[package - main-amd64-default][science/py-PyNE] Failed for py39-PyNE-0.7.7_4 in configure
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Date: Tue, 25 Jul 2023 16:14:36 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/p629834653cee_s789df254cc/logs/py39-PyNE-0.7.7_4.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p629834653cee_s789df254cc
Log:
=>> Building science/py-PyNE
build started at Tue Jul 25 16:09:46 UTC 2023
port directory: /usr/ports/science/py-PyNE
package name: py39-PyNE-0.7.7_4
building for: FreeBSD main-amd64-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
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!!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-PyNE-0.7.7_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-amd64-default-job-08] Installing pkg-1.20.4...
[main-amd64-default-job-08] Extracting pkg-1.20.4: .......... done
===> py39-PyNE-0.7.7_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-PyNE-0.7.7_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PyNE-0.7.7_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PyNE-0.7.7_4 for building
=> SHA256 Checksum OK for PyNE-0.7.7/decay.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/cram.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/decay-linux-clang.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/cram-linux-clang.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/prebuilt_nuc_data.h5.
=> SHA256 Checksum OK for PyNE-0.7.7/pyne-pyne-0.7.7_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PyNE-0.7.7_4 for building
===> Extracting for py39-PyNE-0.7.7_4
=> SHA256 Checksum OK for PyNE-0.7.7/decay.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/cram.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/decay-linux-clang.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/cram-linux-clang.tar.gz.
=> SHA256 Checksum OK for PyNE-0.7.7/prebuilt_nuc_data.h5.
=> SHA256 Checksum OK for PyNE-0.7.7/pyne-pyne-0.7.7_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
<snip>
| | |-|
|-|___________________________________________________________________| |
(@) l /\ / ( ( \ /\ l `\|-|
l / V \ \ V \ l (@)
l/ _) )_ \I
`\ /'
`
-- 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:/usr/lib
-- The ASM compiler identification is Clang with GNU-like command-line
-- Found assembler: /usr/bin/cc
-- CMake Install Prefix: /usr/local
-- Dependency Root Dir (DEPS_ROOT_DIR): /usr
-- Dependency Hints (DEPS_HINTS): HINTS;/usr
-- Dependency Binary Hints (DEPS_BIN_HINTS): HINTS;/usr;/usr/bin
-- Dependency Library Hints (DEPS_LIB_HINTS): HINTS;/usr;/usr/lib
-- Dependency Include Hints (DEPS_INCLUDE_HINTS): HINTS;/usr/include
-- HDF5 Root: /usr/local
-- Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libhdf5_hl.so;hdf5-shared (found version "1.12.2")
-- HDF5 Include directory: /usr/local/include
-- HDF5 Library directories: /usr/local/lib
-- HDF5 Libraries: hdf5-shared
-- HDF5 library version: 1.12.2
-- 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/python3.9 (found version "3.9.17")
-- Found PythonLibs: /usr/local/lib/libpython3.9.so (found version "3.9.17")
-- PYTHON_EXECUTABLE: /usr/local/bin/python3.9
-- PYTHON_SITE_PACKAGES: /usr/local/lib/python3.9/site-packages
-- NUMPY_VERSION_STRING = 1.25.0
-- Found Numpy: 1.25.0
-- The Fortran compiler identification is GNU 12.2.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran12 - skipped
-- CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES: /usr/local/lib/gcc12;/usr/local/bin;/usr/local/lib/gcc12/gcc/x86_64-portbld-freebsd14.0/12.2.0;/usr/local/x86_64-portbld-freebsd14.0/lib
-- CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES: gfortran;m;ssp_nonshared;gcc;gcc_s;quadmath;m;gcc;gcc_s;c;gcc;gcc_s
-- Found Cython: /usr/local/bin/cython
-- LIBS: hdf5-shared;/usr/local/lib/libpython3.9.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-py39/pyne-0.7.7/src: /usr/local/include;/usr/local/include;/usr/local/lib/python3.9/site-packages/numpy/core/include;/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne;/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src
-- Include paths for /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/pyne: /usr/local/include;/usr/local/include;/usr/local/lib/python3.9/site-packages/numpy/core/include;/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne;/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/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-py39/pyne-0.7.7/pyne/xs: /usr/local/include;/usr/local/include;/usr/local/lib/python3.9/site-packages/numpy/core/include;/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne;/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src
-- Configuring done (2.9s)
-- Generating done (0.1s)
-- Build files have been written to: /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
[ 1%] Building C object src/CMakeFiles/pyne.dir/cram.c.o
[ 1%] Built target ReplicatePythonSourceTree
[ 2%] Building CXX object src/CMakeFiles/pyne.dir/decay.cpp.o
[ 3%] Building CXX object src/CMakeFiles/pyne.dir/atomic_data.cpp.o
[ 4%] Building CXX object src/CMakeFiles/pyne.dir/data.cpp.o
[ 5%] Building CXX object src/CMakeFiles/pyne.dir/enrichment.cpp.o
[ 6%] Building CXX object src/CMakeFiles/pyne.dir/enrichment_cascade.cpp.o
[ 7%] Building CXX object src/CMakeFiles/pyne.dir/enrichment_symbolic.cpp.o
[ 9%] Building CXX object src/CMakeFiles/pyne.dir/jsoncpp.cpp.o
/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src/jsoncpp.cpp:2123:74: warning: implicit conversion from 'const 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-py39/pyne-0.7.7/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-py39/pyne-0.7.7/src/jsoncpp.cpp:2149:67: warning: implicit conversion from 'const 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-py39/pyne-0.7.7/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.
