[package - 130releng-armv7-quarterly][science/py-PyNE] Failed for py38-PyNE-0.7.6 in configure
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Date: Wed, 27 Apr 2022 10:12:54 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: http://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/e7d3e65b5acb/logs/py38-PyNE-0.7.6.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=e7d3e65b5acb
Log:
=>> Building science/py-PyNE
build started at Wed Apr 27 09:58:21 UTC 2022
port directory: /usr/ports/science/py-PyNE
package name: py38-PyNE-0.7.6
building for: FreeBSD 130releng-armv7-quarterly-job-08 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 1300139 arm
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py38-PyNE-0.7.6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5_1.pkg
[130releng-armv7-quarterly-job-08] Installing pkg-1.17.5_1...
[130releng-armv7-quarterly-job-08] Extracting pkg-1.17.5_1: .......... done
===> py38-PyNE-0.7.6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py38-PyNE-0.7.6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py38-PyNE-0.7.6 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py38-PyNE-0.7.6 for building
=> SHA256 Checksum OK for PyNE-0.7.6/decay.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.6/cram.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.6/decay-linux-clang.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.6/cram-linux-clang.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.6/prebuilt_nuc_data.h5.
=> SHA256 Checksum OK for PyNE-0.7.6/pyne-pyne-0.7.6_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
<snip>
-- The CXX compiler identification is Clang 11.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /nxb-bin/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: /nxb-bin/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
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-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
/ \
) (( )) (
(@) /|\ ))_(( /|\
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-- Pyne platform defined as: __LINUX__
-- Checking whether to build spatial solvers
-- -- Checking CMAKE_CXX_COMPILER_ID: Clang
-- Build spatial solvers: false
-- Build type: Release
-- PyNE Fast Compile: FALSE
-- CMAKE_INSTALL_RPATH: /usr/local/lib:/nxb-bin/usr/lib
-- The ASM compiler identification is Clang with GNU-like command-line
-- Found assembler: /nxb-bin/usr/bin/cc
-- CMake Install Prefix: /usr/local
-- Dependency Root Dir (DEPS_ROOT_DIR): /nxb-bin/usr
-- Dependency Hints (DEPS_HINTS): HINTS;/nxb-bin/usr
-- Dependency Binary Hints (DEPS_BIN_HINTS): HINTS;/nxb-bin/usr;/nxb-bin/usr/bin
-- Dependency Library Hints (DEPS_LIB_HINTS): HINTS;/nxb-bin/usr;/nxb-bin/usr/lib
-- Dependency Include Hints (DEPS_INCLUDE_HINTS): HINTS;/nxb-bin/usr/include
-- HDF5 Root: /usr/local
-- Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libhdf5_hl.so;/usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so (found version "1.10.6")
-- HDF5 Include directory: /usr/local/include
-- HDF5 Library directories: /usr/local/lib
-- HDF5 Libraries: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so
-- HDF5 library version: 1.10.6
-- MOAB Root: /usr/local
-- Found MOAB: /usr/local/lib/libMOAB.so
-- MOAB header files: /usr/local/include
-- MOAB library: /usr/local/lib/libMOAB.so
-- MOAB Found: TRUE
-- Found PythonInterp: /usr/local/bin/python3.8 (found version "3.8.13")
-- Found PythonLibs: /usr/local/lib/libpython3.8.so (found version "3.8.13")
-- PYTHON_EXECUTABLE: /usr/local/bin/python3.8
-- PYTHON_SITE_PACKAGES: /usr/local/lib/python3.8/site-packages
-- NUMPY_VERSION_STRING = 1.20.3
-- Found Numpy: 1.20.3
-- The Fortran compiler identification is GNU 10.3.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran10 - skipped
-- CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES: /usr/local/lib/gcc10;/usr/local/bin;/usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0;/usr/local/armv7-portbld-freebsd13.0/lib
-- CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES: gfortran;m;ssp_nonshared;gcc;gcc_s;m;gcc;gcc_s;c;gcc;gcc_s
-- Found Cython: /usr/local/bin/cython
-- LIBS: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so;/usr/local/lib/libpython3.8.so
-- Extracting decay.tar.gz
x decay.h
x decay.cpp
-- Extracting decay-linux-clang.tar.gz
x decay-linux-clang.s
-- Extracting cram.tar.gz
x cram.c
x cram.h
-- Extracting cram-linux-clang.tar.gz
x cram-linux-clang.s
-- Not fast compiling decay.cpp since PyNE fast compile is disabled.
-- Not fast compiling cram.c since PyNE fast compile is disabled.
