/third_party/benchmark': checked out '5b7683f49e1e9223cf9927b24f6fd3d6bd82e3f8'
28-Jul-2021 10:52:25 Cloning into 'third_party/bloaty'...
28-Jul-2021 10:52:27 Submodule path 'casatools/grpc-source/third_party/bloaty': checked out '73594cde8c9a52a102c4341c244c833aa61b9c06'
28-Jul-2021 10:52:27 Submodule 'third_party/googletest' (https://github.com/google/googletest.git) registered for path 'third_party/googletest'
28-Jul-2021 10:52:27 Submodule 'third_party/libFuzzer' (https://chromium.googlesource.com/chromium/llvm-project/llvm/lib/Fuzzer) registered for path 'third_party/libFuzzer'
28-Jul-2021 10:52:27 Submodule 'third_party/re2' (https://github.com/google/re2) registered for path 'third_party/re2'
28-Jul-2021 10:52:27 Cloning into 'third_party/googletest'...
28-Jul-2021 10:52:29 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/googletest': checked out 'a2b8a8e07628e5fd60644b6dd99c1b5e7d7f1f47'
28-Jul-2021 10:52:29 Cloning into 'third_party/libFuzzer'...
28-Jul-2021 10:52:30 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/libFuzzer': checked out '1b543d6e5073b56be214394890c9193979a3d7e1'
28-Jul-2021 10:52:30 Cloning into 'third_party/re2'...
28-Jul-2021 10:52:31 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/re2': checked out 'c964d9b07816f9b52ca692e23b8b3dba33beec54'
28-Jul-2021 10:52:31 Cloning into 'third_party/boringssl'...
28-Jul-2021 10:52:53 Submodule path 'casatools/grpc-source/third_party/boringssl': checked out 'be2ee342d3781ddb954f91f8a7e660c6f59e87e5'
28-Jul-2021 10:52:53 Cloning into 'third_party/boringssl-with-bazel'...
28-Jul-2021 10:53:13 Submodule path 'casatools/grpc-source/third_party/boringssl-with-bazel': checked out '886e7d75368e3f4fab3f4d0d3584e4abfc557755'
28-Jul-2021 10:53:13 Cloning into 'third_party/cares/cares'...
28-Jul-2021 10:53:15 Submodule path 'casatools/grpc-source/third_party/cares/cares': checked out '3be1924221e1326df520f8498d704a5c4c8d0cce'
28-Jul-2021 10:53:15 Cloning into 'third_party/gflags'...
28-Jul-2021 10:53:16 Submodule path 'casatools/grpc-source/third_party/gflags': checked out '30dbc81fb5ffdc98ea9b14b1918bfe4e8779b26e'
28-Jul-2021 10:53:16 Submodule 'doc' (https://github.com/gflags/gflags.git) registered for path 'doc'
28-Jul-2021 10:53:16 Cloning into 'doc'...
28-Jul-2021 10:53:17 Submodule path 'casatools/grpc-source/third_party/gflags/doc': checked out '971dd2a4fadac9cdab174c523c22df79efd63aa5'
28-Jul-2021 10:53:17 Cloning into 'third_party/googletest'...
28-Jul-2021 10:53:19 Submodule path 'casatools/grpc-source/third_party/googletest': checked out 'ec44c6c1675c25b9827aacd08c02433cccde7780'
28-Jul-2021 10:53:19 Cloning into 'third_party/protobuf'...
28-Jul-2021 10:53:20 fatal: reference is not a tree: 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 10:53:20 Cloning into 'third_party/zlib'...
28-Jul-2021 10:53:21 Submodule path 'casatools/grpc-source/third_party/zlib': checked out 'cacf7f1d4e3d44d871b605da3b647f07d718623f'
28-Jul-2021 10:53:21 Unable to checkout '2761122b810fe8861004ae785cc3ab39f384d342' in submodule path 'casatools/grpc-source/third_party/protobuf'
28-Jul-2021 10:53:22 Failed to recurse into submodule path 'casatools/grpc-source'
28-Jul-2021 10:53:23 Switched to a new branch 'CAS-13478'
28-Jul-2021 10:53:23 M        casatools/grpc-source
28-Jul-2021 10:53:23 Branch CAS-13478 set up to track remote branch CAS-13478 from origin.
28-Jul-2021 10:53:23 /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source
28-Jul-2021 10:53:23 Cloning into 'casashell'...
28-Jul-2021 10:53:24 error: pathspec 'CAS-13478' did not match any file(s) known to git.
28-Jul-2021 10:53:24 /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source
28-Jul-2021 10:53:24 Finished task 'Clone casa6, shell and casa-build-utils' with result: Success
28-Jul-2021 10:53:24
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:24
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:24 Starting task 'Docker' of type 'com.atlassian.bamboo.plugins.bamboo-docker-plugin:task.docker.cli'
28-Jul-2021 10:53:24 Running image name (casa-docker.nrao.edu:5000/casatools-manylinux2010-py38:2)
28-Jul-2021 10:53:24
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
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28-Jul-2021 10:53:24 cde9e83d14e74302e4a563b2d3d2c141f623a0b15d2e0cee4ebce053dc9a7173
28-Jul-2021 10:53:24 Finished task 'Docker' with result: Success
28-Jul-2021 10:53:24 Starting task 'Update casatestdata' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:53:24
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-1/bamboo-home/temp/CASA-CPY380-P38-6-ScriptBuildTask-3152625762313286738.sh
... in: /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
... using extra environment variables:
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28-Jul-2021 10:53:41 Already on 'master'
28-Jul-2021 10:53:42 Already up-to-date.
28-Jul-2021 10:53:42 Finished task 'Update casatestdata' with result: Success
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:53:42 Starting task 'Build casa' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:53:42
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-1/bamboo-home/temp/CASA-CPY380-P38-6-ScriptBuildTask-3750889716115603236.sh
... in: /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
... using extra environment variables:
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bamboo_planRepository_username=
bamboo_repository_50463083_previous_revision_number=7e25456701d599a4eee9c4af8d1c69c34f0b0062
bamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.232.b09-0.el7_7.x86_64
bamboo_repository_50463083_revision_number=7e25456701d599a4eee9c4af8d1c69c34f0b0062
bamboo_repository_50463085_git_branch=CAS-13478
bamboo_planRepository_1_branchName=CAS-13478
28-Jul-2021 10:54:44 Executing: docker exec build_container /bin/bash -c "useradd -u 9285 casaci"
28-Jul-2021 10:54:44 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 10:54:44 Collecting auditwheel
28-Jul-2021 10:54:44 Downloading auditwheel-4.0.0-py3-none-any.whl (48 kB)
28-Jul-2021 10:54:44 Collecting numpy==1.18.4
28-Jul-2021 10:54:44 Downloading numpy-1.18.4-cp38-cp38-manylinux1_x86_64.whl (20.7 MB)
28-Jul-2021 10:54:44 Collecting scipy==1.4.1
28-Jul-2021 10:54:44 Downloading scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl (26.0 MB)
28-Jul-2021 10:54:44 Collecting matplotlib==3.2.1
28-Jul-2021 10:54:44 Downloading matplotlib-3.2.1-cp38-cp38-manylinux1_x86_64.whl (12.4 MB)
28-Jul-2021 10:54:44 Collecting pyelftools>=0.24
28-Jul-2021 10:54:44 Downloading pyelftools-0.27-py2.py3-none-any.whl (151 kB)
28-Jul-2021 10:54:44 Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
28-Jul-2021 10:54:44 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
28-Jul-2021 10:54:44 Collecting python-dateutil>=2.1
28-Jul-2021 10:54:44 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
28-Jul-2021 10:54:44 Collecting kiwisolver>=1.0.1
28-Jul-2021 10:54:44 Downloading kiwisolver-1.3.1-cp38-cp38-manylinux1_x86_64.whl (1.2 MB)
28-Jul-2021 10:54:44 Collecting cycler>=0.10
28-Jul-2021 10:54:44 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
28-Jul-2021 10:54:44 Collecting six>=1.5
28-Jul-2021 10:54:44 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
28-Jul-2021 10:54:44 Installing collected packages: pyelftools, auditwheel, numpy, scipy, pyparsing, six, python-dateutil, kiwisolver, cycler, matplotlib
28-Jul-2021 10:54:44 Attempting uninstall: numpy
28-Jul-2021 10:54:44 Found existing installation: numpy 1.18.0
28-Jul-2021 10:54:44 Uninstalling numpy-1.18.0:
28-Jul-2021 10:54:44 Successfully uninstalled numpy-1.18.0
28-Jul-2021 10:54:44 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 10:54:44 WARNING: You are using pip version 20.2.3; however, version 21.2.1 is available.
