[package - 141i386-default][science/py-pyprecice] Failed for py311-pyprecice-2.5.0.4 in stage
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Date: Tue, 12 Nov 2024 05:39:10 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/beefy21/data/141i386-default/ea7acb655568/logs/py311-pyprecice-2.5.0.4.log
Build URL: https://pkg-status.freebsd.org/beefy21/build.html?mastername=141i386-default&build=ea7acb655568
Log:
=>> Building science/py-pyprecice
build started at Tue Nov 12 05:38:55 UTC 2024
port directory: /usr/ports/science/py-pyprecice
package name: py311-pyprecice-2.5.0.4
building for: FreeBSD 141i386-default-job-42 14.1-RELEASE-p6 FreeBSD 14.1-RELEASE-p6 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 920 May 21 01:02 /usr/ports/science/py-pyprecice/Makefile
Ports top last git commit: ea7acb6555
Ports top unclean checkout: no
Port dir last git commit: a40e262549
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1401000
Job Id: 42
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--MAINTAINER--
yuri@FreeBSD.org
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--CONFIGURE_ARGS--
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PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pyprecice/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pyprecice/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pyprecice/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-pyprecice/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pyprecice/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-pyprecice/work-py311/.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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--End PLIST_SUB--
--SUB_LIST--
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--End SUB_LIST--
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PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
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# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
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GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
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cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyprecice-2.5.0.4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[141i386-default-job-42] Installing pkg-1.21.3...
[141i386-default-job-42] Extracting pkg-1.21.3: .......... done
===> py311-pyprecice-2.5.0.4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-pyprecice-2.5.0.4
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by py311-pyprecice-2.5.0.4 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by py311-pyprecice-2.5.0.4 for building
=> SHA256 Checksum OK for precice-python-bindings-v2.5.0.4_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by py311-pyprecice-2.5.0.4 for building
===> Extracting for py311-pyprecice-2.5.0.4
=> SHA256 Checksum OK for precice-python-bindings-v2.5.0.4_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for py311-pyprecice-2.5.0.4
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyprecice-2.5.0.4 depends on package: py311-numpy>=1.16,1<1.27,1 - not found
===> Installing existing package /packages/All/py311-numpy-1.26.4_2,1.pkg
[141i386-default-job-42] Installing py311-numpy-1.26.4_2,1...
[141i386-default-job-42] `-- Installing gcc13-13.3.0...
[141i386-default-job-42] | `-- Installing binutils-2.43.1,1...
[141i386-default-job-42] | | `-- Installing indexinfo-0.3.1...
[141i386-default-job-42] | | `-- Extracting indexinfo-0.3.1: .... done
[141i386-default-job-42] | | `-- Installing zstd-1.5.6...
[141i386-default-job-42] | | `-- Installing liblz4-1.10.0,1...
[141i386-default-job-42] | | `-- Extracting liblz4-1.10.0,1: .......... done
[141i386-default-job-42] | | `-- Extracting zstd-1.5.6: .......... done
[141i386-default-job-42] | `-- Extracting binutils-2.43.1,1: .......... done
[141i386-default-job-42] | `-- Installing gmp-6.3.0...
[141i386-default-job-42] | `-- Extracting gmp-6.3.0: .......... done
[141i386-default-job-42] | `-- Installing mpc-1.3.1_1...
[141i386-default-job-42] | | `-- Installing mpfr-4.2.1,1...
[141i386-default-job-42] | | `-- Extracting mpfr-4.2.1,1: .......... done
[141i386-default-job-42] | `-- Extracting mpc-1.3.1_1: ......... done
[141i386-default-job-42] `-- Extracting gcc13-13.3.0: .......... done
[141i386-default-job-42] `-- Installing openblas-0.3.27,2...
[141i386-default-job-42] `-- Extracting openblas-0.3.27,2: .......... done
<snip>
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py311-gdbm databases/py-gdbm@py311
py311-sqlite3 databases/py-sqlite3@py311
py311-tkinter x11-toolkits/py-tkinter@py311
===> py311-pyprecice-2.5.0.4 depends on package: py311-numpy>=1.16,1<1.27,1 - found
===> Returning to build of py311-pyprecice-2.5.0.4
===> py311-pyprecice-2.5.0.4 depends on package: py311-mpi4py>0 - not found
===> Installing existing package /packages/All/py311-mpi4py-4.0.1.pkg
[141i386-default-job-42] Installing py311-mpi4py-4.0.1...
[141i386-default-job-42] `-- Installing openmpi4-4.1.6_1...
[141i386-default-job-42] | `-- Installing hwloc2-2.11.2...
[141i386-default-job-42] | | `-- Installing level-zero-1.17.45...
[141i386-default-job-42] | | `-- Installing libfmt-10.2.1...
