[package - head-powerpc64-default][science/gromacs] Failed for gromacs-2020_1 in configure

pkg-fallout at FreeBSD.org pkg-fallout at FreeBSD.org
Sat Feb 22 09:55:24 UTC 2020


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 at FreeBSD.org
Last committer: antoine at FreeBSD.org
Ident:          $FreeBSD: head/science/gromacs/Makefile 525285 2020-02-05 17:35:05Z antoine $
Log URL:        http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p526244_s356047/logs/gromacs-2020_1.log
Build URL:      http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p526244_s356047
Log:

=>> Building science/gromacs
build started at Sat Feb 22 09:51:52 UTC 2020
port directory: /usr/ports/science/gromacs
package name: gromacs-2020_1
building for: FreeBSD head-powerpc64-default-job-17 13.0-CURRENT FreeBSD 13.0-CURRENT 1300068 powerpc
maintained by: yuri at FreeBSD.org
Makefile ident:      $FreeBSD: head/science/gromacs/Makefile 525285 2020-02-05 17:35:05Z antoine $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300047
Jail OSVERSION: 1300068
Job Id: 17




!!! Jail is newer than host. (Jail: 1300068, Host: 1300047) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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---Begin OPTIONS List---
===> The following configuration options are available for gromacs-2020_1:
     ATLAS=off: Use ATLAS for BLAS and LAPACK
     FLOAT=on: Use single instead of double precision
     OPENCL=off: Heterogeneous computing via OpenCL
     OPENMP=on: Parallel processing support via OpenMP
     SIMD=off: Use CPU-specific optimizations
     X11=on: X11 (graphics) support
====> Multiprocessing: you have to select exactly one of them
     NOMP=off: No multiprocessing support
     MPICH=off: Parallel processing support via MPICH
     OPENMPI=off: Parallel processing support via Open MPI
     THREAD_MPI=on: Build a thread-MPI-based multithreaded version of GROMACS
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
yuri at FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

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--End PLIST_SUB--

--SUB_LIST--
ATLAS="@comment " NO_ATLAS="" FLOAT="" NO_FLOAT="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL="@comment " NO_OPENCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " X11="" NO_X11="@comment " PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/gromacs DOCSDIR=/usr/local/share/doc/gromacs EXAMPLESDIR=/usr/local/share/examples/gromacs  WWWDIR=/usr/local/www/gromacs ETCDIR=/usr/local/etc/gromacs
--End SUB_LIST--

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#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
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MAKE_JOBS_NUMBER=4
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11"
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11"
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x"
CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11"
CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
_OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=powerpc64
PPC_ABI=ELFv1
OPSYS=FreeBSD
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OSREL=13.0
OSVERSION=1300068
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
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GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
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file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  33554432
stack size              (kbytes, -s)  524288
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
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--End resource limits--
=======================<phase: check-sanity   >============================
===>  License LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gromacs-2020_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.13.1.txz
[head-powerpc64-default-job-17] Installing pkg-1.13.1...
[head-powerpc64-default-job-17] Extracting pkg-1.13.1: .......... done
===>   gromacs-2020_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gromacs-2020_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2020_1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2020_1 for building
=> SHA256 Checksum OK for gromacs-2020.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2020_1 for building
===>  Extracting for gromacs-2020_1
=> SHA256 Checksum OK for gromacs-2020.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
<snip>
the second will work as long as perl is in PATH.
=====
Message from python37-3.7.6:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py37-gdbm       databases/py-gdbm at py37
py37-sqlite3    databases/py-sqlite3 at py37
py37-tkinter    x11-toolkits/py-tkinter at py37
===>   gromacs-2020_1 depends on executable: clang90 - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on package: fftw3>0 - not found
===>   Installing existing package /packages/All/fftw3-3.3.8_5.txz
[head-powerpc64-default-job-17] Installing fftw3-3.3.8_5...
[head-powerpc64-default-job-17] Extracting fftw3-3.3.8_5: .......... done
===>   gromacs-2020_1 depends on package: fftw3>0 - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.16.4.txz
[head-powerpc64-default-job-17] Installing cmake-3.16.4...
[head-powerpc64-default-job-17] `-- Installing curl-7.68.0...
[head-powerpc64-default-job-17] |   `-- Installing ca_root_nss-3.50...
[head-powerpc64-default-job-17] |   `-- Extracting ca_root_nss-3.50: ........ done
[head-powerpc64-default-job-17] |   `-- Installing libnghttp2-1.40.0...
[head-powerpc64-default-job-17] |   `-- Extracting libnghttp2-1.40.0: .......... done
[head-powerpc64-default-job-17] `-- Extracting curl-7.68.0: .......... done
[head-powerpc64-default-job-17] `-- Installing expat-2.2.8...
[head-powerpc64-default-job-17] `-- Extracting expat-2.2.8: .......... done
[head-powerpc64-default-job-17] `-- Installing jsoncpp-1.9.2...
[head-powerpc64-default-job-17] `-- Extracting jsoncpp-1.9.2: .......... done
[head-powerpc64-default-job-17] `-- Installing libarchive-3.4.0,1...
[head-powerpc64-default-job-17] |   `-- Installing liblz4-1.9.2_1,1...
[head-powerpc64-default-job-17] |   `-- Extracting liblz4-1.9.2_1,1: .......... done
[head-powerpc64-default-job-17] |   `-- Installing lzo2-2.10_1...
[head-powerpc64-default-job-17] |   `-- Extracting lzo2-2.10_1: .......... done
[head-powerpc64-default-job-17] `-- Extracting libarchive-3.4.0,1: .......... done
[head-powerpc64-default-job-17] `-- Installing libuv-1.34.2...
[head-powerpc64-default-job-17] `-- Extracting libuv-1.34.2: .......... done
[head-powerpc64-default-job-17] `-- Installing rhash-1.3.5...
[head-powerpc64-default-job-17] `-- Extracting rhash-1.3.5: .......... done
[head-powerpc64-default-job-17] Extracting cmake-3.16.4: .......... done
=====
Message from ca_root_nss-3.50:

