[package - main-armv7-default][science/py-PyNE] Failed for py39-PyNE-0.7.7_3 in configure
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Date: Sun, 16 Oct 2022 14:32:35 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://ampere2.nyi.freebsd.org/data/main-armv7-default/pd20a3cf7e848_s91a84eb5b/logs/py39-PyNE-0.7.7_3.log
Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=pd20a3cf7e848_s91a84eb5b
Log:
=>> Building science/py-PyNE
build started at Sun Oct 16 14:21:34 UTC 2022
port directory: /usr/ports/science/py-PyNE
package name: py39-PyNE-0.7.7_3
building for: FreeBSD main-armv7-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400072 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400063
Jail OSVERSION: 1400072
Job Id: 06
!!! Jail is newer than host. (Jail: 1400072, Host: 1400063) !!!
!!! 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_3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-armv7-default-job-06] Installing pkg-1.18.4...
[main-armv7-default-job-06] Extracting pkg-1.18.4: .......... done
===> py39-PyNE-0.7.7_3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-PyNE-0.7.7_3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PyNE-0.7.7_3 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by py39-PyNE-0.7.7_3 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_3 for building
===> Extracting for py39-PyNE-0.7.7_3
=> 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>
Message from openmpi-4.1.4:
--
===> NOTICE:
The openmpi 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
===> py39-PyNE-0.7.7_3 depends on shared library: libMOAB.so - found (/usr/local/lib/libMOAB.so)
===> Returning to build of py39-PyNE-0.7.7_3
===> py39-PyNE-0.7.7_3 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for py39-PyNE-0.7.7_3
setup.py:38: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
/usr/local/bin/cmake
-- The C compiler identification is Clang 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /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: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
/ \
) (( )) (
(@) /|\ ))_(( /|\
|-| / | \ (/\|/\) / | \ (@)
| | -------------------/--|-voV---\`|'/--Vov-|--\---------------------|-|
|-| '^` (o o) '^` | |
| | `\Y/' |-|
|-| | |
| | /\ ___ __ __ /\ |-|
|-| /^~\ / _ \_ _ /\ \ \/__\ /^~\ | |
| | /^~\ / /_)/ | | |/ \/ /_\ /^~\ |-|
|-| /^~\ / ___/| |_| / /\ //__ /^~\ | |
| | ^||` \/ \__, \_\ \/\__/ ^||` |-|
|-| || |____/ || | |
| | ==== ==== |-|
|-| | |
| | |-|
|-|___________________________________________________________________| |
(@) 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 "3.9.14")
-- Found PythonLibs: /usr/local/lib/libpython3.9.so (found version "3.9.14")
-- PYTHON_EXECUTABLE: /usr/local/bin/python3.9
-- PYTHON_SITE_PACKAGES: /usr/local/lib/python3.9/site-packages
-- NUMPY_VERSION_STRING = 1.23.3
-- Found Numpy: 1.23.3
-- The Fortran compiler identification is GNU 11.3.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran11 - skipped
-- CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES: /usr/local/lib/gcc11;/usr/local/bin;/usr/local/lib/gcc11/gcc/armv7-portbld-freebsd14.0/11.3.0;/usr/local/armv7-portbld-freebsd14.0/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: 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
-- Generating done
-- Build files have been written to: /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
Scanning dependencies of target pyne
[ 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
Assertion failed: (!KeyInfoT::isEqual(Val, EmptyKey) && !KeyInfoT::isEqual(Val, TombstoneKey) && "Empty/Tombstone value shouldn't be inserted into map!"), function LookupBucketFor, file /usr/local/poudriere/jails/main-armv7/usr/src/contrib/llvm-project/llvm/include/llvm/ADT/DenseMap.h, line 625.
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: /usr/bin/cc -DH5_BUILT_AS_DYNAMIC_LIB -Dpyne_EXPORTS -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build/pyne -I/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -DNDEBUG -fPIC -O0 -ffast-math -MD -MT src/CMakeFiles/pyne.dir/cram.c.o -MF CMakeFiles/pyne.dir/cram.c.o.d -o CMakeFiles/pyne.dir/cram.c.o -c /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src/cram.c
1. <eof> parser at end of file
2. Optimizer
#0 0x045b5ac8 (/usr/bin/cc+0x45b5ac8)
#1 0x045b3960 (/usr/bin/cc+0x45b3960)
#2 0x0455c978 (/usr/bin/cc+0x455c978)
#3 0x0455cb4c (/usr/bin/cc+0x455cb4c)
#4 0x45ea4148 (/lib/libthr.so.3+0x26148)
cc: error: clang frontend command failed with exit code 134 (use -v to see invocation)
FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c)
Target: armv7-unknown-freebsd14.0-gnueabihf
Thread model: posix
InstalledDir: /usr/bin
cc: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
cc: note: diagnostic msg: /tmp/cram-f8171f.c
cc: note: diagnostic msg: /tmp/cram-f8171f.sh
cc: note: diagnostic msg:
********************
--- src/CMakeFiles/pyne.dir/cram.c.o ---
*** [src/CMakeFiles/pyne.dir/cram.c.o] Error code 134
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
--- src/CMakeFiles/pyne.dir/all ---
*** [src/CMakeFiles/pyne.dir/all] Error code 2
make[2]: stopped in /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
1 error
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