[package - main-armv7-default][science/py-pyscf] Failed for py39-pyscf-2.1.0_2 in build
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Date: Thu, 08 Dec 2022 07:30:50 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/ampere2/data/main-armv7-default/p634ed29b7bad_sd1f3abc892/logs/py39-pyscf-2.1.0_2.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p634ed29b7bad_sd1f3abc892
Log:
=>> Building science/py-pyscf
build started at Thu Dec 8 07:30:23 UTC 2022
port directory: /usr/ports/science/py-pyscf
package name: py39-pyscf-2.1.0_2
building for: FreeBSD main-armv7-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400073 arm
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-pyscf-2.1.0_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-armv7-default-job-10] Installing pkg-1.18.4...
[main-armv7-default-job-10] Extracting pkg-1.18.4: .......... done
===> py39-pyscf-2.1.0_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-pyscf-2.1.0_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-pyscf-2.1.0_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-pyscf-2.1.0_2 for building
=> SHA256 Checksum OK for pyscf-pyscf-v2.1.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-pyscf-2.1.0_2 for building
===> Extracting for py39-pyscf-2.1.0_2
=> SHA256 Checksum OK for pyscf-pyscf-v2.1.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-pyscf-2.1.0_2
===> Applying FreeBSD patches for py39-pyscf-2.1.0_2 from /usr/ports/science/py-pyscf/files
===========================================================================
=======================<phase: build-depends >============================
===> py39-pyscf-2.1.0_2 depends on package: py39-numpy>=1.16,1<1.24,1 - not found
===> Installing existing package /packages/All/py39-numpy-1.23.5,1.pkg
[main-armv7-default-job-10] Installing py39-numpy-1.23.5,1...
[main-armv7-default-job-10] `-- Installing gcc11-11.3.0_5...
[main-armv7-default-job-10] | `-- Installing binutils-2.39,1...
[main-armv7-default-job-10] | | `-- Installing gettext-runtime-0.21.1...
[main-armv7-default-job-10] | | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-10] | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-10] | | `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv7-default-job-10] | `-- Extracting binutils-2.39,1: .......... done
[main-armv7-default-job-10] | `-- Installing gmp-6.2.1...
[main-armv7-default-job-10] | `-- Extracting gmp-6.2.1: .......... done
[main-armv7-default-job-10] | `-- Installing mpc-1.2.1...
[main-armv7-default-job-10] | | `-- Installing mpfr-4.1.1...
[main-armv7-default-job-10] | | `-- Extracting mpfr-4.1.1: .......... done
<snip>
[main-armv7-default-job-10] `-- Installing jsoncpp-1.9.5...
[main-armv7-default-job-10] `-- Extracting jsoncpp-1.9.5: .......... done
[main-armv7-default-job-10] `-- Installing libuv-1.44.2...
[main-armv7-default-job-10] `-- Extracting libuv-1.44.2: .......... done
[main-armv7-default-job-10] `-- Installing rhash-1.4.3...
[main-armv7-default-job-10] `-- Extracting rhash-1.4.3: .......... done
[main-armv7-default-job-10] Extracting cmake-core-3.24.3_2: .......... done
===> py39-pyscf-2.1.0_2 depends on executable: cmake - found
===> Returning to build of py39-pyscf-2.1.0_2
===> py39-pyscf-2.1.0_2 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-armv7-default-job-10] Installing gmake-4.3_2...
[main-armv7-default-job-10] Extracting gmake-4.3_2: .......... done
===> py39-pyscf-2.1.0_2 depends on executable: gmake - found
===> Returning to build of py39-pyscf-2.1.0_2
===> py39-pyscf-2.1.0_2 depends on executable: gfortran11 - found
===> py39-pyscf-2.1.0_2 depends on package: py39-setuptools>=63.1.0 - found
===> py39-pyscf-2.1.0_2 depends on file: /usr/local/bin/python3.9 - found
===> py39-pyscf-2.1.0_2 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===> py39-pyscf-2.1.0_2 depends on shared library: libcint.so - not found
===> Installing existing package /packages/All/libcint-5.1.6.pkg
[main-armv7-default-job-10] Installing libcint-5.1.6...
[main-armv7-default-job-10] Extracting libcint-5.1.6: ........ done
===> py39-pyscf-2.1.0_2 depends on shared library: libcint.so - found (/usr/local/lib/libcint.so)
===> Returning to build of py39-pyscf-2.1.0_2
===> py39-pyscf-2.1.0_2 depends on shared library: libxc.so - not found
===> Installing existing package /packages/All/libxc-6.0.0.pkg
[main-armv7-default-job-10] Installing libxc-6.0.0...
