[package - main-amd64-default][science/py-hoomd-blue] Failed for py39-hoomd-blue-4.0.0 in build
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Date: Mon, 26 Jun 2023 15:09:45 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p4785b313b958_se8efee297c/logs/py39-hoomd-blue-4.0.0.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p4785b313b958_se8efee297c
Log:
=>> Building science/py-hoomd-blue
build started at Mon Jun 26 15:04:56 UTC 2023
port directory: /usr/ports/science/py-hoomd-blue
package name: py39-hoomd-blue-4.0.0
building for: FreeBSD main-amd64-default-job-01 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400091
Job Id: 01
!!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for py39-hoomd-blue-4.0.0:
TBB=on: Enable support for Threading Building Blocks (TBB)
====> MPI (Message Passing Interface) support: you have to select exactly one of them
NOMPI=off: Build without parallel processing support
MPICH=on: Parallel processing support via MPICH 3
OPENMPI=off: Parallel processing support via Open MPI
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
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--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
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PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-hoomd-blue/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-hoomd-blue/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-hoomd-blue/work/.cache HOME=/wrkdirs/usr/ports/science/py-hoomd-blue/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-hoomd-blue/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-hoomd-blue/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-hoomd-blue-4.0.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-01] Installing pkg-1.19.1_1...
[main-amd64-default-job-01] Extracting pkg-1.19.1_1: .......... done
===> py39-hoomd-blue-4.0.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-hoomd-blue-4.0.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py39-hoomd-blue-4.0.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py39-hoomd-blue-4.0.0 for building
=> SHA256 Checksum OK for glotzerlab-hoomd-blue-v4.0.0_GH0.tar.gz.
=> SHA256 Checksum OK for glotzerlab-upp11-0c1fb8d_GH0.tar.gz.
=> SHA256 Checksum OK for glotzerlab-nano-signal-slot-34223a4_GH0.tar.gz.
=> SHA256 Checksum OK for glotzerlab-quickhull-a706b5b_GH0.tar.gz.
=> SHA256 Checksum OK for glotzerlab-random123-a2c4f04_GH0.tar.gz.
=> SHA256 Checksum OK for glotzerlab-HIP-d211f99_GH0.tar.gz.
=> SHA256 Checksum OK for glotzerlab-hipCUB-c70e193_GH0.tar.gz.
=> SHA256 Checksum OK for mphowardlab-neighbor-ba0f068_GH0.tar.gz.
=> SHA256 Checksum OK for mphowardlab-hipper-b6da049_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
<snip>
===========================================================================
=======================<phase: lib-depends >============================
===> py39-hoomd-blue-4.0.0 depends on shared library: libtbb.so - not found
===> Installing existing package /packages/All/onetbb-2021.9.0.pkg
[main-amd64-default-job-01] Installing onetbb-2021.9.0...
[main-amd64-default-job-01] `-- Installing hwloc2-2.8.0...
[main-amd64-default-job-01] | `-- Installing level-zero-1.12.0...
[main-amd64-default-job-01] | `-- Extracting level-zero-1.12.0: .......... done
[main-amd64-default-job-01] | `-- Installing libpciaccess-0.17...
[main-amd64-default-job-01] | `-- Extracting libpciaccess-0.17: ........ done
[main-amd64-default-job-01] | `-- Installing libxml2-2.10.4...
[main-amd64-default-job-01] | `-- Extracting libxml2-2.10.4: .......... done
[main-amd64-default-job-01] `-- Extracting hwloc2-2.8.0: .......... done
[main-amd64-default-job-01] Extracting onetbb-2021.9.0: .......... done
=====
Message from level-zero-1.12.0:
--
===> NOTICE:
The level-zero port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> py39-hoomd-blue-4.0.0 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so)
===> Returning to build of py39-hoomd-blue-4.0.0
===> py39-hoomd-blue-4.0.0 depends on shared library: libmpich.so - not found
===> Installing existing package /packages/All/mpich-3.4.3_2.pkg
[main-amd64-default-job-01] Installing mpich-3.4.3_2...
[main-amd64-default-job-01] `-- Installing bash-5.2.15...
[main-amd64-default-job-01] `-- Extracting bash-5.2.15: .......... done
[main-amd64-default-job-01] `-- Installing json-c-0.16...
[main-amd64-default-job-01] `-- Extracting json-c-0.16: .......... done
[main-amd64-default-job-01] `-- Installing libepoll-shim-0.0.20230411...
[main-amd64-default-job-01] `-- Extracting libepoll-shim-0.0.20230411: .......... done
[main-amd64-default-job-01] `-- Installing libfabric-1.15.1_1...
[main-amd64-default-job-01] `-- Extracting libfabric-1.15.1_1: .......... done
[main-amd64-default-job-01] `-- Installing perl5-5.32.1_3...
[main-amd64-default-job-01] `-- Extracting perl5-5.32.1_3: .......... done
[main-amd64-default-job-01] `-- Installing slurm-wlm-20.02.7_3...
[main-amd64-default-job-01] | `-- Installing hdf5-1.12.2_2,1...
[main-amd64-default-job-01] | | `-- Installing libaec-1.0.6...
[main-amd64-default-job-01] | | `-- Extracting libaec-1.0.6: .......... done
[main-amd64-default-job-01] | `-- Extracting hdf5-1.12.2_2,1: .......... done
[main-amd64-default-job-01] | `-- Installing libsysinfo-0.0.3_2...
[main-amd64-default-job-01] | `-- Extracting libsysinfo-0.0.3_2: ......... done
[main-amd64-default-job-01] | `-- Installing lua54-5.4.6...
[main-amd64-default-job-01] | | `-- Installing libedit-3.1.20221030,1...