28-Jul-2021 10:54:44 You should consider upgrading via the '/opt/_internal/cpython-3.8.6/bin/python3.8 -m pip install --upgrade pip' command.
28-Jul-2021 10:54:44 Executing: docker exec -u casaci build_container /bin/bash -c "mkdir ~/.casa && mkdir -p ~/.config/pip"
28-Jul-2021 10:54:44 Executing: docker cp /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/casa-build-utils/devbuild/config/config.py build_container:/home/casaci/.casa/config.py
28-Jul-2021 10:54:44 Executing: docker cp /export/home/cbt-el7-1/bamboo-home/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 10:54:44 Executing: docker exec -u casaci build_container /bin/bash -c "ccache -M 50G"
28-Jul-2021 10:54:44 Set cache size limit to 50.0 Gbytes
28-Jul-2021 10:54:44 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 10:54:44 found java version 1.8
28-Jul-2021 10:54:44 configuring CASAtools... this may take a little while...
28-Jul-2021 10:54:44 configure: host os is linux
28-Jul-2021 10:54:44 checking for g++... g++
28-Jul-2021 10:54:44 checking whether the C++ compiler works... yes
28-Jul-2021 10:54:44 checking for C++ compiler default output file name... a.out
28-Jul-2021 10:54:44 checking for suffix of executables...
28-Jul-2021 10:54:44 checking whether we are cross compiling... no
28-Jul-2021 10:54:44 checking for suffix of object files... o
28-Jul-2021 10:54:44 checking whether we are using the GNU C++ compiler... yes
28-Jul-2021 10:54:44 checking whether g++ accepts -g... yes
28-Jul-2021 10:54:44 checking for OpenMP flag of C++ compiler... -fopenmp
28-Jul-2021 10:54:44 checking whether we are using the GNU C++ compiler... yes
28-Jul-2021 10:54:44 checking whether g++ accepts -g... yes
28-Jul-2021 10:54:44 checking whether g++ supports C++11 features by default... no
28-Jul-2021 10:54:44 checking whether g++ supports C++11 features with -std=c++11... yes
28-Jul-2021 10:54:44 checking for OpenMP flag of C++ compiler... -fopenmp
28-Jul-2021 10:54:44 configure: C++11 compiler /opt/rh/devtoolset-4/root/usr/bin/g++
28-Jul-2021 10:54:44 checking for std::defaultfloat... yes
28-Jul-2021 10:54:44 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 10:54:44 checking for mpiCC,... no
28-Jul-2021 10:54:44 checking for mpicxx,... no
28-Jul-2021 10:54:44 checking for mpic++... /opt/casa/03/bin//mpic++
28-Jul-2021 10:54:44 configure: After looking for an MPI wrapper, the C++ compiler is: /opt/casa/03/bin//mpic++
28-Jul-2021 10:54:44 checking for mpicc... /opt/casa/03/bin//mpicc
28-Jul-2021 10:54:44 configure: After looking for an MPI wrapper, the C compiler is: /opt/casa/03/bin//mpicc
28-Jul-2021 10:54:44 checking whether to compile using MPI... yes
28-Jul-2021 10:54:48 checking whether we are using the GNU C++ compiler... (cached) yes
28-Jul-2021 10:54:48 checking whether /opt/casa/03/bin//mpic++ accepts -g... (cached) yes
28-Jul-2021 10:54:48 checking for function MPI_Init... yes
28-Jul-2021 10:54:48 checking for mpi.h... yes
28-Jul-2021 10:54:48 checking whether C++ compiler accepts -fcx-fortran-rules... yes
28-Jul-2021 10:54:48 checking for flags to support C++11 libc++... no
28-Jul-2021 10:54:48 configure: c++ compiler is /opt/casa/03/bin//mpic++
28-Jul-2021 10:54:48 configure:  temporary directory /tmp/casatools-config-668
28-Jul-2021 10:54:48 configure: creating /tmp/casatools-config-668
28-Jul-2021 10:54:48 checking whether we are using the GNU C compiler... no
28-Jul-2021 10:54:48 checking whether /opt/casa/03/bin//mpicc accepts -g... no
28-Jul-2021 10:54:48 checking for /opt/casa/03/bin//mpicc option to accept ISO C89... unsupported
28-Jul-2021 10:54:48 configure: C compiler /opt/casa/03/bin//mpicc
28-Jul-2021 10:54:48 checking whether C compiler accepts -fcx-fortran-rules... no
28-Jul-2021 10:54:48 checking for gfortran-mp-9... no
28-Jul-2021 10:54:48 checking for gfortran-mp-8... no
28-Jul-2021 10:54:48 checking for gfortran-mp-5... no
28-Jul-2021 10:54:48 checking for gfortran-mp-4.9... no
28-Jul-2021 10:54:48 checking for gfortran-mp-4.8... no
28-Jul-2021 10:54:48 checking for gfortran... no
28-Jul-2021 10:54:48 checking whether we are using the GNU Fortran compiler... no
28-Jul-2021 10:54:48 checking whether  accepts -g... no
28-Jul-2021 10:54:48 checking for gfortran-mp-9... no
28-Jul-2021 10:54:48 checking for gfortran-mp-8... no
28-Jul-2021 10:54:48 checking for gfortran-mp-5... no
28-Jul-2021 10:54:48 checking for gfortran-mp-4.9... no
28-Jul-2021 10:54:48 checking for gfortran-mp-4.8... no
28-Jul-2021 10:54:48 checking for gfortran... gfortran
28-Jul-2021 10:54:48 checking whether we are using the GNU Fortran compiler... (cached) no
28-Jul-2021 10:54:48 checking whether gfortran accepts -g... (cached) no
28-Jul-2021 10:54:48 configure: Fortran compiler /opt/rh/devtoolset-4/root/usr/bin/gfortran
28-Jul-2021 10:54:48 checking for ccache... /usr/bin/ccache
28-Jul-2021 10:54:48 checking for pread... yes
28-Jul-2021 10:54:48 checking for pwrite... yes
28-Jul-2021 10:54:48 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 10:54:48 checking for python... /opt/python/cp38-cp38/bin/python
28-Jul-2021 10:54:48 checking for a version of Python >= '2.1.0'... yes
28-Jul-2021 10:54:48 checking for a version of Python >= '2.7.0'... yes
28-Jul-2021 10:54:48 checking for the distutils Python package... yes
28-Jul-2021 10:54:48 checking for Python include path... /opt/python/cp38-cp38/include/python3.8
28-Jul-2021 10:54:48 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 10:54:48
28-Jul-2021 10:54:48 checking for Python site-packages path... /opt/python/cp38-cp38/lib/python3.8/site-packages
28-Jul-2021 10:54:48 checking python extra libraries... -lcrypt -lpthread -ldl  -lutil -lrt -lm -lm
28-Jul-2021 10:54:48 checking python extra linking flags... -Xlinker -export-dynamic
28-Jul-2021 10:54:48 checking consistency of all components of python development environment... hmmm...
28-Jul-2021 10:54:48 configure: looking harder for shared library flags...
28-Jul-2021 10:54:48 checking for python-config... no
28-Jul-2021 10:54:48 configure: WARNING:
28-Jul-2021 10:54:48 Could not link test program to Python. Maybe the main Python library has been
28-Jul-2021 10:54:48 installed in some non-standard library path. If so, pass it to configure,
28-Jul-2021 10:54:48 via the LIBS environment variable.
28-Jul-2021 10:54:48 Example: ./configure LIBS="-L/usr/non-standard-path/python/lib"
28-Jul-2021 10:54:48 ============================================================================
28-Jul-2021 10:54:48 ERROR!
28-Jul-2021 10:54:48 You probably have to install the development version of the Python package
28-Jul-2021 10:54:48 for your distribution.  The exact name of this package varies among them.
