Date: Sat, 31 Oct 2015 12:44:11 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][science/gromacs] Failed for gromacs-5.0.6 in configure Message-ID: <201510311244.t9VCiBoI007556@beefy8.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: freebsd@skysmurf.nl Last committer: amdmi3@FreeBSD.org Ident: $FreeBSD: head/science/gromacs/Makefile 394419 2015-08-16 21:31:41Z amdmi3 $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p400328_s290048/logs/gromacs-5.0.6.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p400328_s290048 Log: ====>> Building science/gromacs build started at Sat Oct 31 12:38:10 UTC 2015 port directory: /usr/ports/science/gromacs building for: FreeBSD head-armv6-default-job-05 11.0-CURRENT FreeBSD 11.0-CURRENT r290048 arm maintained by: freebsd@skysmurf.nl Makefile ident: $FreeBSD: head/science/gromacs/Makefile 394419 2015-08-16 21:31:41Z amdmi3 $ Poudriere version: 3.1.9 Host OSVERSION: 1100079 Jail OSVERSION: 1100083 !!! Jail is newer than host. (Jail: 1100083, Host: 1100079) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1100083 UNAME_v=FreeBSD 11.0-CURRENT r290048 UNAME_r=11.0-CURRENT LC_COLLATE=C BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=gromacs-5.0.6 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.9 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for gromacs-5.0.6: ATLAS=off: Use ATLAS for BLAS and LAPACK FLOAT=on: Use single instead of double precision OPENMP=on: Parallel processing support via OpenMP SIMD=off: Use CPU-specific optimizations X11=on: X11 (graphics) support ====> MPI (Message Passing Interface) support: you can only select none or one of them MPICH2=off: Parallel processing support via MPICH2 OPENMPI=off: Parallel processing support via Open MPI ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" NO_PIE=yes SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc48" CFLAGS="-O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing" CPP="cpp48" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -B/usr/local/bin -L/usr/local/lib - Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS="" CXX="g++48" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- ATLAS="@comment " NO_ATLAS="" FLOAT="" NO_FLOAT="@comment " OPENMP="" NO_OPENMP="@comment " SIMD="@comment " NO_SIMD="" X11="" NO_X11="@comment " MPICH2="@comment " NO_MPICH2="" OPENMPI="@comment " NO_OPENMPI="" SUFFIX_D="" SUFFIX_MPI="" CMAKE_BUILD_TYPE="release" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" PERL_VERSION=5.20.3 PERL_VER=5.20 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.20 DOCSDIR="share/doc/gromacs" EXAMPLESDIR="share/examples/gromacs" DATADIR="share/gromacs" WWWDIR="www/gromacs" ETCDIR="etc/gromacs" --End PLIST_SUB-- --SUB_LIST-- ATLAS="@comment " NO_ATLAS="" FLOAT="" NO_FLOAT="@comment " OPENMP="" NO_OPENMP="@comment " SIMD="@comment " NO_SIMD="" X11="" NO_X11="@comment " MPICH2="@comment " NO_MPICH2="" OPENMPI="@comment " NO_OPENMPI="" 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-- ---Begin make.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip <snip> [head-armv6-default-job-05] `-- Installing curl-7.45.0... [head-armv6-default-job-05] | `-- Installing ca_root_nss-3.20... [head-armv6-default-job-05] | `-- Extracting ca_root_nss-3.20: ....... done [head-armv6-default-job-05] `-- Extracting curl-7.45.0: .......... done [head-armv6-default-job-05] `-- Installing libarchive-3.1.2_4,1... [head-armv6-default-job-05] | `-- Installing lzo2-2.09... [head-armv6-default-job-05] | `-- Extracting lzo2-2.09: .......... done [head-armv6-default-job-05] `-- Extracting libarchive-3.1.2_4,1: .......... done [head-armv6-default-job-05] `-- Installing jsoncpp-0.6.0.r2_2... [head-armv6-default-job-05] `-- Extracting jsoncpp-0.6.0.r2_2: .......... done [head-armv6-default-job-05] Extracting cmake-3.3.1: .......... done Message from ca_root_nss-3.20: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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-5.0.6 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on executable: gfortran48 - not found ===> Installing existing package /packages/All/gcc-4.8.5.txz [head-armv6-default-job-05] Installing gcc-4.8.5... [head-armv6-default-job-05] `-- Installing mpc-1.0.3... [head-armv6-default-job-05] | `-- Installing gmp-5.1.3_2... [head-armv6-default-job-05] | `-- Extracting gmp-5.1.3_2: .......... done [head-armv6-default-job-05] | `-- Installing mpfr-3.1.2_2... [head-armv6-default-job-05] | `-- Extracting mpfr-3.1.2_2: .......... done [head-armv6-default-job-05] `-- Extracting mpc-1.0.3: ...... done [head-armv6-default-job-05] `-- Installing binutils-2.25.1... [head-armv6-default-job-05] | `-- Installing gettext-runtime-0.19.6... [head-armv6-default-job-05] | `-- Extracting gettext-runtime-0.19.6: .......... done [head-armv6-default-job-05] `-- Extracting