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Date:      Sat, 14 Nov 2020 01:52:37 GMT
From:      pkg-fallout@FreeBSD.org
To:        yuri@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - 114i386-quarterly][misc/py-xgboost] Failed for py37-xgboost-1.2.1 in build
Message-ID:  <202011140152.0AE1qbpb008297@beefy1.nyi.freebsd.org>

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Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri@FreeBSD.org
Last committer: yuri@FreeBSD.org
Ident:          $FreeBSD: branches/2020Q4/misc/py-xgboost/Makefile 553406 2020-10-27 01:45:30Z yuri $
Log URL:        http://beefy1.nyi.freebsd.org/data/114i386-quarterly/555065/logs/py37-xgboost-1.2.1.log
Build URL:      http://beefy1.nyi.freebsd.org/build.html?mastername=114i386-quarterly&build=555065
Log:

=>> Building misc/py-xgboost
build started at Sat Nov 14 01:49:50 UTC 2020
port directory: /usr/ports/misc/py-xgboost
package name: py37-xgboost-1.2.1
building for: FreeBSD 114i386-quarterly-job-14 11.4-RELEASE-p4 FreeBSD 11.4-RELEASE-p4 i386
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2020Q4/misc/py-xgboost/Makefile 553406 2020-10-27 01:45:30Z yuri $
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=======================<phase: check-sanity   >============================
===>  License APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   py37-xgboost-1.2.1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.15.10.txz
[114i386-quarterly-job-14] Installing pkg-1.15.10...
[114i386-quarterly-job-14] Extracting pkg-1.15.10: .......... done
===>   py37-xgboost-1.2.1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py37-xgboost-1.2.1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License APACHE20 accepted by the user
===> Fetching all distfiles required by py37-xgboost-1.2.1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License APACHE20 accepted by the user
===> Fetching all distfiles required by py37-xgboost-1.2.1 for building
=> SHA256 Checksum OK for dmlc-xgboost-v1.2.1_GH0.tar.gz.
=> SHA256 Checksum OK for dmlc-rabit-4acdd7c6f68debe1c39ae07ca75466d74d194dd1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License APACHE20 accepted by the user
===> Fetching all distfiles required by py37-xgboost-1.2.1 for building
===>  Extracting for py37-xgboost-1.2.1
=> SHA256 Checksum OK for dmlc-xgboost-v1.2.1_GH0.tar.gz.
=> SHA256 Checksum OK for dmlc-rabit-4acdd7c6f68debe1c39ae07ca75466d74d194dd1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for py37-xgboost-1.2.1
===>  Applying FreeBSD patches for py37-xgboost-1.2.1 from /usr/ports/misc/py-xgboost/files
===========================================================================
=======================<phase: build-depends  >============================
===>   py37-xgboost-1.2.1 depends on executable: cmake - not found
===>   Installing existing package /packages/All/cmake-3.18.3.txz
[114i386-quarterly-job-14] Installing cmake-3.18.3...
[114i386-quarterly-job-14] `-- Installing curl-7.72.0...
[114i386-quarterly-job-14] |   `-- Installing ca_root_nss-3.58...
[114i386-quarterly-job-14] |   `-- Extracting ca_root_nss-3.58: ........ done
[114i386-quarterly-job-14] |   `-- Installing libnghttp2-1.41.0...
[114i386-quarterly-job-14] |   `-- Extracting libnghttp2-1.41.0: .......... done
[114i386-quarterly-job-14] `-- Extracting curl-7.72.0: .......... done
[114i386-quarterly-job-14] `-- Installing expat-2.2.8...
[114i386-quarterly-job-14] `-- Extracting expat-2.2.8: .......... done
[114i386-quarterly-job-14] `-- Installing jsoncpp-1.9.4...
[114i386-quarterly-job-14] `-- Extracting jsoncpp-1.9.4: .......... done
<snip>
[ 18%] Building CXX object rabit/CMakeFiles/rabit_mock.dir/src/allreduce_robust.cc.o
[ 19%] Building CXX object rabit/CMakeFiles/rabit_mock.dir/src/engine_mock.cc.o
[ 20%] Building CXX object rabit/CMakeFiles/rabit_empty.dir/src/c_api.cc.o
[ 22%] Building CXX object rabit/CMakeFiles/rabit_mock.dir/src/c_api.cc.o
[ 23%] Linking CXX static library librabit_empty.a
[ 23%] Built target rabit_empty
[ 24%] Linking CXX static library librabit_base.a
[ 24%] Built target rabit_base
[ 25%] Linking CXX shared library librabit_mock.so
[ 25%] Built target rabit_mock
[ 27%] Linking CXX static library librabit_mock_static.a
[ 27%] Built target rabit_mock_static
[ 28%] Linking CXX static library librabit.a
[ 28%] Built target rabit
Scanning dependencies of target objxgboost
[ 29%] Building CXX object src/CMakeFiles/objxgboost.dir/c_api/c_api.cc.o
[ 31%] Building CXX object src/CMakeFiles/objxgboost.dir/c_api/c_api_error.cc.o
[ 33%] Building CXX object src/CMakeFiles/objxgboost.dir/common/charconv.cc.o
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[ 49%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gblinear.cc.o
[ 51%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gblinear_model.cc.o
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[ 58%] Building CXX object src/CMakeFiles/objxgboost.dir/learner.cc.o
[ 59%] Building CXX object src/CMakeFiles/objxgboost.dir/linear/linear_updater.cc.o
[ 61%] Building CXX object src/CMakeFiles/objxgboost.dir/linear/updater_coordinate.cc.o
[ 62%] Building CXX object src/CMakeFiles/objxgboost.dir/linear/updater_shotgun.cc.o
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[ 87%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/tree_updater.cc.o
[ 88%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_colmaker.cc.o
[ 89%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_histmaker.cc.o
[ 90%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_prune.cc.o
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[ 96%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_sync.cc.o
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Scanning dependencies of target runxgboost
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src/CMakeFiles/objxgboost.dir/linear/updater_coordinate.cc.o: In function `.omp_outlined..71':
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updater_coordinate.cc:(.text+0xaa2): undefined reference to `__atomic_load'
src/CMakeFiles/objxgboost.dir/linear/updater_coordinate.cc.o: In function `.omp_outlined..73':
updater_coordinate.cc:(.text+0xe35): undefined reference to `__atomic_load'
updater_coordinate.cc:(.text+0xe7f): undefined reference to `__atomic_load'
src/CMakeFiles/objxgboost.dir/linear/updater_shotgun.cc.o: In function `.omp_outlined..40':
updater_shotgun.cc:(.text+0xba5): undefined reference to `__atomic_load'
src/CMakeFiles/objxgboost.dir/linear/updater_shotgun.cc.o:updater_shotgun.cc:(.text+0xbf2): more undefined references to `__atomic_load' follow
c++: error: linker command failed with exit code 1 (use -v to see invocation)
--- xgboost/xgboost ---
*** [xgboost/xgboost] Error code 1

