[package - main-amd64-default][science/nest] Failed for nest-3.3 in build
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Date: Fri, 13 May 2022 04:17:57 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://beefy18.nyi.freebsd.org/data/main-amd64-default/pf0c279ef0f2b_s5326ebfd05/logs/nest-3.3.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=pf0c279ef0f2b_s5326ebfd05
Log:
=>> Building science/nest
build started at Fri May 13 04:07:07 UTC 2022
port directory: /usr/ports/science/nest
package name: nest-3.3
building for: FreeBSD main-amd64-default-job-01 14.0-CURRENT FreeBSD 14.0-CURRENT 1400058 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
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!!! Jail is newer than host. (Jail: 1400058, Host: 1400050) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for nest-3.3:
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PYTHON=on: Python bindings or support
===> Use 'make config' to modify these settings
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yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> nest-3.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5_1.pkg
[main-amd64-default-job-01] Installing pkg-1.17.5_1...
[main-amd64-default-job-01] Extracting pkg-1.17.5_1: .......... done
===> nest-3.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of nest-3.3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
=> nest-nest-simulator-v3.3_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/nest/nest-simulator/tar.gz/v3.3?dummy=/nest-nest-simulator-v3.3_GH0.tar.gz
fetch: https://codeload.github.com/nest/nest-simulator/tar.gz/v3.3?dummy=/nest-nest-simulator-v3.3_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/nest/nest-simulator/tar.gz/v3.3?dummy=/nest-nest-simulator-v3.3_GH0.tar.gz: size of remote file is not known
nest-nest-simulator-v3.3_GH0.tar.gz 10 MB 12 MBps 01s
===> Fetching all distfiles required by nest-3.3 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by nest-3.3 for building
=> SHA256 Checksum OK for nest-nest-simulator-v3.3_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by nest-3.3 for building
===> Extracting for nest-3.3
=> SHA256 Checksum OK for nest-nest-simulator-v3.3_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for nest-3.3
===> Applying FreeBSD patches for nest-3.3 from /usr/ports/science/nest/files
===========================================================================
<snip>
-- Looking for NAN - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for M_E
-- Looking for M_E - found
-- Looking for M_PI
-- Looking for M_PI - found
-- Looking for expm1
-- Looking for expm1 - not found
-- Host triple: amd64-pc-freebsd
-- Target triple: amd64-pc-freebsd
-- Found Python: /usr/local/bin/python3.8 (found suitable exact version "3.8.13") found components: Interpreter Development.Module
-- Found Cython: /usr/local/bin/cython-3.8 (found suitable version "0.29.28", minimum required is "0.28.3")
-- Found LTDL: /usr/local/lib/libltdl.so
-- Found Readline: /usr/local/lib/libreadline.so (found version "8.1")
-- Found PkgConfig: /usr/local/bin/pkgconf (found version "1.8.0")
-- Found GSL: /usr/local/include (found version "2.7.1")
-- Found OpenMP_C: -fopenmp=libomp (found version "5.0")
-- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0")
-- Found Boost: /usr/local/include (found suitable version "1.72.0", minimum required is "1.69.0")
-- Check the abort exitcode.
-- Check the abort exitcode. 134
-- Check the segmentation fault exitcode.
-- Check the segmentation fault exitcode. 139
-- Check whether the compiler ignores cmath makros.
-- Check whether the compiler ignores cmath makros. OFF
-- Check whether the compiler does NOT include <*.h> headers ISO conformant.
-- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF
-- Check whether the compiler respects symbolic signal names in signal.h.
-- Check whether the compiler respects symbolic signal names in signal.h. OFF
-- Check static template member declaration.
-- Check static template member declaration. OFF
-- Check for STL vector capacity base unity.
-- Check for STL vector capacity base unity. ON
-- Check for STL vector capacity doubling strategy.
-- Check for STL vector capacity doubling strategy. ON
-- Check whether the compiler fails with ICE.
-- Check whether the compiler fails with ICE. OFF
-- Check if ::nan is available from cmath.
-- Check if ::nan is available from cmath. ON
-- Check if ::isnan is available from cmath.
-- Check if ::isnan is available from cmath. ON
-- Check if Random123 generators work.