--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.

Assessment and verification of trust is the complete responsibility of the
system administrator.


This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.

This enables SSL Certificate Verification by client software without manual
intervention.

If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.

  * /etc/ssl/cert.pem
  * /usr/local/etc/ssl/cert.pem
  * /usr/local/openssl/cert.pem
===>   gromacs-2020_1 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on executable: gfortran9 - found
===>   gromacs-2020_1 depends on package: pkgconf>=1.3.0_1 - not found
===>   Installing existing package /packages/All/pkgconf-1.6.3,1.txz
[head-powerpc64-default-job-17] Installing pkgconf-1.6.3,1...
[head-powerpc64-default-job-17] Extracting pkgconf-1.6.3,1: .......... done
===>   gromacs-2020_1 depends on package: pkgconf>=1.3.0_1 - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on file: /usr/local/bin/as - found
===>   gromacs-2020_1 depends on package: perl5>=5.30.r1<5.31 - found
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/ice.pc - not found
===>   Installing existing package /packages/All/libICE-1.0.10,1.txz
[head-powerpc64-default-job-17] Installing libICE-1.0.10,1...
[head-powerpc64-default-job-17] Extracting libICE-1.0.10,1: .......... done
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/sm.pc - not found
===>   Installing existing package /packages/All/libSM-1.2.3,1.txz
[head-powerpc64-default-job-17] Installing libSM-1.2.3,1...
[head-powerpc64-default-job-17] Extracting libSM-1.2.3,1: .......... done
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/xext.pc - not found
===>   Installing existing package /packages/All/libXext-1.3.4,1.txz
[head-powerpc64-default-job-17] Installing libXext-1.3.4,1...
[head-powerpc64-default-job-17] `-- Installing libX11-1.6.9,1...
[head-powerpc64-default-job-17] |   `-- Installing libXau-1.0.9...
[head-powerpc64-default-job-17] |   `-- Extracting libXau-1.0.9: .......... done
[head-powerpc64-default-job-17] |   `-- Installing libXdmcp-1.1.3...
[head-powerpc64-default-job-17] |   | `-- Installing xorgproto-2019.2...
[head-powerpc64-default-job-17] |   | `-- Extracting xorgproto-2019.2: .......... done
[head-powerpc64-default-job-17] |   `-- Extracting libXdmcp-1.1.3: ......... done
[head-powerpc64-default-job-17] |   `-- Installing libxcb-1.13.1...
[head-powerpc64-default-job-17] |   | `-- Installing libpthread-stubs-0.4...
[head-powerpc64-default-job-17] |   | `-- Extracting libpthread-stubs-0.4: .... done
[head-powerpc64-default-job-17] |   `-- Extracting libxcb-1.13.1: .......... done
[head-powerpc64-default-job-17] `-- Extracting libX11-1.6.9,1: .......... done
[head-powerpc64-default-job-17] Extracting libXext-1.3.4,1: .......... done
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   gromacs-2020_1 depends on shared library: libhwloc.so - not found
===>   Installing existing package /packages/All/hwloc-1.11.11.txz
[head-powerpc64-default-job-17] Installing hwloc-1.11.11...
[head-powerpc64-default-job-17] `-- Installing libpciaccess-0.16...
[head-powerpc64-default-job-17] |   `-- Installing pciids-20200125...
[head-powerpc64-default-job-17] |   `-- Extracting pciids-20200125: ..... done
[head-powerpc64-default-job-17] `-- Extracting libpciaccess-0.16: ......... done
[head-powerpc64-default-job-17] Extracting hwloc-1.11.11: .......... done
===>   gromacs-2020_1 depends on shared library: libhwloc.so - found (/usr/local/lib/libhwloc.so)
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on shared library: libfftw3f.so - not found