[main-amd64-default-job-01] | | `-- Extracting libedit-3.1.20221030,1: .......... done
[main-amd64-default-job-01] | `-- Extracting lua54-5.4.6: .......... done
[main-amd64-default-job-01] | `-- Installing munge-0.5.15...
[main-amd64-default-job-01] | | `-- Installing libgcrypt-1.9.4_1...
[main-amd64-default-job-01] | | `-- Installing libgpg-error-1.47...
[main-amd64-default-job-01] | | `-- Extracting libgpg-error-1.47: .......... done
[main-amd64-default-job-01] | | `-- Extracting libgcrypt-1.9.4_1: .......... done
[main-amd64-default-job-01] | `-- Extracting munge-0.5.15: ......... done
===> Creating groups.
Creating group 'slurm' with gid '468'.
===> Creating users
Creating user 'slurm' with uid '468'.
[main-amd64-default-job-01] `-- Extracting slurm-wlm-20.02.7_3: .......... done
[main-amd64-default-job-01] Extracting mpich-3.4.3_2: .......... done
=====
Message from slurm-wlm-20.02.7_3:
--
===> NOTICE:
The slurm-wlm port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
=====
Message from mpich-3.4.3_2:
--
===> NOTICE:
The mpich port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> py39-hoomd-blue-4.0.0 depends on shared library: libmpich.so - found (/usr/local/lib/libmpich.so)
===> Returning to build of py39-hoomd-blue-4.0.0
===========================================================================
=======================<phase: configure >============================
===> Configuring for py39-hoomd-blue-4.0.0
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/py-hoomd-blue/work/.build
-- The C compiler identification is Clang 16.0.6
-- The CXX compiler identification is Clang 16.0.6
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring HOOMD 4.0.0
-- Found MPI_C: /usr/local/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/local/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found cereal: /usr/local/lib/cmake/cereal
-- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.17", minimum required is "3")
-- Found PythonLibs: /usr/local/lib/libpython3.9.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Success
-- Found pybind11: /usr/local/include (found version "2.10.4")
-- Found pybind11: /usr/local/share/cmake/pybind11 /usr/local/include (version 2.10.4)
-- Installing hoomd python module to: /usr/local/lib/python3.9/site-packages/hoomd
-- Found eigen: /usr/local/share/eigen3/cmake /usr/local/include/eigen3 (version 3.4.0)
-- Found TBB: /usr/local/lib/cmake/TBB /usr/local/lib/libtbb.so.12.9 /usr/local/include
-- Found plugin: example_plugins/pair_plugin
-- Found plugin: example_plugins/updater_plugin
-- Configuring done (2.2s)
-- Generating done (0.1s)
CMake Warning:
Manually-specified variables were not used by the project:
BOOST_PYTHON_SUFFIX
CMAKE_COLOR_MAKEFILE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
FETCHCONTENT_FULLY_DISCONNECTED
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/science/py-hoomd-blue/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for py39-hoomd-blue-4.0.0
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-4.0.0/hoomd/Messenger.cc
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oomd-blue-4.0.0/hoomd/ParticleData.cc
FAILED: hoomd/CMakeFiles/_hoomd.dir/ParticleData.cc.o
/usr/bin/c++ -DEIGEN_MPL2_ONLY -DENABLE_MPI -DENABLE_TBB -DHOOMD_LONGREAL_SIZE=64 -DHOOMD_SHORTREAL_SIZE=32 -D_REENTRANT -D_hoomd_EXPORTS -I/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.0.0 -I/wrkdirs/usr/ports/science/py-hoomd-blue/work/.build/hoomd/include -isystem /usr/local/include/python3.9 -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wconversion -Wno-sign-conversion -Wno-unknown-pragmas -Wno-deprecated-declarations -Wno-unused-result -fcolor-diagnostics -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -fPIC -fvisibility=hidden -fsized-deallocation -MD -MT hoomd/CMakeFiles/_hoomd.dir/ParticleData.cc.o -MF hoomd/CMakeFiles/_hoomd.dir/ParticleData.cc.o.d -o hoomd/CMakeFiles/_hoomd.dir/ParticleData.cc.o -c /wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.0.
0/hoomd/ParticleData.cc
/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.0.0/hoomd/ParticleData.cc:2893:32: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct comm_flag_select : std::unary_function<const unsigned int, bool>
~~~~~^~~~~~~~~~~~~~
__unary_function
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
1 error generated.
[ 6% 31/472] /usr/bin/c++ -DEIGEN_MPL2_ONLY -DENABLE_MPI -DENABLE_TBB -DHOOMD_LONGREAL_SIZE=64 -DHOOMD_SHORTREAL_SIZE=32 -D_REENTRANT -D_hoomd_EXPORTS -I/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.0.0 -I/wrkdirs/usr/ports/science/py-hoomd-blue/work/.build/hoomd/include -isystem /usr/local/include/python3.9 -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wconversion -Wno-sign-conversion -Wno-unknown-pragmas -Wno-deprecated-declarations -Wno-unused-result -fcolor-diagnostics -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -fPIC -fvisibility=hidden -fsized-deallocation -MD -MT hoomd/CMakeFiles/_hoomd.dir/ParticleGroup.cc.o -MF hoomd/CMakeFiles/_hoomd.dir/ParticleGroup.cc.o.d -o hoomd/CMakeFiles/_hoomd.dir/ParticleGroup.cc.o -c /wrkdirs/usr/ports/science/py-hoomd-blue/wor
k/hoomd-blue-4.0.0/hoomd/ParticleGroup.cc
ninja: build stopped: subcommand failed.
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-hoomd-blue