28-Jul-2021 10:54:48 ============================================================================
28-Jul-2021 10:54:48
28-Jul-2021 10:54:48 checking for python... /opt/python/cp38-cp38/bin/python
28-Jul-2021 10:54:48 checking for numpy includedir... /opt/python/cp38-cp38/lib/python3.8/site-packages/numpy/core/include
28-Jul-2021 10:54:48 checking whether linking to numpy library works... yes
28-Jul-2021 10:54:48 checking for readline in -lreadline... yes
28-Jul-2021 10:54:48 checking for flex... flex
28-Jul-2021 10:54:48 checking lex output file root... lex.yy
28-Jul-2021 10:54:48 checking lex library... none needed
28-Jul-2021 10:54:48 checking whether yytext is a pointer... no
28-Jul-2021 10:54:48 checking for bison... bison -y
28-Jul-2021 10:54:48 checking if compiler needs -Werror to reject unknown flags... no
28-Jul-2021 10:54:48 checking for the pthreads library -lpthreads... no
28-Jul-2021 10:54:48 checking whether pthreads work without any flags... yes
28-Jul-2021 10:54:48 checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
28-Jul-2021 10:54:48 checking if more special flags are required for pthreads... no
28-Jul-2021 10:55:39 checking for PTHREAD_PRIO_INHERIT... no
28-Jul-2021 10:55:39 checking for pkg-config... /usr/bin/pkg-config
28-Jul-2021 10:55:39 checking pkg-config is at least version 0.9.0... yes
28-Jul-2021 10:55:39 checking how to run the C++ preprocessor... /opt/casa/03/bin//mpic++ -E
28-Jul-2021 10:55:39 checking for grep that handles long lines and -e... /bin/grep
28-Jul-2021 10:55:39 checking for egrep... /bin/grep -E
28-Jul-2021 10:55:39 checking for ANSI C header files... yes
28-Jul-2021 10:55:39 checking for sys/types.h... yes
28-Jul-2021 10:55:39 checking for sys/stat.h... yes
28-Jul-2021 10:55:39 checking for stdlib.h... yes
28-Jul-2021 10:55:39 checking for string.h... yes
28-Jul-2021 10:55:39 checking for memory.h... yes
28-Jul-2021 10:55:39 checking for strings.h... yes
28-Jul-2021 10:55:39 checking for inttypes.h... yes
28-Jul-2021 10:55:39 checking for stdint.h... yes
28-Jul-2021 10:55:39 checking for unistd.h... yes
28-Jul-2021 10:55:39 checking for CFITSIO... yes
28-Jul-2021 10:55:39 checking for WCSLIB... yes
28-Jul-2021 10:55:39 checking for rpfitsin_ in -lrpfits... yes
28-Jul-2021 10:55:39 checking for gsl-config... /usr/local/bin/gsl-config
28-Jul-2021 10:55:39 checking requested gsl version (2.0)... yes
28-Jul-2021 10:55:39 checking for swig3... no
28-Jul-2021 10:55:39 checking for swig... /usr/local/bin/swig
28-Jul-2021 10:55:39 checking swig version... 3.0.12
28-Jul-2021 10:55:39 checking requested swig version (3.0.0)... yes
28-Jul-2021 10:55:39 checking for libxml2 library... checking for xml2-config... /usr/bin/xml2-config
28-Jul-2021 10:55:39 yes
28-Jul-2021 10:55:39 checking for EIGEN... yes
28-Jul-2021 10:55:39 configure: removing /tmp/casatools-config-668
28-Jul-2021 10:55:39 configure: creating ./config.status
28-Jul-2021 10:55:39 config.status: creating build.properties
28-Jul-2021 10:55:39 config.status: creating setup.py
28-Jul-2021 10:55:39 conflicts: 8 shift/reduce
28-Jul-2021 10:55:39 _debug_build_: False
28-Jul-2021 10:55:39 _rel_with_deb_info_: True
28-Jul-2021 10:55:39 _strip_syms_: True
28-Jul-2021 10:55:39 Using /opt/casa/03 for third party libraries
28-Jul-2021 10:55:39 6.3.0.23 dirty
28-Jul-2021 10:55:39
28-Jul-2021 10:55:39
28-Jul-2021 10:55:39 Latest commit doesn't have a tag. Adding -dirty flag to version string.
28-Jul-2021 10:55:39 6.3.0.23
28-Jul-2021 10:55:39 6 3 0 23 100  +dirty
28-Jul-2021 10:55:39 6.3.0.23a100.dev+dirty
28-Jul-2021 10:55:39 generating version header...
28-Jul-2021 10:55:39 <inc> coordsys, image, synthesisimstore, componentlist, msmetadata, table
28-Jul-2021 10:55:39 <tgt> libmsmetadata < msmetadata
28-Jul-2021 10:55:39 <tgt> libtable < table
28-Jul-2021 10:55:39 <tgt> libcomponentlistcoordsysimage < componentlist coordsys image
28-Jul-2021 10:55:39 <tgt> libsynthesisimstore < synthesisimstore
28-Jul-2021 10:55:39 <tgt> synthesismaskhandler : synthesismaskhandler
28-Jul-2021 10:55:39 <tgt> utils : utils
28-Jul-2021 10:55:39 <tgt> miriadfiller : miriadfiller
28-Jul-2021 10:55:39 <tgt> coordsys : libcomponentlistcoordsysimage
28-Jul-2021 10:55:39 <tgt> mstransformer : mstransformer
28-Jul-2021 10:55:39 <tgt> vpmanager : vpmanager
28-Jul-2021 10:55:39 <tgt> image : libcomponentlistcoordsysimage
28-Jul-2021 10:55:39 <tgt> sidebandseparator : sidebandseparator
28-Jul-2021 10:55:39 <tgt> measures : measures
28-Jul-2021 10:55:39 <tgt> sakura : sakura
28-Jul-2021 10:55:39 <tgt> atmosphere : atmosphere
28-Jul-2021 10:55:39 <tgt> quanta : quanta
28-Jul-2021 10:55:39 <tgt> vlafiller : vlafiller
28-Jul-2021 10:55:39 <tgt> synthesisdeconvolver : synthesisdeconvolver
28-Jul-2021 10:55:39 <tgt> synthesisimstore : libsynthesisimstore
28-Jul-2021 10:55:39 <tgt> synthesisnormalizer : libsynthesisimstore synthesisnormalizer
28-Jul-2021 10:55:39 <tgt> regionmanager : regionmanager
28-Jul-2021 10:55:39 <tgt> calanalysis : calanalysis
28-Jul-2021 10:55:39 <tgt> iterbotsink : iterbotsink
28-Jul-2021 10:55:39 <tgt> singledishms : singledishms
28-Jul-2021 10:55:39 <tgt> synthesisimager : libsynthesisimstore synthesisimager
28-Jul-2021 10:55:39 <tgt> linearmosaic : linearmosaic
28-Jul-2021 10:55:39 <tgt> imager : imager
28-Jul-2021 10:55:39 <tgt> simulator : simulator
28-Jul-2021 10:55:39 <tgt> componentlist : libcomponentlistcoordsysimage
28-Jul-2021 10:55:39 <tgt> spectralline : spectralline
28-Jul-2021 10:55:39 <tgt> msmetadata : libmsmetadata
28-Jul-2021 10:55:39 <tgt> imagepol : imagepol libcomponentlistcoordsysimage
28-Jul-2021 10:55:39 <tgt> agentflagger : agentflagger
28-Jul-2021 10:55:39 <tgt> sdm : sdm
28-Jul-2021 10:55:39 <tgt> atcafiller : atcafiller
28-Jul-2021 10:55:39 <tgt> imagemetadata : imagemetadata
28-Jul-2021 10:55:39 <tgt> calibrater : calibrater
28-Jul-2021 10:55:39 <tgt> logsink : logsink
28-Jul-2021 10:55:39 <tgt> functional : functional
28-Jul-2021 10:55:39 <tgt> ms : libmsmetadata libtable ms
28-Jul-2021 10:55:39 <tgt> synthesisutils : libsynthesisimstore synthesisutils
28-Jul-2021 10:55:39 <tgt> table : libtable
28-Jul-2021 10:55:39
28-Jul-2021 10:55:39 Casacore version 3.4.0
28-Jul-2021 10:55:39 copying the grpc source directory...
28-Jul-2021 10:55:39 ]=> ['rsync', '-aq', 'grpc-source/', 'build/grpc.linux-x86_64-3.8'] (cwd: /source/casa6/casatools)
28-Jul-2021 10:55:39
28-Jul-2021 10:55:39 checking out google protobuf...
28-Jul-2021 10:55:39 ]=> ['git', 'submodule', 'update', '--init', '--recursive', 'grpc-source'] (cwd: /source/casa6/casatools)
28-Jul-2021 10:55:39 failure...
28-Jul-2021 10:55:39 fatal: remote error: upload-pack: not our ref 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 10:55:39 fatal: the remote end hung up unexpectedly
28-Jul-2021 10:55:39 Fetched in submodule path 'grpc-source/third_party/protobuf', but it did not contain 2761122b810fe8861004ae785cc3ab39f384d342. Direct fetching of that commit failed.
28-Jul-2021 10:55:39 Failed to recurse into submodule path 'grpc-source'
28-Jul-2021 10:55:39
28-Jul-2021 10:55:39 fatal: remote error: upload-pack: not our ref 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 10:55:39 fatal: the remote end hung up unexpectedly
28-Jul-2021 10:55:39 Fetched in submodule path 'grpc-source/third_party/protobuf', but it did not contain 2761122b810fe8861004ae785cc3ab39f384d342. Direct fetching of that commit failed.
