[package - main-i386-default][science/py-PyNE] Failed for py39-PyNE-0.7.7_4 in configure
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Date: Sat, 30 Dec 2023 08:01:07 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/beefy17/data/main-i386-default/padd1ba90ee22_s84b4342c0d/logs/py39-PyNE-0.7.7_4.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=padd1ba90ee22_s84b4342c0d
Log:
=>> Building science/py-PyNE
build started at Sat Dec 30 07:55:42 UTC 2023
port directory: /usr/ports/science/py-PyNE
package name: py39-PyNE-0.7.7_4
building for: FreeBSD main-i386-default-job-12 15.0-CURRENT FreeBSD 15.0-CURRENT 1500008 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2685 Aug 22 01:01 /usr/ports/science/py-PyNE/Makefile
Ports top last git commit: add1ba90ee2
Ports top unclean checkout: no
Port dir last git commit: ac878217a90
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.0
Host OSVERSION: 1500006
Jail OSVERSION: 1500008
Job Id: 12
!!! Jail is newer than host. (Jail: 1500008, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-PyNE-0.7.7_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[main-i386-default-job-12] Installing pkg-1.20.9...
[main-i386-default-job-12] Extracting pkg-1.20.9: .......... 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 >============================
===== 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 BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PyNE-0.7.7_4 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> 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>============================
===== 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 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 >============================
===== 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 py39-PyNE-0.7.7_4
===> Applying FreeBSD patches for py39-PyNE-0.7.7_4 from /usr/ports/science/py-PyNE/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-PyNE-0.7.7_4 depends on executable: cmake - not found
<snip>
This warning is for project developers. Use -Wno-dev to suppress it.
-- 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 (4.2s)
-- 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
[ 2%] Building CXX object src/CMakeFiles/pyne.dir/decay.cpp.o
[ 2%] Built target ReplicatePythonSourceTree
[ 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]
2123 | 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'
1429 | #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]
2149 | 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'
1429 | #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
[ 17%] Building CXX object src/CMakeFiles/pyne.dir/rxname.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]
35 | virtual std::string fluka() {}
| ^
1 warning generated.
[ 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]
78 | 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
[ 26%] Compiling Cython CXX source for data...
[ 27%] Compiling Cython CXX source for ace...
[ 28%] Compiling Cython CXX source for bins...
[ 29%] 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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
[ 30%] Building CXX object pyne/CMakeFiles/ace.dir/ace.cxx.o
[ 31%] Building CXX object pyne/CMakeFiles/data.dir/data.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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
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:1404:48: error: no member named 'std' in namespace 'std'; did you mean simply 'std'?
1404 | if (__x.real() == 0 && (__x.imag() == 0 || std::isnan(__x.imag())))
| ^
/usr/include/c++/v1/complex:249:1: note: 'std' declared here
249 | _LIBCPP_BEGIN_NAMESPACE_STD
| ^
/usr/include/c++/v1/__config:845:49: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
845 | # define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
| ^
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/data.cxx:790:
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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/data.cxx:1018:
/usr/include/c++/v1/complex:1404:48: error: no member named 'std' in namespace 'std'; did you mean simply 'std'?
1404 | if (__x.real() == 0 && (__x.imag() == 0 || std::isnan(__x.imag())))
| ^
/usr/include/c++/v1/complex:249:1: note: 'std' declared here
249 | _LIBCPP_BEGIN_NAMESPACE_STD
| ^
/usr/include/c++/v1/__config:845:49: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
845 | # define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
| ^
1 warning generated.
[ 32%] Linking CXX shared module bins.so
[ 32%] Built target bins
[ 34%] Compiling Cython CXX source for dtypes...
/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/ace.cxx:35015:63: warning: result of comparison of constant 9007199254740992 with expression of type 'long' is always true [-Wtautological-constant-out-of-range-compare]
35015 | if ((8 * sizeof(long) <= 53 || likely(labs(a) <= ((PY_LONG_LONG)1 << 53)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/ace.cxx:985:43: note: expanded from macro 'likely'
985 | #define likely(x) __builtin_expect(!!(x), 1)
| ^
1 warning and 1 error generated.
[ 35%] Building CXX object pyne/CMakeFiles/dtypes.dir/dtypes.cxx.o
--- pyne/CMakeFiles/data.dir/data.cxx.o ---
*** [pyne/CMakeFiles/data.dir/data.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/data.dir/all ---
*** [pyne/CMakeFiles/data.dir/all] Error code 2
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
2 warnings 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
In file included from /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne/dtypes.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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
1 warning generated.
--- pyne/CMakeFiles/dtypes.dir/all ---
*** [pyne/CMakeFiles/dtypes.dir/all] Error code 6
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
3 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', '-j3']' 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