make[3]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
1 error

make[3]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
--- CMakeFiles/runxgboost.dir/all ---
*** [CMakeFiles/runxgboost.dir/all] Error code 2

make[2]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
1 error

make[2]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
*** [all] Error code 2

make[1]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
1 error

make[1]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
WARNING:XGBoost build_ext:Disabling OpenMP support.
INFO:XGBoost build_ext:Run CMake command: ['cmake', 'xgboost', '-GUnix Makefiles', '-DUSE_OPENMP=1', '-DUSE_CUDA=0', '-DUSE_NCCL=0', '-DBUILD_WITH_SHARED_NCCL=0', '-DHIDE_CXX_SYMBOLS=1', '-DUSE_HDFS=0', '-DUSE_AZURE=0', '-DUSE_S3=0', '-DPLUGIN_LZ4=0', '-DPLUGIN_DENSE_PARSER=0']
-- CMake version 3.18.3
-- xgboost VERSION: 1.2.1
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5") 
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5") 
DMLC_ROOT point to /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7/xgboost/rabit/../dmlc-core
-- Configuring done
-- Generating done
-- Build files have been written to: /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
[  6%] Built target rabit
[ 12%] Built target rabit_mock_static
[ 19%] Built target rabit_mock
[ 24%] Built target rabit_base
[ 28%] Built target rabit_empty
[ 96%] Built target objxgboost
[ 97%] Linking CXX executable xgboost/xgboost
src/CMakeFiles/objxgboost.dir/linear/updater_coordinate.cc.o: In function `.omp_outlined..71':
updater_coordinate.cc:(.text+0xa55): undefined reference to `__atomic_load'
updater_coordinate.cc:(.text+0xaa2): undefined reference to `__atomic_load'
src/CMakeFiles/objxgboost.dir/linear/updater_coordinate.cc.o: In function `.omp_outlined..73':
updater_coordinate.cc:(.text+0xe35): undefined reference to `__atomic_load'
updater_coordinate.cc:(.text+0xe7f): undefined reference to `__atomic_load'
src/CMakeFiles/objxgboost.dir/linear/updater_shotgun.cc.o: In function `.omp_outlined..40':
updater_shotgun.cc:(.text+0xba5): undefined reference to `__atomic_load'
src/CMakeFiles/objxgboost.dir/linear/updater_shotgun.cc.o:updater_shotgun.cc:(.text+0xbf2): more undefined references to `__atomic_load' follow
c++: error: linker command failed with exit code 1 (use -v to see invocation)
--- xgboost/xgboost ---
*** [xgboost/xgboost] Error code 1

make[3]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
1 error

make[3]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
--- CMakeFiles/runxgboost.dir/all ---
*** [CMakeFiles/runxgboost.dir/all] Error code 2

make[2]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
1 error

make[2]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
*** [all] Error code 2

make[1]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
1 error

make[1]: stopped in /wrkdirs/usr/ports/misc/py-xgboost/work-py37/xgboost-1.2.1/python-package/build/temp.freebsd-11.4-RELEASE-p4-i386-3.7
Traceback (most recent call last):
  File "setup.py", line 162, in build_cmake_extension
    self.build(src_dir, build_dir, gen, build_tool, use_omp=1)
  File "setup.py", line 115, in build
    cwd=build_dir)
  File "/usr/local/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', '-j24']' returned non-zero exit status 2.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "setup.py", line 318, in <module>
    url='https://github.com/dmlc/xgboost')
  File "/usr/local/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/usr/local/lib/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/local/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.7/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/usr/local/lib/python3.7/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/local/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.7/site-packages/setuptools/command/build_ext.py", line 84, in run
    _build_ext.run(self)
  File "/usr/local/lib/python3.7/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/usr/local/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
    self._build_extensions_serial()
  File "/usr/local/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
    self.build_extension(ext)
  File "setup.py", line 170, in build_extension
    self.build_cmake_extension()
  File "setup.py", line 165, in build_cmake_extension
    self.build(src_dir, build_dir, gen, build_tool, use_omp=0)
  File "setup.py", line 115, in build
    cwd=build_dir)
  File "/usr/local/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', '-j24']' returned non-zero exit status 2.
*** Error code 1

Stop.
make: stopped in /usr/ports/misc/py-xgboost



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