28-Jul-2021 10:56:13 Failed to recurse into submodule path 'grpc-source'
28-Jul-2021 10:56:13
28-Jul-2021 10:56:13 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 10:56:13 /bin/bash: line 0: cd: /source/casa6/casatools/dist: No such file or directory
28-Jul-2021 10:56:13 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 10:56:13 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 10:56:13 cannot find CASAtasks (https://open-bitbucket.nrao.edu/projects/CASA/repos/casatasks/browse) in PYTHONPATH
28-Jul-2021 10:56:13 Executing: docker exec -u casaci build_container /bin/bash -c "mkdir /source/extralibs"
28-Jul-2021 10:56:13 Executing: docker exec -u casaci build_container /bin/bash -c "cp /usr/lib64/libgfortran.so.3 /source/extralibs"
28-Jul-2021 10:56:13 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 10:56:13 6.3.0.23 dirty
28-Jul-2021 10:56:13
28-Jul-2021 10:56:13
28-Jul-2021 10:56:13 Latest commit doesn't have a tag. Adding -dirty flag to version string.
28-Jul-2021 10:56:13 6.3.0.23
28-Jul-2021 10:56:13 6 3 0 23 100  +dirty
28-Jul-2021 10:56:13 6.3.0.23a100.dev+dirty
28-Jul-2021 10:56:13 running build
28-Jul-2021 10:56:13 running build_py
28-Jul-2021 10:56:13 creating build
28-Jul-2021 10:56:13 creating build/lib
28-Jul-2021 10:56:13 creating build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/weblog.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/restfreqtool.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/selection_syntax.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/check.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/extractcasascript.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/testhelper.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/xmlhelper.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/filltsys.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/runtest.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/__init__.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/listing.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 copying casatestutils/compare.py -> build/lib/casatestutils
28-Jul-2021 10:56:13 creating build/lib/casatestutils/datahelpers
28-Jul-2021 10:56:13 copying casatestutils/datahelpers/selectTaql.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 10:56:13 copying casatestutils/datahelpers/__init__.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 10:56:13 copying casatestutils/datahelpers/getTelescope.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 10:56:13 creating build/lib/casatestutils/imagerhelpers
28-Jul-2021 10:56:13 copying casatestutils/imagerhelpers/imagetesthelpers.py -> build/lib/casatestutils/imagerhelpers
28-Jul-2021 10:56:13 copying casatestutils/imagerhelpers/__init__.py -> build/lib/casatestutils/imagerhelpers
28-Jul-2021 10:56:13 copying casatestutils/component_to_test_map.json -> build/lib/casatestutils
28-Jul-2021 10:56:13 /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 10:56:13 warnings.warn(tmpl.format(**locals()))
28-Jul-2021 10:56:13 cp: cannot stat ‘/export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source/casashell/dist/*.whl’: No such file or directory
28-Jul-2021 10:56:13 cp: cannot stat ‘/export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatools/dist/wheelhouse/*.whl’: No such file or directory
28-Jul-2021 10:56:13 cp: cannot stat ‘/export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatasks/dist/*.whl’: No such file or directory
28-Jul-2021 10:56:13 Failing task since return code of [/export/home/cbt-el7-1/bamboo-home/temp/CASA-CPY380-P38-6-ScriptBuildTask-3750889716115603236.sh] was 1 while expected 0
28-Jul-2021 10:56:13 Finished task 'Build casa' with result: Failed
28-Jul-2021 10:56:13 Starting task 'Stop casalith-container' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:56:13
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
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28-Jul-2021 10:56:13 Error response from daemon: No such container: casalith-container
28-Jul-2021 10:56:13 Error: No such container: casalith-container
28-Jul-2021 10:56:13 Removed casalith-container
28-Jul-2021 10:56:13 Finished task 'Stop casalith-container' with result: Success
28-Jul-2021 10:56:13 Starting task 'Stop build_container' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 10:56:13
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-1/bamboo-home/temp/CASA-CPY380-P38-6-ScriptBuildTask-4313701176812854396.sh
... in: /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 10:56:14 Error response from daemon: No such container: build-container
28-Jul-2021 10:56:14 Error: No such container: build-container
28-Jul-2021 10:56:14 Removed casalith-container
28-Jul-2021 10:56:14 Finished task 'Stop build_container' with result: Success
28-Jul-2021 10:56:14 Running post build plugin 'Docker Container Cleanup'
28-Jul-2021 10:56:14
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/bin/docker rm -f build_container
... in: /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 10:56:14 build_container
28-Jul-2021 10:56:14 Running post build plugin 'NCover Results Collector'
28-Jul-2021 10:56:14 Running post build plugin 'Clover Results Collector'
28-Jul-2021 10:56:14 Running post build plugin 'npm Cache Cleanup'
28-Jul-2021 10:56:14 Running post build plugin 'Artifact Copier'
28-Jul-2021 10:56:14 Publishing an artifact: casatools python 3.8
28-Jul-2021 10:56:14 Unable to publish artifact [casatools python 3.8]: the source directory /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatools/dist/wheelhouse does not exist.
28-Jul-2021 10:56:14 The artifact is required, build will now fail.
28-Jul-2021 10:56:14 The artifact hasn't been successfully published after 624.2 μs
28-Jul-2021 10:56:14 Publishing an artifact: casatasks
28-Jul-2021 10:56:14 Unable to publish artifact [casatasks]: the source directory /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/source/casa6/casatools/dist does not exist.
28-Jul-2021 10:56:14 The artifact is required, build will now fail.
28-Jul-2021 10:56:14 The artifact hasn't been successfully published after 228.4 μs
28-Jul-2021 10:56:14 Publishing an artifact: casashell
28-Jul-2021 10:56:14 Unable to publish artifact [casashell]: the source directory /export/home/cbt-el7-1/bamboo-home/xml-data/build-dir/CASA-CPY380-P38/casashell/dist does not exist.
28-Jul-2021 10:56:14 The artifact is required, build will now fail.
28-Jul-2021 10:56:14 The artifact hasn't been successfully published after 176.2 μs
28-Jul-2021 10:56:14 Finalising the build...
28-Jul-2021 10:56:14 Stopping timer.
28-Jul-2021 10:56:14 Build CASA-CPY380-P38-6 completed.
28-Jul-2021 10:56:14 Running on server: post build plugin 'NCover Results Collector'
28-Jul-2021 10:56:14 Running on server: post build plugin 'Build Hanging Detection Configuration'
28-Jul-2021 10:56:14 Running on server: post build plugin 'Clover Delta Calculator'
28-Jul-2021 10:56:14 Running on server: post build plugin 'Maven Dependencies Postprocessor'
28-Jul-2021 10:56:14 All post build plugins have finished
28-Jul-2021 10:56:14 Generating build results summary...
28-Jul-2021 10:56:14 Saving build results to disk...
28-Jul-2021 10:56:14 Logging substituted variables...
28-Jul-2021 10:56:15 Indexing build results...
28-Jul-2021 10:56:15 Finished building CASA-CPY380-P38-6.
28-Jul-2021 11:00:14 Build CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6) started building on agent cbt-el7-10.cv.nrao.edu
28-Jul-2021 11:00:14 Remote agent on host cbt-el7-10.cv.nrao.edu
28-Jul-2021 11:00:14 Build working directory is /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:00:14 Executing build CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)
28-Jul-2021 11:00:14 Starting task 'Clean working directory task' of type 'com.atlassian.bamboo.plugins.bamboo-artifact-downloader-plugin:cleanWorkingDirectoryTask'
28-Jul-2021 11:00:14 Cleaning working directory '/export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38'
28-Jul-2021 11:00:17 Finished task 'Clean working directory task' with result: Success
28-Jul-2021 11:00:17 Running pre-build action: VCS Version Collector
28-Jul-2021 11:00:17
Substituting variable: ${bamboo.planRepository.branchName} with CAS-13478
28-Jul-2021 11:00:17 Starting task 'Clone casa6, shell and casa-build-utils' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 11:00:17
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-6-ScriptBuildTask-8206951107090260559.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 11:00:17 branch: CAS-13478
28-Jul-2021 11:00:17 Cloning into 'casa-build-utils'...
28-Jul-2021 11:00:19 Switched to a new branch 'CAS-13478'
28-Jul-2021 11:00:19 Branch CAS-13478 set up to track remote branch CAS-13478 from origin.
28-Jul-2021 11:00:19 /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:00:19 Cloning into 'casa6'...
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28-Jul-2021 11:00:38 Checking out files: 100% (10892/10892), done.
28-Jul-2021 11:00:38 Submodule 'casatools/casacore' (https://github.com/casacore/casacore.git) registered for path 'casatools/casacore'
28-Jul-2021 11:00:38 Submodule 'casatools/grpc-source' (https://github.com/grpc/grpc) registered for path 'casatools/grpc-source'
28-Jul-2021 11:00:38 Cloning into 'casatools/casacore'...