-- Check if Random123 generators work. ON
-- NEST version: 3.3
--------------------------------------------------------------------------------
NEST Configuration Summary
--------------------------------------------------------------------------------
Build type : Release
Target System : FreeBSD
Cross Compiling : FALSE
C compiler : Clang 13.0.0 (/usr/bin/cc)
C compiler flags : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing
C++ compiler : Clang 13.0.0 (/usr/bin/c++)
C++ compiler flags : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing
Build dynamic : ON
Built-in modules : models
User modules : None
Python bindings : Yes (Python 3.8.13: /usr/local/bin/python3.8)
Includes : /usr/local/include/python3.8/
Libraries :
Cython bindings : Yes (Cython 0.29.28: /usr/local/bin/cython-3.8)
MPI4PY header : NO
Use threading : Yes (OpenMP: -fopenmp=libomp)
Use GSL : Yes (GSL 2.7.1)
Includes : /usr/local/include
Libraries : /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so
Use Readline : Yes (GNU Readline 8.1)
Includes : /usr/local/include
Libraries : /usr/local/lib/libreadline.so;/usr/lib/libncurses.so
Use libltdl : Yes (LTDL )
Includes : /usr/local/include
Libraries : /usr/local/lib/libltdl.so
Use doxygen : No
Use MPI : No
Detailed timers : No
Use MUSIC : No
Use libneurosim : No
Use Boost : Yes (Boost 1.72.0)
Includes : /usr/local/include
Libraries :
Use SIONlib : No
--------------------------------------------------------------------------------
The NEST executable will be installed to:
/usr/local/bin/
NEST dynamic libraries and user modules will be installed to:
/usr/local/lib/nest/
Documentation and examples will be installed to:
/usr/local/share/doc/nest/
PyNEST will be installed to:
/usr/local/lib/python3.8/site-packages
To set necessary environment variables, add the following line
to your ~/.bashrc :
source /usr/local/bin/nest_vars.sh
--------------------------------------------------------------------------------
You can now build and install NEST with
make
make install
make installcheck
If you experience problems with the installation or the use of NEST,
please see https://www.nest-simulator.org/frequently_asked_questions
or go to https://www.nest-simulator.org/community to find out how to
join the user mailing list.
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BOOST_PYTHON_SUFFIX
CMAKE_COLOR_MAKEFILE
CMAKE_VERBOSE_MAKEFILE
Python_ADDITIONAL_VERSIONS
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/science/nest/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for nest-3.3
[ 0% 2/232] /usr/bin/c++ -Dnestutil_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -MD -MT libnestutil/CMakeFiles/nestutil.dir/numerics.cpp.o -MF libnestutil/CMakeFiles/nestutil.dir/numerics.cpp.o.d -o libnestutil/CMakeFiles/nestutil.dir/numerics.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil/numerics.cpp
[ 0% 3/232] /usr/bin/c++ -Dnestutil_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -MD -MT libnestutil/CMakeFiles/nestutil.dir/propagator_stability.cpp.o -MF libnestutil/CMakeFiles/nestutil.dir/propagator_stability.cpp.o.d -o libnestutil/CMakeFiles/nestutil.dir/propagator_stability.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil/propagator_stability.cpp
[ 1% 4/232] /usr/bin/c++ -Dnestutil_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -MD -MT libnestutil/CMakeFiles/nestutil.dir/logging_event.cpp.o -MF libnestutil/CMakeFiles/nestutil.dir/logging_event.cpp.o.d -o libnestutil/CMakeFiles/nestutil.dir/logging_event.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil/logging_event.cpp
[ 1% 5/232] /usr/bin/c++ -Dnestutil_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -MD -MT libnestutil/CMakeFiles/nestutil.dir/stopwatch.cpp.o -MF libnestutil/CMakeFiles/nestutil.dir/stopwatch.cpp.o.d -o libnestutil/CMakeFiles/nestutil.dir/stopwatch.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil/stopwatch.cpp
[ 2% 6/232] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -fstack-protector-strong -shared -Wl,-soname,libnestutil.so -o libnestutil/libnestutil.so libnestutil/CMakeFiles/nestutil.dir/logging_event.cpp.o libnestutil/CMakeFiles/nestutil.dir/numerics.cpp.o libnestutil/CMakeFiles/nestutil.dir/propagator_stability.cpp.o libnestutil/CMakeFiles/nestutil.dir/stopwatch.cpp.o -Wl,-rpath,:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: /usr/local/lib/libgsl.so /usr/local/lib/libgslcblas.so && :
[ 2% 7/232] /usr/bin/c++ -Dmodels_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/thirdparty -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/sli -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/nestkernel -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp=libomp -MD -MT models/CMakeFiles/models.dir/ac_generator.cpp.o -MF models/CMakeFiles/models.dir/ac_generator.cpp.o.d -o models/CMakeFiles/models.dir/ac_generator.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/models/ac_generator.cpp
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FAILED: models/CMakeFiles/models.dir/iaf_psc_alpha_multisynapse.cpp.o
/usr/bin/c++ -Dmodels_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/thirdparty -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/sli -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/nestkernel -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp=libomp -MD -MT models/CMakeFiles/models.dir/iaf_psc_alpha_multisynapse.cpp.o -MF models/CMakeFiles/models.dir/iaf_psc_alpha_multisynapse.cpp.o.d -o models/CMakeFiles/models.dir/iaf_psc_alpha_multisynapse.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/models/iaf_psc_alpha_multisynapse.cpp
[ 21% 49/232] /usr/bin/c++ -Dmodels_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/thirdparty -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/sli -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/nestkernel -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp=libomp -MD -MT models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o -MF models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o.d -o models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/models/iaf_psc_alpha_canon.cpp
FAILED: models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o
/usr/bin/c++ -Dmodels_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/thirdparty -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/libnestutil -I/wrkdirs/usr/ports/science/nest/work/.build/libnestutil -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/sli -I/wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/nestkernel -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -std=c++11 -Wall -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp=libomp -MD -MT models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o -MF models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o.d -o models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o -c /wrkdirs/usr/ports/science/nest/work/nest-simulator-3.3/models/iaf_psc_alpha_canon.cpp
ninja: build stopped: subcommand failed.
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/nest