-- Include paths for /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src: /usr/local/include;/usr/local/include;/usr/local/lib/python3.8/site-packages/numpy/core/include;/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build/pyne;/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src
-- Include paths for /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/pyne: /usr/local/include;/usr/local/include;/usr/local/lib/python3.8/site-packages/numpy/core/include;/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build/pyne;/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src
-- Modules to Cythonize: ace;bins;data;dtypes;endf;enrichment;extra_types;jsoncpp;material;material_library;nucname;particle;pyne_config;rxname;source;stlcontainers;tally;transmuters;_utils;source_sampling
-- F2PY F90 FLAGS:
-- Include paths for /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/pyne/xs: /usr/local/include;/usr/local/include;/usr/local/lib/python3.8/site-packages/numpy/core/include;/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build/pyne;/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src
-- Configuring done
-- Generating done
-- Build files have been written to: /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build
[ -3%] Built target ReplicatePythonSourceTree
Scanning dependencies of target pyne
[ -3%] Building C object src/CMakeFiles/pyne.dir/cram.c.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/decay.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/atomic_data.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/data.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/enrichment.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/enrichment_cascade.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/enrichment_symbolic.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/jsoncpp.cpp.o
/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/jsoncpp.cpp:2123:74: warning: implicit conversion from 'const Json::Int64' (aka 'const long long') to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion]
JSON_ASSERT_MESSAGE( value_.real_ >= minInt64 && value_.real_ <= maxInt64, "Real out of Int64 range" );
~~ ^~~~~~~~
/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/jsoncpp.cpp:1429:58: note: expanded from macro 'JSON_ASSERT_MESSAGE'
#define JSON_ASSERT_MESSAGE( condition, message ) if (!( condition )) JSON_FAIL_MESSAGE( message )
^~~~~~~~~
/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/jsoncpp.cpp:2149:67: warning: implicit conversion from 'const Json::UInt64' (aka 'const unsigned long long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
JSON_ASSERT_MESSAGE( value_.real_ >= 0 && value_.real_ <= maxUInt64, "Real out of UInt64 range" );
~~ ^~~~~~~~~
/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/jsoncpp.cpp:1429:58: note: expanded from macro 'JSON_ASSERT_MESSAGE'
#define JSON_ASSERT_MESSAGE( condition, message ) if (!( condition )) JSON_FAIL_MESSAGE( message )
^~~~~~~~~
2 warnings generated.
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/jsoncustomwriter.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/material.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/material_library.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/nucname.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/particle.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/source.cpp.o
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/source.cpp:10:
/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/source.h:35:32: warning: non-void function does not return a value [-Wreturn-type]
virtual std::string fluka() {}
^
1 warning generated.
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/rxname.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/tally.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/transmuters.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/utils.cpp.o
[ -3%] Building Fortran object src/CMakeFiles/pyne.dir/endftod.f90.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/measure.cpp.o
[ -3%] Building CXX object src/CMakeFiles/pyne.dir/source_sampling.cpp.o
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/source_sampling.cpp:2:
/wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/src/source_sampling.h:78:23: warning: 'read_e_bounds' has C-linkage specified, but returns incomplete type 'std::vector<double>' which could be incompatible with C [-Wreturn-type-c-linkage]
std::vector<double> read_e_bounds(std::string e_bounds_file);
^
1 warning generated.
[ -3%] Linking CXX shared library libpyne.so
CMakeFiles/pyne.dir/cram.c.o: in function `pyne_cram_solve_complex':
cram.c:(.text+0x58a3cc): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58a654): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58a7f4): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58a988): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58ab1c): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58acb0): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58ae44): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58afd8): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58b170): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58b2cc): relocation truncated to fit: R_ARM_CALL against symbol `__muldc3' defined in .text section in /usr/local/lib/gcc10/gcc/armv7-portbld-freebsd13.0/10.3.0/libgcc.a(_muldc3.o)
cram.c:(.text+0x58b410): additional relocation overflows omitted from the output
c++: error: linker command failed with exit code 1 (use -v to see invocation)
*** Error code 1
Stop.
make[3]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py38/pyne-0.7.6/build
setup.py:38: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "setup.py", line 419, in <module>
main()
File "setup.py", line 403, in main
main_safe(ns)
File "setup.py", line 395, in main_safe
main_body(ns)
File "setup.py", line 378, in main_body
rtn = subprocess.check_call(['make'] + ns.make_args, cwd=ns.build_dir)
File "/usr/local/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 1.
Writing atomic_data.h
Writing atomic_data.cpp
CMake command is
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local -DHDF5_ROOT=/usr/local -DHDF5_LIBRARIES=/usr/local/lib/libhdf5.so;/usr/local/lib/libhdf5_hl.so -DHDF5_LIBRARY_DIRS=/usr/local/lib -DHDF5_INCLUDE_DIRS=/usr/local/include -DWITH_MOAB=ON -DMOAB_ROOT=/usr/local -DPYNE_FAST_COMPILE=FALSE -DENABLE_SPATIAL_SOLVERS=ON -DPYTHON_EXECUTABLE=/usr/local/bin/python3.8
--------------------
If you are having issues building pyne, please report your problem to pyne-dev@googlegroups.com or look for help at http://pyne.io
--------------------
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-PyNE