28-Jul-2021 11:01:00 Submodule path 'casatools/casacore': checked out 'dc540dcbada16af64d2c00e3e211e10e691dc260'
28-Jul-2021 11:01:00 Cloning into 'casatools/grpc-source'...
28-Jul-2021 11:01:49 Submodule path 'casatools/grpc-source': checked out 'cca868ac8f3641df4003a82b7fc54c921e14f765'
28-Jul-2021 11:01:49 Submodule 'third_party/abseil-cpp' (https://github.com/abseil/abseil-cpp) registered for path 'third_party/abseil-cpp'
28-Jul-2021 11:01:49 Submodule 'third_party/benchmark' (https://github.com/google/benchmark) registered for path 'third_party/benchmark'
28-Jul-2021 11:01:49 Submodule 'third_party/bloaty' (https://github.com/google/bloaty.git) registered for path 'third_party/bloaty'
28-Jul-2021 11:01:49 Submodule 'third_party/boringssl' (https://github.com/google/boringssl.git) registered for path 'third_party/boringssl'
28-Jul-2021 11:01:49 Submodule 'third_party/boringssl-with-bazel' (https://github.com/google/boringssl.git) registered for path 'third_party/boringssl-with-bazel'
28-Jul-2021 11:01:49 Submodule 'third_party/cares/cares' (https://github.com/c-ares/c-ares.git) registered for path 'third_party/cares/cares'
28-Jul-2021 11:01:49 Submodule 'third_party/gflags' (https://github.com/gflags/gflags.git) registered for path 'third_party/gflags'
28-Jul-2021 11:01:49 Submodule 'third_party/googletest' (https://github.com/google/googletest.git) registered for path 'third_party/googletest'
28-Jul-2021 11:01:49 Submodule 'third_party/protobuf' (https://github.com/google/protobuf.git) registered for path 'third_party/protobuf'
28-Jul-2021 11:01:49 Submodule 'third_party/zlib' (https://github.com/madler/zlib) registered for path 'third_party/zlib'
28-Jul-2021 11:01:50 Cloning into 'third_party/abseil-cpp'...
28-Jul-2021 11:01:52 Submodule path 'casatools/grpc-source/third_party/abseil-cpp': checked out 'cc4bed2d74f7c8717e31f9579214ab52a9c9c610'
28-Jul-2021 11:01:52 Cloning into 'third_party/benchmark'...
28-Jul-2021 11:01:54 Submodule path 'casatools/grpc-source/third_party/benchmark': checked out '5b7683f49e1e9223cf9927b24f6fd3d6bd82e3f8'
28-Jul-2021 11:01:54 Cloning into 'third_party/bloaty'...
28-Jul-2021 11:01:58 Submodule path 'casatools/grpc-source/third_party/bloaty': checked out '73594cde8c9a52a102c4341c244c833aa61b9c06'
28-Jul-2021 11:01:58 Submodule 'third_party/googletest' (https://github.com/google/googletest.git) registered for path 'third_party/googletest'
28-Jul-2021 11:01:58 Submodule 'third_party/libFuzzer' (https://chromium.googlesource.com/chromium/llvm-project/llvm/lib/Fuzzer) registered for path 'third_party/libFuzzer'
28-Jul-2021 11:01:58 Submodule 'third_party/re2' (https://github.com/google/re2) registered for path 'third_party/re2'
28-Jul-2021 11:01:59 Cloning into 'third_party/googletest'...
28-Jul-2021 11:02:01 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/googletest': checked out 'a2b8a8e07628e5fd60644b6dd99c1b5e7d7f1f47'
28-Jul-2021 11:02:01 Cloning into 'third_party/libFuzzer'...
28-Jul-2021 11:02:04 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/libFuzzer': checked out '1b543d6e5073b56be214394890c9193979a3d7e1'
28-Jul-2021 11:02:04 Cloning into 'third_party/re2'...
28-Jul-2021 11:02:05 Submodule path 'casatools/grpc-source/third_party/bloaty/third_party/re2': checked out 'c964d9b07816f9b52ca692e23b8b3dba33beec54'
28-Jul-2021 11:02:05 Cloning into 'third_party/boringssl'...
28-Jul-2021 11:02:35 Submodule path 'casatools/grpc-source/third_party/boringssl': checked out 'be2ee342d3781ddb954f91f8a7e660c6f59e87e5'
28-Jul-2021 11:02:35 Cloning into 'third_party/boringssl-with-bazel'...
28-Jul-2021 11:03:00 Submodule path 'casatools/grpc-source/third_party/boringssl-with-bazel': checked out '886e7d75368e3f4fab3f4d0d3584e4abfc557755'
28-Jul-2021 11:03:00 Cloning into 'third_party/cares/cares'...
28-Jul-2021 11:03:02 Submodule path 'casatools/grpc-source/third_party/cares/cares': checked out '3be1924221e1326df520f8498d704a5c4c8d0cce'
28-Jul-2021 11:03:02 Cloning into 'third_party/gflags'...
28-Jul-2021 11:03:04 Submodule path 'casatools/grpc-source/third_party/gflags': checked out '30dbc81fb5ffdc98ea9b14b1918bfe4e8779b26e'
28-Jul-2021 11:03:04 Submodule 'doc' (https://github.com/gflags/gflags.git) registered for path 'doc'
28-Jul-2021 11:03:04 Cloning into 'doc'...
28-Jul-2021 11:03:05 Submodule path 'casatools/grpc-source/third_party/gflags/doc': checked out '971dd2a4fadac9cdab174c523c22df79efd63aa5'
28-Jul-2021 11:03:05 Cloning into 'third_party/googletest'...
28-Jul-2021 11:03:09 Submodule path 'casatools/grpc-source/third_party/googletest': checked out 'ec44c6c1675c25b9827aacd08c02433cccde7780'
28-Jul-2021 11:03:11 Cloning into 'third_party/protobuf'...
28-Jul-2021 11:03:12 fatal: reference is not a tree: 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 11:03:12 Cloning into 'third_party/zlib'...
28-Jul-2021 11:03:16 Submodule path 'casatools/grpc-source/third_party/zlib': checked out 'cacf7f1d4e3d44d871b605da3b647f07d718623f'
28-Jul-2021 11:03:16 Unable to checkout '2761122b810fe8861004ae785cc3ab39f384d342' in submodule path 'casatools/grpc-source/third_party/protobuf'
28-Jul-2021 11:03:16 Failed to recurse into submodule path 'casatools/grpc-source'
28-Jul-2021 11:03:17 Switched to a new branch 'CAS-13478'
28-Jul-2021 11:03:17 M        casatools/grpc-source
28-Jul-2021 11:03:17 Branch CAS-13478 set up to track remote branch CAS-13478 from origin.
28-Jul-2021 11:03:17 /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source
28-Jul-2021 11:03:17 Cloning into 'casashell'...
28-Jul-2021 11:03:18 error: pathspec 'CAS-13478' did not match any file(s) known to git.
28-Jul-2021 11:03:18 /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38/source
28-Jul-2021 11:03:18 Finished task 'Clone casa6, shell and casa-build-utils' with result: Success
28-Jul-2021 11:03:18
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:18
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:18 Starting task 'Docker' of type 'com.atlassian.bamboo.plugins.bamboo-docker-plugin:task.docker.cli'
28-Jul-2021 11:03:18 Running image name (casa-docker.nrao.edu:5000/casatools-manylinux2010-py38:2)
28-Jul-2021 11:03:18
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... 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
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28-Jul-2021 11:03:28 8ec74c6092f4e52ce1a1f6934fe64e2dc7f22985abb2cc1b995e7dfa56e62e42
28-Jul-2021 11:03:30 Finished task 'Docker' with result: Success
28-Jul-2021 11:03:30 Starting task 'Update casatestdata' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 11:03:30
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-6-ScriptBuildTask-1730053870546111691.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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28-Jul-2021 11:03:31 Already on 'master'
28-Jul-2021 11:03:32 Already up-to-date.
