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Date:      Tue, 16 Apr 2019 22:26:21 GMT
From:      pkg-fallout@FreeBSD.org
To:        yuri@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-i386-default][science/gromacs] Failed for gromacs-2019.1_1 in build
Message-ID:  <201904162226.x3GMQLQB071791@beefy11.nyi.freebsd.org>

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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
Last committer: jbeich@FreeBSD.org
Ident:          $FreeBSD: head/science/gromacs/Makefile 498698 2019-04-12 06:36:31Z jbeich $
Log URL:        http://beefy11.nyi.freebsd.org/data/head-i386-default/p499067_s346255/logs/gromacs-2019.1_1.log
Build URL:      http://beefy11.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p499067_s346255
Log:

=>> Building science/gromacs
build started at Tue Apr 16 22:00:06 UTC 2019
port directory: /usr/ports/science/gromacs
package name: gromacs-2019.1_1
building for: FreeBSD head-i386-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300018 i386
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: head/science/gromacs/Makefile 498698 2019-04-12 06:36:31Z jbeich $
Poudriere version: 3.2.8-3-g02cc9753
Host OSVERSION: 1300009
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!!! Jail is newer than host. (Jail: 1300018, Host: 1300009) !!!
!!! 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 gromacs-2019.1_1:
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     THREAD_MPI=on: Build a thread-MPI-based multithreaded version of GROMACS
===> Use 'make config' to modify these settings
---End OPTIONS List---

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=======================<phase: check-sanity   >============================
===>  License LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gromacs-2019.1_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[head-i386-default-job-05] Installing pkg-1.10.5_5...
[head-i386-default-job-05] Extracting pkg-1.10.5_5: .......... done
===>   gromacs-2019.1_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gromacs-2019.1_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2019.1_1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2019.1_1 for building
=> SHA256 Checksum OK for gromacs-2019.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
<snip>
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp
[ 88%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/mdlib/wall.cpp
[ 88%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/mdlib/wnblist.cpp
[ 88%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp
[ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/bonded.cpp
[ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/disre.cpp
[ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/gpubonded-impl.cpp
[ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o
cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11   -O2 -pipe -fstack-protector -fno-strict-aliasing   -fPIC   -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/listed-forces.cpp
[ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o
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c++: error: linker command failed with exit code 1 (use -v to see invocation)
*** Error code 1

Stop.
make[3]: stopped in /wrkdirs/usr/ports/science/gromacs/work/.build
*** Error code 1

Stop.
make[2]: stopped in /wrkdirs/usr/ports/science/gromacs/work/.build
*** Error code 1

Stop.
make[1]: stopped in /wrkdirs/usr/ports/science/gromacs/work/.build
*** Error code 1

Stop.
make: stopped in /usr/ports/science/gromacs



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