[141i386-default-job-42] | | `-- Extracting libfmt-10.2.1: .......... done
[141i386-default-job-42] | | `-- Installing spdlog-1.14.1...
[141i386-default-job-42] | | `-- Extracting spdlog-1.14.1: .......... done
[141i386-default-job-42] | | `-- Extracting level-zero-1.17.45: .......... done
[141i386-default-job-42] | | `-- Installing libpciaccess-0.18.1...
[141i386-default-job-42] | | `-- Extracting libpciaccess-0.18.1: ........ done
[141i386-default-job-42] | | `-- Installing libxml2-2.11.9...
[141i386-default-job-42] | | `-- Extracting libxml2-2.11.9: .......... done
[141i386-default-job-42] | `-- Extracting hwloc2-2.11.2: .......... done
[141i386-default-job-42] | `-- Installing libevent-2.1.12...
[141i386-default-job-42] | `-- Extracting libevent-2.1.12: .......... done
[141i386-default-job-42] | `-- Installing libltdl-2.4.7...
[141i386-default-job-42] | `-- Extracting libltdl-2.4.7: .......... done
[141i386-default-job-42] | `-- Installing munge-0.5.16...
[141i386-default-job-42] | | `-- Installing libgcrypt-1.11.0...
[141i386-default-job-42] | | `-- Installing libgpg-error-1.50...
[141i386-default-job-42] | | `-- Extracting libgpg-error-1.50: .......... done
[141i386-default-job-42] | | `-- Extracting libgcrypt-1.11.0: .......... done
[141i386-default-job-42] | `-- Extracting munge-0.5.16: ......... done
[141i386-default-job-42] `-- Extracting openmpi4-4.1.6_1: .......... done
[141i386-default-job-42] Extracting py311-mpi4py-4.0.1: .......... done
=====
Message from openmpi4-4.1.6_1:
--
===> NOTICE:
The openmpi4 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
===> py311-pyprecice-2.5.0.4 depends on package: py311-mpi4py>0 - found
===> Returning to build of py311-pyprecice-2.5.0.4
===> py311-pyprecice-2.5.0.4 depends on package: py311-pkgconfig>0 - not found
===> Installing existing package /packages/All/py311-pkgconfig-1.5.5_2,1.pkg
[141i386-default-job-42] Installing py311-pkgconfig-1.5.5_2,1...
[141i386-default-job-42] `-- Installing pkgconf-2.3.0,1...
[141i386-default-job-42] `-- Extracting pkgconf-2.3.0,1: .......... done
[141i386-default-job-42] Extracting py311-pkgconfig-1.5.5_2,1: .......... done
===> py311-pyprecice-2.5.0.4 depends on package: py311-pkgconfig>0 - found
===> Returning to build of py311-pyprecice-2.5.0.4
===> py311-pyprecice-2.5.0.4 depends on package: pkgconf>=1.3.0_1 - found
===> py311-pyprecice-2.5.0.4 depends on executable: cython-3.11 - not found
===> Installing existing package /packages/All/py311-cython-0.29.37_1.pkg
[141i386-default-job-42] Installing py311-cython-0.29.37_1...
[141i386-default-job-42] Extracting py311-cython-0.29.37_1: .......... done
===> py311-pyprecice-2.5.0.4 depends on executable: cython-3.11 - found
===> Returning to build of py311-pyprecice-2.5.0.4
===> py311-pyprecice-2.5.0.4 depends on package: py311-setuptools>=63.1.0 - found
===> py311-pyprecice-2.5.0.4 depends on file: /usr/local/bin/python3.11 - found
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyprecice-2.5.0.4 depends on shared library: libprecice.so - not found
===> Installing existing package /packages/All/precice-3.1.2.pkg
[141i386-default-job-42] Installing precice-3.1.2...
[141i386-default-job-42] `-- Installing boost-libs-1.85.0...
[141i386-default-job-42] | `-- Installing icu-74.2_1,1...
[141i386-default-job-42] | `-- Extracting icu-74.2_1,1: .......... done
[141i386-default-job-42] `-- Extracting boost-libs-1.85.0: .......... done
[141i386-default-job-42] `-- Installing mpich-4.2.3...
[141i386-default-job-42] | `-- Installing json-c-0.18...
[141i386-default-job-42] | `-- Extracting json-c-0.18: .......... done
[141i386-default-job-42] | `-- Installing libepoll-shim-0.0.20240608...
[141i386-default-job-42] | `-- Extracting libepoll-shim-0.0.20240608: .......... done
[141i386-default-job-42] | `-- Installing libfabric-1.15.1_2...
[141i386-default-job-42] | `-- Extracting libfabric-1.15.1_2: .......... done
[141i386-default-job-42] | `-- Installing perl5-5.36.3_2...