28-Jul-2021 11:03:32 Finished task 'Update casatestdata' with result: Success
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32
Substituting variable: ${bamboo.working.directory} with /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
28-Jul-2021 11:03:32 Starting task 'Build casa' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 11:03:32
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-6-ScriptBuildTask-5365114857623215377.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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bamboo_build_commandline_com_atlassian_bamboo_plugins_bamboo_docker_plugin_task_docker_cli_3=/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
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bamboo_repository_50463083_revision_number=7e25456701d599a4eee9c4af8d1c69c34f0b0062
28-Jul-2021 11:04:50 Executing: docker exec build_container /bin/bash -c "useradd -u 9285 casaci"
28-Jul-2021 11:04:50 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 11:04:50 Collecting auditwheel
28-Jul-2021 11:04:50 Downloading auditwheel-4.0.0-py3-none-any.whl (48 kB)
28-Jul-2021 11:04:50 Collecting numpy==1.18.4
28-Jul-2021 11:04:50 Downloading numpy-1.18.4-cp38-cp38-manylinux1_x86_64.whl (20.7 MB)
28-Jul-2021 11:04:50 Collecting scipy==1.4.1
28-Jul-2021 11:04:50 Downloading scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl (26.0 MB)
28-Jul-2021 11:04:50 Collecting matplotlib==3.2.1
28-Jul-2021 11:04:50 Downloading matplotlib-3.2.1-cp38-cp38-manylinux1_x86_64.whl (12.4 MB)
28-Jul-2021 11:04:50 Collecting pyelftools>=0.24
28-Jul-2021 11:04:50 Downloading pyelftools-0.27-py2.py3-none-any.whl (151 kB)
28-Jul-2021 11:04:50 Collecting cycler>=0.10
28-Jul-2021 11:04:50 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
28-Jul-2021 11:04:50 Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
28-Jul-2021 11:04:50 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
28-Jul-2021 11:04:50 Collecting kiwisolver>=1.0.1
28-Jul-2021 11:04:50 Downloading kiwisolver-1.3.1-cp38-cp38-manylinux1_x86_64.whl (1.2 MB)
28-Jul-2021 11:04:50 Collecting python-dateutil>=2.1
28-Jul-2021 11:04:50 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
28-Jul-2021 11:04:50 Collecting six
28-Jul-2021 11:04:50 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
28-Jul-2021 11:04:50 Installing collected packages: pyelftools, auditwheel, numpy, scipy, six, cycler, pyparsing, kiwisolver, python-dateutil, matplotlib
28-Jul-2021 11:04:50 Attempting uninstall: numpy
28-Jul-2021 11:04:50 Found existing installation: numpy 1.18.0
28-Jul-2021 11:04:50 Uninstalling numpy-1.18.0:
28-Jul-2021 11:04:50 Successfully uninstalled numpy-1.18.0
28-Jul-2021 11:04:50 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 11:04:50 WARNING: You are using pip version 20.2.3; however, version 21.2.1 is available.
28-Jul-2021 11:04:50 You should consider upgrading via the '/opt/_internal/cpython-3.8.6/bin/python3.8 -m pip install --upgrade pip' command.
28-Jul-2021 11:04:50 Executing: docker exec -u casaci build_container /bin/bash -c "mkdir ~/.casa && mkdir -p ~/.config/pip"
28-Jul-2021 11:04:50 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 11:04:50 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 11:04:50 Executing: docker exec -u casaci build_container /bin/bash -c "ccache -M 50G"
28-Jul-2021 11:04:50 Set cache size limit to 50.0 Gbytes
28-Jul-2021 11:04:50 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 11:04:50 found java version 1.8
28-Jul-2021 11:04:50 configuring CASAtools... this may take a little while...
28-Jul-2021 11:04:50 configure: host os is linux
28-Jul-2021 11:04:50 checking for g++... g++
28-Jul-2021 11:04:50 checking whether the C++ compiler works... yes
28-Jul-2021 11:04:50 checking for C++ compiler default output file name... a.out
28-Jul-2021 11:04:50 checking for suffix of executables...
28-Jul-2021 11:04:50 checking whether we are cross compiling... no
28-Jul-2021 11:04:50 checking for suffix of object files... o
28-Jul-2021 11:04:50 checking whether we are using the GNU C++ compiler... yes
28-Jul-2021 11:04:50 checking whether g++ accepts -g... yes
28-Jul-2021 11:04:50 checking for OpenMP flag of C++ compiler... -fopenmp
28-Jul-2021 11:04:50 checking whether we are using the GNU C++ compiler... yes
28-Jul-2021 11:04:50 checking whether g++ accepts -g... yes
28-Jul-2021 11:04:50 checking whether g++ supports C++11 features by default... no
28-Jul-2021 11:04:50 checking whether g++ supports C++11 features with -std=c++11... yes
28-Jul-2021 11:04:50 checking for OpenMP flag of C++ compiler... -fopenmp
28-Jul-2021 11:04:50 configure: C++11 compiler /opt/rh/devtoolset-4/root/usr/bin/g++
28-Jul-2021 11:04:50 checking for std::defaultfloat... yes
28-Jul-2021 11:04:50 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 11:04:50 checking for mpiCC,... no
28-Jul-2021 11:04:50 checking for mpicxx,... no
28-Jul-2021 11:04:50 checking for mpic++... /opt/casa/03/bin//mpic++
28-Jul-2021 11:04:50 configure: After looking for an MPI wrapper, the C++ compiler is: /opt/casa/03/bin//mpic++
28-Jul-2021 11:04:50 checking for mpicc... /opt/casa/03/bin//mpicc
28-Jul-2021 11:04:50 configure: After looking for an MPI wrapper, the C compiler is: /opt/casa/03/bin//mpicc
28-Jul-2021 11:04:50 checking whether to compile using MPI... yes
28-Jul-2021 11:04:55 checking whether we are using the GNU C++ compiler... (cached) yes
28-Jul-2021 11:04:55 checking whether /opt/casa/03/bin//mpic++ accepts -g... (cached) yes
28-Jul-2021 11:04:55 checking for function MPI_Init... yes
28-Jul-2021 11:04:55 checking for mpi.h... yes
28-Jul-2021 11:04:55 checking whether C++ compiler accepts -fcx-fortran-rules... yes
28-Jul-2021 11:04:55 checking for flags to support C++11 libc++... no
28-Jul-2021 11:04:55 configure: c++ compiler is /opt/casa/03/bin//mpic++
28-Jul-2021 11:04:55 configure:  temporary directory /tmp/casatools-config-870
28-Jul-2021 11:04:55 configure: creating /tmp/casatools-config-870
28-Jul-2021 11:04:55 checking whether we are using the GNU C compiler... no
28-Jul-2021 11:04:55 checking whether /opt/casa/03/bin//mpicc accepts -g... no
28-Jul-2021 11:04:55 checking for /opt/casa/03/bin//mpicc option to accept ISO C89... unsupported
28-Jul-2021 11:04:55 configure: C compiler /opt/casa/03/bin//mpicc
28-Jul-2021 11:04:55 checking whether C compiler accepts -fcx-fortran-rules... no
28-Jul-2021 11:04:55 checking for gfortran-mp-9... no
28-Jul-2021 11:04:55 checking for gfortran-mp-8... no
28-Jul-2021 11:04:55 checking for gfortran-mp-5... no
28-Jul-2021 11:04:55 checking for gfortran-mp-4.9... no
28-Jul-2021 11:04:55 checking for gfortran-mp-4.8... no
28-Jul-2021 11:04:55 checking for gfortran... no
28-Jul-2021 11:04:55 checking whether we are using the GNU Fortran compiler... no
28-Jul-2021 11:04:55 checking whether  accepts -g... no
28-Jul-2021 11:04:55 checking for gfortran-mp-9... no
28-Jul-2021 11:04:55 checking for gfortran-mp-8... no
28-Jul-2021 11:04:55 checking for gfortran-mp-5... no
28-Jul-2021 11:04:55 checking for gfortran-mp-4.9... no
28-Jul-2021 11:04:55 checking for gfortran-mp-4.8... no
28-Jul-2021 11:04:55 checking for gfortran... gfortran
28-Jul-2021 11:04:55 checking whether we are using the GNU Fortran compiler... (cached) no
28-Jul-2021 11:04:55 checking whether gfortran accepts -g... (cached) no
28-Jul-2021 11:04:55 configure: Fortran compiler /opt/rh/devtoolset-4/root/usr/bin/gfortran
28-Jul-2021 11:04:55 checking for ccache... /usr/bin/ccache
28-Jul-2021 11:04:55 checking for pread... yes
28-Jul-2021 11:04:55 checking for pwrite... yes
28-Jul-2021 11:04:55 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 11:04:55 checking for python... /opt/python/cp38-cp38/bin/python
28-Jul-2021 11:04:55 checking for a version of Python >= '2.1.0'... yes
28-Jul-2021 11:04:55 checking for a version of Python >= '2.7.0'... yes
28-Jul-2021 11:04:55 checking for the distutils Python package... yes
28-Jul-2021 11:04:55 checking for Python include path... /opt/python/cp38-cp38/include/python3.8
28-Jul-2021 11:04:55 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 11:04:55
28-Jul-2021 11:04:55 checking for Python site-packages path... /opt/python/cp38-cp38/lib/python3.8/site-packages
28-Jul-2021 11:04:55 checking python extra libraries... -lcrypt -lpthread -ldl  -lutil -lrt -lm -lm
28-Jul-2021 11:04:55 checking python extra linking flags... -Xlinker -export-dynamic
28-Jul-2021 11:04:55 checking consistency of all components of python development environment... hmmm...