===>   Installing existing package /packages/All/fftw3-float-3.3.8_5.txz
[head-powerpc64-default-job-17] Installing fftw3-float-3.3.8_5...
[head-powerpc64-default-job-17] Extracting fftw3-float-3.3.8_5: .......... done
===>   gromacs-2020_1 depends on shared library: libfftw3f.so - found (/usr/local/lib/libfftw3f.so)
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on shared library: libomp.so - found (/usr/local/llvm90/lib/libomp.so)
===>   gromacs-2020_1 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===>   gromacs-2020_1 depends on shared library: libblas.so - not found
===>   Installing existing package /packages/All/blas-3.5.0_6.txz
[head-powerpc64-default-job-17] Installing blas-3.5.0_6...
[head-powerpc64-default-job-17] Extracting blas-3.5.0_6: ....... done
===>   gromacs-2020_1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===>   Returning to build of gromacs-2020_1
===>   gromacs-2020_1 depends on shared library: liblapack.so - not found
===>   Installing existing package /packages/All/lapack-3.5.0_8.txz
[head-powerpc64-default-job-17] Installing lapack-3.5.0_8...
[head-powerpc64-default-job-17] Extracting lapack-3.5.0_8: .......... done
===>   gromacs-2020_1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===>   Returning to build of gromacs-2020_1
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for gromacs-2020_1
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/gromacs/work/.build
-- The C compiler identification is Clang 9.0.1
-- The CXX compiler identification is Clang 9.0.1
-- Check for working C compiler: /usr/local/bin/clang90
-- Check for working C compiler: /usr/local/bin/clang90 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/local/bin/clang++90
-- Check for working CXX compiler: /usr/local/bin/clang++90 -- broken
CMake Error at /usr/local/share/cmake/Modules/CMakeTestCXXCompiler.cmake:53 (message):
  The C++ compiler

    "/usr/local/bin/clang++90"

  is not able to compile a simple test program.

  It fails with the following output:

    Change Dir: /wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeTmp
    
    Run Build Command(s):/usr/bin/make cmTC_4a315/fast && /usr/bin/make -f CMakeFiles/cmTC_4a315.dir/build.make CMakeFiles/cmTC_4a315.dir/build
    Building CXX object CMakeFiles/cmTC_4a315.dir/testCXXCompiler.cxx.o
    /usr/local/bin/clang++90    -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o CMakeFiles/cmTC_4a315.dir/testCXXCompiler.cxx.o -c /wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
    Linking CXX executable cmTC_4a315
    /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_4a315.dir/link.txt --verbose=1
    /usr/local/bin/clang++90  -O2 -pipe -fstack-protector-strong -fno-strict-aliasing    -Wl,-rpath=/usr/local/lib/gcc9  -L/usr/local/lib/gcc9 -B/usr/local/bin -L/usr/local/lib -fstack-protector-strong  CMakeFiles/cmTC_4a315.dir/testCXXCompiler.cxx.o  -o cmTC_4a315 
    /usr/local/bin/ld: cannot find -lc++
    clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
    *** Error code 1
    
    Stop.
    make[2]: stopped in /wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeTmp
    *** Error code 1
    
    Stop.
    make[1]: stopped in /wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeTmp
    
    

  

  CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
  CMakeLists.txt:57 (project)


-- Configuring incomplete, errors occurred!
See also "/wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeOutput.log".
See also "/wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeError.log".
*** Error code 1

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


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