[ 10%] Building CXX object src/CMakeFiles/pyne.dir/jsoncustomwriter.cpp.o
[ 11%] Building CXX object src/CMakeFiles/pyne.dir/material.cpp.o
[ 12%] Building CXX object src/CMakeFiles/pyne.dir/material_library.cpp.o
[ 13%] Building CXX object src/CMakeFiles/pyne.dir/nucname.cpp.o
[ 14%] Building CXX object src/CMakeFiles/pyne.dir/particle.cpp.o
[ 15%] Building CXX object src/CMakeFiles/pyne.dir/source.cpp.o
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src/source.cpp:10:
/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src/source.h:35:32: warning: non-void function does not return a value [-Wreturn-type]
virtual std::string fluka() {}
^
1 warning generated.
[ 17%] Building CXX object src/CMakeFiles/pyne.dir/rxname.cpp.o
[ 18%] Building CXX object src/CMakeFiles/pyne.dir/tally.cpp.o
[ 19%] Building CXX object src/CMakeFiles/pyne.dir/transmuters.cpp.o
[ 20%] Building CXX object src/CMakeFiles/pyne.dir/utils.cpp.o
[ 21%] Building Fortran object src/CMakeFiles/pyne.dir/endftod.f90.o
[ 22%] Building CXX object src/CMakeFiles/pyne.dir/measure.cpp.o
[ 23%] Building CXX object src/CMakeFiles/pyne.dir/source_sampling.cpp.o
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src/source_sampling.cpp:2:
/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/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.
[ 25%] Linking CXX shared library libpyne.so
[ 25%] Built target pyne
[ 27%] Compiling Cython CXX source for ace...
[ 27%] Compiling Cython CXX source for bins...
[ 28%] Building CXX object pyne/CMakeFiles/bins.dir/bins.cxx.o
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/bins.cxx:766:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.9/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]
#warning "Using deprecated NumPy API, disable it with " \
^
[ 29%] Building CXX object pyne/CMakeFiles/ace.dir/ace.cxx.o
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/ace.cxx:766:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.9/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]
#warning "Using deprecated NumPy API, disable it with " \
^
1 warning generated.
[ 30%] Linking CXX shared module bins.so
[ 30%] Built target bins
[ 31%] Compiling Cython CXX source for data...
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/ace.cxx:1017:
/usr/include/c++/v1/complex:1401:48: error: no member named 'std' in namespace 'std'; did you mean simply 'std'?
if (__x.real() == 0 && (__x.imag() == 0 || std::isnan(__x.imag())))
^
/usr/include/c++/v1/complex:250:1: note: 'std' declared here
_LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/include/c++/v1/__config:663:49: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
# define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
^
1 warning and 1 error generated.
--- pyne/CMakeFiles/ace.dir/ace.cxx.o ---
*** [pyne/CMakeFiles/ace.dir/ace.cxx.o] Error code 1
make[3]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
1 error
make[3]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
--- pyne/CMakeFiles/ace.dir/all ---
*** [pyne/CMakeFiles/ace.dir/all] Error code 2
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
--- pyne/CMakeFiles/data.dir/all ---
*** [pyne/CMakeFiles/data.dir/all] Error code 6
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
2 errors
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
*** [all] Error code 2
make[1]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
1 error
make[1]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "setup.py", line 481, in <module>
main()
File "setup.py", line 464, in main
main_safe(ns)
File "setup.py", line 456, in main_safe
main_body(ns)
File "setup.py", line 438, in main_body
rtn = subprocess.check_call(["make"] + ns.make_args, cwd=ns.build_dir)
File "/usr/local/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', '-j2']' returned non-zero exit status 2.
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/python3.9
--------------------
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