[141i386-default-job-42] | `-- Extracting perl5-5.36.3_2: .......... done
[141i386-default-job-42] `-- Extracting mpich-4.2.3: .......... done
[141i386-default-job-42] Extracting precice-3.1.2: .......... done
=====
Message from boost-libs-1.85.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> py311-pyprecice-2.5.0.4 depends on shared library: libprecice.so - found (/usr/local/lib/libprecice.so)
===> Returning to build of py311-pyprecice-2.5.0.4
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for py311-pyprecice-2.5.0.4
setup.py:11: UserWarning: It looks like you are not using pip for installation. Installing the package via 'pip3 install --user .' is recommended. You can still use 'python3 setup.py install --user', if you want and if the bindings work correctly, you do not have to worry. However, if you face problems during installation or running pyprecice, this means that you have to make sure that all dependencies are installed correctly and repeat the installation of pyprecice. Refer to pyproject.toml for a list of dependencies.
warnings.warn(
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
running config
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for py311-pyprecice-2.5.0.4
setup.py:11: UserWarning: It looks like you are not using pip for installation. Installing the package via 'pip3 install --user .' is recommended. You can still use 'python3 setup.py install --user', if you want and if the bindings work correctly, you do not have to worry. However, if you face problems during installation or running pyprecice, this means that you have to make sure that all dependencies are installed correctly and repeat the installation of pyprecice. Refer to pyproject.toml for a list of dependencies.
warnings.warn(
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
running build
running build_py
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
creating build
creating build/lib
creating build/lib/precice
copying precice/__init__.py -> build/lib/precice
copying precice/_version.py -> build/lib/precice
UPDATING build/lib/precice/_version.py
set build/lib/precice/_version.py to '2.5.0.4'
===========================================================================
=======================<phase: run-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pyprecice-2.5.0.4 depends on package: py311-numpy>=1.16,1<1.27,1 - found
===> py311-pyprecice-2.5.0.4 depends on package: py311-mpi4py>0 - found
===> py311-pyprecice-2.5.0.4 depends on package: py311-setuptools>=63.1.0 - found
===> py311-pyprecice-2.5.0.4 depends on file: /usr/local/bin/python3.11 - found
===========================================================================
=======================<phase: stage >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Staging for py311-pyprecice-2.5.0.4
===> Generating temporary packing list
setup.py:11: UserWarning: It looks like you are not using pip for installation. Installing the package via 'pip3 install --user .' is recommended. You can still use 'python3 setup.py install --user', if you want and if the bindings work correctly, you do not have to worry. However, if you face problems during installation or running pyprecice, this means that you have to make sure that all dependencies are installed correctly and repeat the installation of pyprecice. Refer to pyproject.toml for a list of dependencies.
warnings.warn(
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
running install
/usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
warning: cyprecice/cyprecice.pyx:1231:61: local variable '_value' referenced before assignment
warning: cyprecice/cyprecice.pyx:1233:81: local variable '_value' referenced before assignment
warning: cyprecice/cyprecice.pyx:1235:15: local variable '_value' referenced before assignment
Compiling /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice/cyprecice.pyx because it changed.
[1/1] Cythonizing /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice/cyprecice.pyx
running build
running build_py
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
creating build/lib.freebsd-14.1-RELEASE-p6-i386-cpython-311
creating build/lib.freebsd-14.1-RELEASE-p6-i386-cpython-311/precice
copying precice/__init__.py -> build/lib.freebsd-14.1-RELEASE-p6-i386-cpython-311/precice
copying precice/_version.py -> build/lib.freebsd-14.1-RELEASE-p6-i386-cpython-311/precice
UPDATING build/lib.freebsd-14.1-RELEASE-p6-i386-cpython-311/precice/_version.py
set build/lib.freebsd-14.1-RELEASE-p6-i386-cpython-311/precice/_version.py to '2.5.0.4'
running build_ext
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
Failed to load config from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/pyproject.toml: 'tool'
Try to load it from setup.cfg
building 'cyprecice' extension
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports/science
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports/science/py-pyprecice
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports/science/py-pyprecice/work-py311
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4
creating build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice
cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -I/usr/local/include/python3.11 -c /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice/cyprecice.cpp -o build/temp.freebsd-14.1-RELEASE-p6-i386-cpython-311/wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice/cyprecice.o -std=c++11 -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include
In file included from /wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice/cyprecice.cpp:789:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
/wrkdirs/usr/ports/science/py-pyprecice/work-py311/python-bindings-2.5.0.4/cyprecice/cyprecice.cpp:816:10: fatal error: 'precice/SolverInterface.hpp' file not found
816 | #include "precice/SolverInterface.hpp"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-pyprecice