[package - main-i386-default][science/py-PyNE] Failed for py39-PyNE-0.7.7_4 in configure
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Date: Tue, 17 Oct 2023 12:03:52 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/p1fa9afdc10b7_s6e8bf24073/logs/py39-PyNE-0.7.7_4.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p1fa9afdc10b7_s6e8bf24073
Log:
=>> Building science/py-PyNE
build started at Tue Oct 17 11:58:58 UTC 2023
port directory: /usr/ports/science/py-PyNE
package name: py39-PyNE-0.7.7_4
building for: FreeBSD main-i386-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500001 i386
maintained by: yuri@FreeBSD.org
Makefile ident:
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Host OSVERSION: 1500000
Jail OSVERSION: 1500001
Job Id: 01
!!! Jail is newer than host. (Jail: 1500001, Host: 1500000) !!!
!!! 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-1.20.8.pkg
[main-i386-default-job-01] Installing pkg-1.20.8...
[main-i386-default-job-01] Extracting pkg-1.20.8: .......... 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.
<snip>
-- 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 "3.9.18")
-- Found PythonLibs: /usr/local/lib/libpython3.9.so (found version "3.9.18")
-- 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/i386-portbld-freebsd15.0/12.2.0;/usr/local/i386-portbld-freebsd15.0/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 (4.4s)
-- Generating done (0.1s)
-- Build files have been written to: /wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/build
[ 2%] 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]
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.
LLVM ERROR: out of memory
Allocation failed
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. Code generation
3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/science/py-PyNE/work-py39/pyne-0.7.7/src/cram.c'.
4. Running pass 'X86 Assembly Printer' on function '@pyne_cram_solve_special'
#0 0x055b4854 (/usr/bin/cc+0x55b4854)
#1 0x055b4cb0 (/usr/bin/cc+0x55b4cb0)
#2 0x055b2b6e (/usr/bin/cc+0x55b2b6e)
#3 0x0555bb21 (/usr/bin/cc+0x555bb21)
#4 0x27003f39 (/lib/libthr.so.3+0x18f39)
#5 0x27003409 (/lib/libthr.so.3+0x18409)
#6 0xffffe294 ([vdso]+0x294)
#7 0x2728bbcf thr_kill (/lib/libc.so.7+0x121bcf)
#8 0x2720911b _raise (/lib/libc.so.7+0x9f11b)
#9 0x272b453b abort (/lib/libc.so.7+0x14a53b)
#10 0x05562d1f (/usr/bin/cc+0x5562d1f)
#11 0x055b6295 (/usr/bin/cc+0x55b6295)
#12 0x025bf2b3 (/usr/bin/cc+0x25bf2b3)
#13 0x052f2041 (/usr/bin/cc+0x52f2041)
#14 0x05304673 (/usr/bin/cc+0x5304673)
#15 0x062556ab (/usr/bin/cc+0x62556ab)
#16 0x05618dac (/usr/bin/cc+0x5618dac)
#17 0x0625067e (/usr/bin/cc+0x625067e)
#18 0x04d003e7 (/usr/bin/cc+0x4d003e7)
#19 0x051dfcbd (/usr/bin/cc+0x51dfcbd)
#20 0x051e5621 (/usr/bin/cc+0x51e5621)
#21 0x051e037d (/usr/bin/cc+0x51e037d)
#22 0x051e59f1 (/usr/bin/cc+0x51e59f1)
#23 0x02f216c3 (/usr/bin/cc+0x2f216c3)
#24 0x03258d17 (/usr/bin/cc+0x3258d17)
#25 0x0379d199 (/usr/bin/cc+0x379d199)
#26 0x03194d04 (/usr/bin/cc+0x3194d04)
#27 0x03256c45 (/usr/bin/cc+0x3256c45)
#28 0x031945ea (/usr/bin/cc+0x31945ea)
#29 0x031141de (/usr/bin/cc+0x31141de)
#30 0x03251a13 (/usr/bin/cc+0x3251a13)
#31 0x025a8fed (/usr/bin/cc+0x25a8fed)
#32 0x025b83e7 (/usr/bin/cc+0x25b83e7)
#33 0x02fb0383 (/usr/bin/cc+0x2fb0383)
#34 0x0555b8ab (/usr/bin/cc+0x555b8ab)
#35 0x02fafdcf (/usr/bin/cc+0x2fafdcf)
#36 0x02f75c4f (/usr/bin/cc+0x2f75c4f)
#37 0x02f75f13 (/usr/bin/cc+0x2f75f13)
#38 0x02f91b6b (/usr/bin/cc+0x2f91b6b)
#39 0x025b79e7 (/usr/bin/cc+0x25b79e7)
#40 0x271df945 __libc_start1 (/lib/libc.so.7+0x75945)
cc: error: clang frontend command failed with exit code 134 (use -v to see invocation)
FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152)
Target: i386-unknown-freebsd15.0
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-0d0afb.c
cc: note: diagnostic msg: /tmp/cram-0d0afb.sh
cc: note: diagnostic msg:
********************
--- src/CMakeFiles/pyne.dir/cram.c.o ---
*** [src/CMakeFiles/pyne.dir/cram.c.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
--- 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', '-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