28-Jul-2021 11:04:55 configure: looking harder for shared library flags...
28-Jul-2021 11:04:55 checking for python-config... no
28-Jul-2021 11:04:55 configure: WARNING:
28-Jul-2021 11:04:55 Could not link test program to Python. Maybe the main Python library has been
28-Jul-2021 11:04:55 installed in some non-standard library path. If so, pass it to configure,
28-Jul-2021 11:04:55 via the LIBS environment variable.
28-Jul-2021 11:04:55 Example: ./configure LIBS="-L/usr/non-standard-path/python/lib"
28-Jul-2021 11:04:55 ============================================================================
28-Jul-2021 11:04:55 ERROR!
28-Jul-2021 11:04:55 You probably have to install the development version of the Python package
28-Jul-2021 11:04:55 for your distribution.  The exact name of this package varies among them.
28-Jul-2021 11:04:55 ============================================================================
28-Jul-2021 11:04:55
28-Jul-2021 11:04:55 checking for python... /opt/python/cp38-cp38/bin/python
28-Jul-2021 11:04:55 checking for numpy includedir... /opt/python/cp38-cp38/lib/python3.8/site-packages/numpy/core/include
28-Jul-2021 11:04:55 checking whether linking to numpy library works... yes
28-Jul-2021 11:04:55 checking for readline in -lreadline... yes
28-Jul-2021 11:04:55 checking for flex... flex
28-Jul-2021 11:04:55 checking lex output file root... lex.yy
28-Jul-2021 11:04:55 checking lex library... none needed
28-Jul-2021 11:04:55 checking whether yytext is a pointer... no
28-Jul-2021 11:04:55 checking for bison... bison -y
28-Jul-2021 11:04:55 checking if compiler needs -Werror to reject unknown flags... no
28-Jul-2021 11:04:55 checking for the pthreads library -lpthreads... no
28-Jul-2021 11:04:55 checking whether pthreads work without any flags... yes
28-Jul-2021 11:04:55 checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
28-Jul-2021 11:04:55 checking if more special flags are required for pthreads... no
28-Jul-2021 11:05:45 checking for PTHREAD_PRIO_INHERIT... no
28-Jul-2021 11:05:45 checking for pkg-config... /usr/bin/pkg-config
28-Jul-2021 11:05:45 checking pkg-config is at least version 0.9.0... yes
28-Jul-2021 11:05:45 checking how to run the C++ preprocessor... /opt/casa/03/bin//mpic++ -E
28-Jul-2021 11:05:45 checking for grep that handles long lines and -e... /bin/grep
28-Jul-2021 11:05:45 checking for egrep... /bin/grep -E
28-Jul-2021 11:05:45 checking for ANSI C header files... yes
28-Jul-2021 11:05:45 checking for sys/types.h... yes
28-Jul-2021 11:05:45 checking for sys/stat.h... yes
28-Jul-2021 11:05:45 checking for stdlib.h... yes
28-Jul-2021 11:05:45 checking for string.h... yes
28-Jul-2021 11:05:45 checking for memory.h... yes
28-Jul-2021 11:05:45 checking for strings.h... yes
28-Jul-2021 11:05:45 checking for inttypes.h... yes
28-Jul-2021 11:05:45 checking for stdint.h... yes
28-Jul-2021 11:05:45 checking for unistd.h... yes
28-Jul-2021 11:05:45 checking for CFITSIO... yes
28-Jul-2021 11:05:45 checking for WCSLIB... yes
28-Jul-2021 11:05:45 checking for rpfitsin_ in -lrpfits... yes
28-Jul-2021 11:05:45 checking for gsl-config... /usr/local/bin/gsl-config
28-Jul-2021 11:05:45 checking requested gsl version (2.0)... yes
28-Jul-2021 11:05:45 checking for swig3... no
28-Jul-2021 11:05:45 checking for swig... /usr/local/bin/swig
28-Jul-2021 11:05:45 checking swig version... 3.0.12
28-Jul-2021 11:05:45 checking requested swig version (3.0.0)... yes
28-Jul-2021 11:05:45 checking for libxml2 library... checking for xml2-config... /usr/bin/xml2-config
28-Jul-2021 11:05:45 yes
28-Jul-2021 11:05:45 checking for EIGEN... yes
28-Jul-2021 11:05:45 configure: removing /tmp/casatools-config-870
28-Jul-2021 11:05:45 configure: creating ./config.status
28-Jul-2021 11:05:45 config.status: creating build.properties
28-Jul-2021 11:05:45 config.status: creating setup.py
28-Jul-2021 11:05:45 conflicts: 8 shift/reduce
28-Jul-2021 11:05:45 _debug_build_: False
28-Jul-2021 11:05:45 _rel_with_deb_info_: True
28-Jul-2021 11:05:45 _strip_syms_: True
28-Jul-2021 11:05:45 Using /opt/casa/03 for third party libraries
28-Jul-2021 11:05:45 6.3.0.23 dirty
28-Jul-2021 11:05:45
28-Jul-2021 11:05:45
28-Jul-2021 11:05:45 Latest commit doesn't have a tag. Adding -dirty flag to version string.
28-Jul-2021 11:05:45 6.3.0.23
28-Jul-2021 11:05:45 6 3 0 23 100  +dirty
28-Jul-2021 11:05:45 6.3.0.23a100.dev+dirty
28-Jul-2021 11:05:45 generating version header...
28-Jul-2021 11:05:45 <inc> coordsys, image, synthesisimstore, componentlist, msmetadata, table
28-Jul-2021 11:05:45 <tgt> libmsmetadata < msmetadata
28-Jul-2021 11:05:45 <tgt> libtable < table
28-Jul-2021 11:05:45 <tgt> libcomponentlistcoordsysimage < componentlist coordsys image
28-Jul-2021 11:05:45 <tgt> libsynthesisimstore < synthesisimstore
28-Jul-2021 11:05:45 <tgt> synthesismaskhandler : synthesismaskhandler
28-Jul-2021 11:05:45 <tgt> utils : utils
28-Jul-2021 11:05:45 <tgt> miriadfiller : miriadfiller
28-Jul-2021 11:05:45 <tgt> coordsys : libcomponentlistcoordsysimage
28-Jul-2021 11:05:45 <tgt> mstransformer : mstransformer
28-Jul-2021 11:05:45 <tgt> vpmanager : vpmanager
28-Jul-2021 11:05:45 <tgt> image : libcomponentlistcoordsysimage
28-Jul-2021 11:05:45 <tgt> sidebandseparator : sidebandseparator
28-Jul-2021 11:05:45 <tgt> measures : measures
28-Jul-2021 11:05:45 <tgt> sakura : sakura
28-Jul-2021 11:05:45 <tgt> atmosphere : atmosphere
28-Jul-2021 11:05:45 <tgt> quanta : quanta
28-Jul-2021 11:05:45 <tgt> vlafiller : vlafiller
28-Jul-2021 11:05:45 <tgt> synthesisdeconvolver : synthesisdeconvolver
28-Jul-2021 11:05:45 <tgt> synthesisimstore : libsynthesisimstore
28-Jul-2021 11:05:45 <tgt> synthesisnormalizer : libsynthesisimstore synthesisnormalizer
28-Jul-2021 11:05:45 <tgt> regionmanager : regionmanager
28-Jul-2021 11:05:45 <tgt> calanalysis : calanalysis
28-Jul-2021 11:05:45 <tgt> iterbotsink : iterbotsink
28-Jul-2021 11:05:45 <tgt> singledishms : singledishms
28-Jul-2021 11:05:45 <tgt> synthesisimager : libsynthesisimstore synthesisimager
28-Jul-2021 11:05:45 <tgt> linearmosaic : linearmosaic
28-Jul-2021 11:05:45 <tgt> imager : imager
28-Jul-2021 11:05:45 <tgt> simulator : simulator
28-Jul-2021 11:05:45 <tgt> componentlist : libcomponentlistcoordsysimage
28-Jul-2021 11:05:45 <tgt> spectralline : spectralline
28-Jul-2021 11:05:45 <tgt> msmetadata : libmsmetadata
28-Jul-2021 11:05:45 <tgt> imagepol : imagepol libcomponentlistcoordsysimage
28-Jul-2021 11:05:45 <tgt> agentflagger : agentflagger
28-Jul-2021 11:05:45 <tgt> sdm : sdm
28-Jul-2021 11:05:45 <tgt> atcafiller : atcafiller
28-Jul-2021 11:05:45 <tgt> imagemetadata : imagemetadata
28-Jul-2021 11:05:45 <tgt> calibrater : calibrater
28-Jul-2021 11:05:45 <tgt> logsink : logsink
28-Jul-2021 11:05:45 <tgt> functional : functional
28-Jul-2021 11:05:45 <tgt> ms : libmsmetadata libtable ms
28-Jul-2021 11:05:45 <tgt> synthesisutils : libsynthesisimstore synthesisutils
28-Jul-2021 11:05:45 <tgt> table : libtable
28-Jul-2021 11:05:45
28-Jul-2021 11:05:45 Casacore version 3.4.0
28-Jul-2021 11:05:45 copying the grpc source directory...