[main-armv7-default-job-10] Extracting libxc-6.0.0: .......... done
===> py39-pyscf-2.1.0_2 depends on shared library: libxc.so - found (/usr/local/lib/libxc.so)
===> Returning to build of py39-pyscf-2.1.0_2
===> py39-pyscf-2.1.0_2 depends on shared library: libxcfun.so - not found
===> Installing existing package /packages/All/xcfun-2.1.1.1.pkg
[main-armv7-default-job-10] Installing xcfun-2.1.1.1...
[main-armv7-default-job-10] Extracting xcfun-2.1.1.1: .......... done
===> py39-pyscf-2.1.0_2 depends on shared library: libxcfun.so - found (/usr/local/lib/libxcfun.so)
===> Returning to build of py39-pyscf-2.1.0_2
===> py39-pyscf-2.1.0_2 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for py39-pyscf-2.1.0_2
running config
===========================================================================
=======================<phase: build >============================
===> Building for py39-pyscf-2.1.0_2
running build
running build_ext
Configuring extensions
cmake -S/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib -Bbuild/temp.freebsd-14.0-CURRENT-arm-cpython-39
-- The C compiler identification is Clang 14.0.5
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-- Detecting C compiler ABI info
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-- 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
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-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/local/lib/libopenblas.so
-- Looking for ffsll
-- Looking for ffsll - found
-- BLAS libraries: /usr/local/lib/libopenblas.so
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- Configuring done
-- Generating done
-- Build files have been written to: /wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39
Building binaries
cmake --build build/temp.freebsd-14.0-CURRENT-arm-cpython-39 -j2
gmake[1]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[2]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
[ 1%] Building C object dft/CMakeFiles/xc_itrf.dir/libxc_itrf.c.o
[ 2%] Building C object np_helper/CMakeFiles/np_helper.dir/transpose.c.o
[ 3%] Building C object np_helper/CMakeFiles/np_helper.dir/pack_tril.c.o
[ 4%] Linking C shared library /wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/libxc_itrf.so
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
[ 4%] Built target xc_itrf
[ 6%] Building C object np_helper/CMakeFiles/np_helper.dir/npdot.c.o
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
[ 7%] Building C object dft/CMakeFiles/xcfun_itrf.dir/xcfun_itrf.c.o
[ 8%] Building C object np_helper/CMakeFiles/np_helper.dir/condense.c.o
[ 9%] Linking C shared library /wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/libxcfun_itrf.so
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
[ 9%] Built target xcfun_itrf
[ 10%] Building C object np_helper/CMakeFiles/np_helper.dir/omp_reduce.c.o
[ 12%] Building C object np_helper/CMakeFiles/np_helper.dir/np_helper.c.o
[ 13%] Linking C shared library /wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/libnp_helper.so
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
[ 13%] Built target np_helper
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
gmake[3]: Entering directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
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[ 14%] Building C object mcscf/CMakeFiles/fci.dir/fci_contract.c.o
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/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:228:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma GCC ivdep
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:245:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma GCC ivdep
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:262:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma GCC ivdep
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:288:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma GCC ivdep
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:298:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma GCC ivdep
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:494:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma GCC ivdep
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:635:9: error: unknown type name 'int8_t'; did you mean '__int8_t'?
int8_t *empty = (int8_t *)(csz + nz);
^~~~~~
__int8_t
/usr/include/sys/_types.h:45:22: note: '__int8_t' declared here
typedef signed char __int8_t;
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:635:34: error: expected expression
int8_t *empty = (int8_t *)(csz + nz);
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:635:26: error: use of undeclared identifier 'int8_t'
int8_t *empty = (int8_t *)(csz + nz);
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:636:9: error: unknown type name 'int8_t'; did you mean '__int8_t'?
int8_t *xempty = empty;
^~~~~~
__int8_t
/usr/include/sys/_types.h:45:22: note: '__int8_t' declared here
typedef signed char __int8_t;
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:637:9: error: unknown type name 'int8_t'; did you mean '__int8_t'?
int8_t *yempty = xempty + nx;
^~~~~~
__int8_t
/usr/include/sys/_types.h:45:22: note: '__int8_t' declared here
typedef signed char __int8_t;
^
/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/pyscf/lib/gto/ft_ao.c:638:9: error: unknown type name 'int8_t'; did you mean '__int8_t'?
int8_t *zempty = yempty + ny;
^~~~~~
__int8_t
/usr/include/sys/_types.h:45:22: note: '__int8_t' declared here
typedef signed char __int8_t;
^
6 warnings and 6 errors generated.
gmake[3]: *** [gto/CMakeFiles/cgto.dir/build.make:146: gto/CMakeFiles/cgto.dir/ft_ao.c.o] Error 1
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gmake[1]: *** [Makefile:91: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/py-pyscf/work-py39/pyscf-2.1.0/build/temp.freebsd-14.0-CURRENT-arm-cpython-39'
error: command '/usr/local/bin/cmake' failed with exit code 2
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-pyscf