28-Jul-2021 11:05:45 ]=> ['rsync', '-aq', 'grpc-source/', 'build/grpc.linux-x86_64-3.8'] (cwd: /source/casa6/casatools)
28-Jul-2021 11:05:45
28-Jul-2021 11:05:45 checking out google protobuf...
28-Jul-2021 11:05:45 ]=> ['git', 'submodule', 'update', '--init', '--recursive', 'grpc-source'] (cwd: /source/casa6/casatools)
28-Jul-2021 11:05:45 failure...
28-Jul-2021 11:05:45 fatal: remote error: upload-pack: not our ref 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 11:05:45 fatal: the remote end hung up unexpectedly
28-Jul-2021 11:05:45 Fetched in submodule path 'grpc-source/third_party/protobuf', but it did not contain 2761122b810fe8861004ae785cc3ab39f384d342. Direct fetching of that commit failed.
28-Jul-2021 11:05:45 Failed to recurse into submodule path 'grpc-source'
28-Jul-2021 11:05:45
28-Jul-2021 11:05:45 fatal: remote error: upload-pack: not our ref 2761122b810fe8861004ae785cc3ab39f384d342
28-Jul-2021 11:05:45 fatal: the remote end hung up unexpectedly
28-Jul-2021 11:05:45 Fetched in submodule path 'grpc-source/third_party/protobuf', but it did not contain 2761122b810fe8861004ae785cc3ab39f384d342. Direct fetching of that commit failed.
28-Jul-2021 11:06:18 Failed to recurse into submodule path 'grpc-source'
28-Jul-2021 11:06:18
28-Jul-2021 11:06:18 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 11:06:18 /bin/bash: line 0: cd: /source/casa6/casatools/dist: No such file or directory
28-Jul-2021 11:06:18 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 11:06:18 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 11:06:18 cannot find CASAtasks (https://open-bitbucket.nrao.edu/projects/CASA/repos/casatasks/browse) in PYTHONPATH
28-Jul-2021 11:06:18 Executing: docker exec -u casaci build_container /bin/bash -c "mkdir /source/extralibs"
28-Jul-2021 11:06:18 Executing: docker exec -u casaci build_container /bin/bash -c "cp /usr/lib64/libgfortran.so.3 /source/extralibs"
28-Jul-2021 11:06:18 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 11:06:18 6.3.0.23 dirty
28-Jul-2021 11:06:18
28-Jul-2021 11:06:18
28-Jul-2021 11:06:18 Latest commit doesn't have a tag. Adding -dirty flag to version string.
28-Jul-2021 11:06:18 6.3.0.23
28-Jul-2021 11:06:18 6 3 0 23 100  +dirty
28-Jul-2021 11:06:18 6.3.0.23a100.dev+dirty
28-Jul-2021 11:06:18 running build
28-Jul-2021 11:06:18 running build_py
28-Jul-2021 11:06:18 creating build
28-Jul-2021 11:06:18 creating build/lib
28-Jul-2021 11:06:18 creating build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/testhelper.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/weblog.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/xmlhelper.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/runtest.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/extractcasascript.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/compare.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/__init__.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/filltsys.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/selection_syntax.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/listing.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/check.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 copying casatestutils/restfreqtool.py -> build/lib/casatestutils
28-Jul-2021 11:06:18 creating build/lib/casatestutils/datahelpers
28-Jul-2021 11:06:18 copying casatestutils/datahelpers/getTelescope.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 11:06:18 copying casatestutils/datahelpers/selectTaql.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 11:06:18 copying casatestutils/datahelpers/__init__.py -> build/lib/casatestutils/datahelpers
28-Jul-2021 11:06:18 creating build/lib/casatestutils/imagerhelpers
28-Jul-2021 11:06:18 copying casatestutils/imagerhelpers/imagetesthelpers.py -> build/lib/casatestutils/imagerhelpers
28-Jul-2021 11:06:18 copying casatestutils/imagerhelpers/__init__.py -> build/lib/casatestutils/imagerhelpers
28-Jul-2021 11:06:18 copying casatestutils/component_to_test_map.json -> build/lib/casatestutils
28-Jul-2021 11:06:18 /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 11:06:18 warnings.warn(tmpl.format(**locals()))
28-Jul-2021 11:06:18 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 11:06:18 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 11:06:18 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 11:06:18 Failing task since return code of [/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-6-ScriptBuildTask-5365114857623215377.sh] was 1 while expected 0
28-Jul-2021 11:06:18 Finished task 'Build casa' with result: Failed
28-Jul-2021 11:06:18 Starting task 'Stop casalith-container' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 11:06:18
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
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28-Jul-2021 11:06:18 Error response from daemon: No such container: casalith-container
28-Jul-2021 11:06:18 Error: No such container: casalith-container
28-Jul-2021 11:06:18 Removed casalith-container
28-Jul-2021 11:06:19 Finished task 'Stop casalith-container' with result: Success
28-Jul-2021 11:06:19 Starting task 'Stop build_container' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
28-Jul-2021 11:06:19
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... running command line:
/export/home/cbt-el7-10/bamboohome/temp/CASA-CPY380-P38-6-ScriptBuildTask-5152171544295041743.sh
... in: /export/home/cbt-el7-10/bamboohome/xml-data/build-dir/CASA-CPY380-P38
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bamboo_repository_50463083_revision_number=7e25456701d599a4eee9c4af8d1c69c34f0b0062
28-Jul-2021 11:06:19 Error response from daemon: No such container: build-container
28-Jul-2021 11:06:19 Error: No such container: build-container
28-Jul-2021 11:06:19 Removed casalith-container
28-Jul-2021 11:06:19 Finished task 'Stop build_container' with result: Success
28-Jul-2021 11:06:19 Running post build plugin 'Docker Container Cleanup'
28-Jul-2021 11:06:19
Beginning to execute external process for build 'CASA - Casa6 Linux Py3.8 package - CAS-13478 - Python 3.8 #6 (CASA-CPY380-P38-6)'
... 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 11:06:23 build_container
28-Jul-2021 11:06:23 Running post build plugin 'NCover Results Collector'
28-Jul-2021 11:06:23 Running post build plugin 'Clover Results Collector'
28-Jul-2021 11:06:23 Running post build plugin 'npm Cache Cleanup'
28-Jul-2021 11:06:23 Running post build plugin 'Artifact Copier'
28-Jul-2021 11:06:23 Publishing an artifact: casatools python 3.8
28-Jul-2021 11:06:23 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 11:06:23 The artifact is required, build will now fail.
28-Jul-2021 11:06:23 The artifact hasn't been successfully published after 230.1 μs
28-Jul-2021 11:06:23 Publishing an artifact: casatasks
28-Jul-2021 11:06:23 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 11:06:23 The artifact is required, build will now fail.
28-Jul-2021 11:06:23 The artifact hasn't been successfully published after 150.5 μs
28-Jul-2021 11:06:23 Publishing an artifact: casashell
28-Jul-2021 11:06:23 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 11:06:23 The artifact is required, build will now fail.
28-Jul-2021 11:06:23 The artifact hasn't been successfully published after 87.65 μs
28-Jul-2021 11:06:23 Finalising the build...
28-Jul-2021 11:06:23 Stopping timer.
28-Jul-2021 11:06:23 Build CASA-CPY380-P38-6 completed.
28-Jul-2021 11:06:23 Running on server: post build plugin 'NCover Results Collector'
28-Jul-2021 11:06:23 Running on server: post build plugin 'Build Hanging Detection Configuration'
28-Jul-2021 11:06:23 Running on server: post build plugin 'Clover Delta Calculator'
28-Jul-2021 11:06:23 Running on server: post build plugin 'Maven Dependencies Postprocessor'
28-Jul-2021 11:06:23 All post build plugins have finished
28-Jul-2021 11:06:23 Generating build results summary...
28-Jul-2021 11:06:23 Saving build results to disk...
28-Jul-2021 11:06:24 Logging substituted variables...
28-Jul-2021 11:06:24 Indexing build results...
28-Jul-2021 11:06:24 Finished building CASA-CPY380-P38-6.