binutils-2.25.1: .......... done [head-armv6-default-job-05] Extracting gcc-4.8.5: .......... done Message from gcc-4.8.5: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc48 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> gromacs-5.0.6 depends on executable: gfortran48 - found ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on executable: pkgconf - not found ===> Installing existing package /packages/All/pkgconf-0.9.12_1.txz [head-armv6-default-job-05] Installing pkgconf-0.9.12_1... [head-armv6-default-job-05] Extracting pkgconf-0.9.12_1: ....... done ===> gromacs-5.0.6 depends on executable: pkgconf - found ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on executable: gcc48 - found ===> gromacs-5.0.6 depends on file: /usr/local/bin/as - found ===> gromacs-5.0.6 depends on file: /usr/local/libdata/pkgconfig/xext.pc - not found ===> Installing existing package /packages/All/libXext-1.3.3_1,1.txz [head-armv6-default-job-05] Installing libXext-1.3.3_1,1... [head-armv6-default-job-05] `-- Installing xproto-7.0.28... [head-armv6-default-job-05] `-- Extracting xproto-7.0.28: .......... done [head-armv6-default-job-05] `-- Installing libXau-1.0.8_3... [head-armv6-default-job-05] `-- Extracting libXau-1.0.8_3: .......... done [head-armv6-default-job-05] `-- Installing libX11-1.6.3,1... [head-armv6-default-job-05] | `-- Installing kbproto-1.0.7... [head-armv6-default-job-05] | `-- Extracting kbproto-1.0.7: .......... done [head-armv6-default-job-05] | `-- Installing libXdmcp-1.1.2... [head-armv6-default-job-05] | `-- Extracting libXdmcp-1.1.2: ......... done [head-armv6-default-job-05] | `-- Installing libxcb-1.11.1... [head-armv6-default-job-05] | | `-- Installing libxml2-2.9.2_3... [head-armv6-default-job-05] | | `-- Extracting libxml2-2.9.2_3: .......... done [head-armv6-default-job-05] | | `-- Installing libpthread-stubs-0.3_6... [head-armv6-default-job-05] | | `-- Extracting libpthread-stubs-0.3_6: ..... done [head-armv6-default-job-05] | `-- Extracting libxcb-1.11.1: .......... done [head-armv6-default-job-05] `-- Extracting libX11-1.6.3,1: .......... done [head-armv6-default-job-05] `-- Installing xextproto-7.3.0... [head-armv6-default-job-05] `-- Extracting xextproto-7.3.0: .......... done [head-armv6-default-job-05] Extracting libXext-1.3.3_1,1: .......... done ===> gromacs-5.0.6 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> gromacs-5.0.6 depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_8.txz [head-armv6-default-job-05] Installing perl5-5.20.3_8... [head-armv6-default-job-05] Extracting perl5-5.20.3_8: .......... done Message from perl5-5.20.3_8: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> gromacs-5.0.6 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of gromacs-5.0.6 =========================================================================== =======================<phase: lib-depends >============================ ===> gromacs-5.0.6 depends on shared library: libfftw3f.so - not found ===> Installing existing package /packages/All/fftw3-float-3.3.3_2.txz [head-armv6-default-job-05] Installing fftw3-float-3.3.3_2... [head-armv6-default-job-05] Extracting fftw3-float-3.3.3_2: .......... done ===> gromacs-5.0.6 depends on shared library: libfftw3f.so - found (/usr/local/lib/libfftw3f.so) ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on shared library: libblas.so - not found ===> Installing existing package /packages/All/blas-3.5.0_3.txz [head-armv6-default-job-05] Installing blas-3.5.0_3... [head-armv6-default-job-05] Extracting blas-3.5.0_3: ....... done ===> gromacs-5.0.6 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.5.0.txz [head-armv6-default-job-05] Installing lapack-3.5.0... [head-armv6-default-job-05] Extracting lapack-3.5.0: .......... done ===> gromacs-5.0.6 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of gromacs-5.0.6 ===> gromacs-5.0.6 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for gromacs-5.0.6 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6 -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/local/bin/gcc48 CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_d890d/fast" -- Check for working C compiler: /usr/local/bin/gcc48 -- broken CMake Error at /usr/local/share/cmake/Modules/CMakeTestCCompiler.cmake:61 (message): The C compiler "/usr/local/bin/gcc48" is not able to compile a simple test program. It fails with the following output: Change Dir: /wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeTmp Run Build Command:"/usr/bin/make" "cmTC_d890d/fast" /nxb-bin/usr/bin/make -f CMakeFiles/cmTC_d890d.dir/build.make CMakeFiles/cmTC_d890d.dir/build Building C object CMakeFiles/cmTC_d890d.dir/testCCompiler.c.o /usr/local/bin/gcc48 -O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -o CMakeFiles/cmTC_d890d.dir/testCCompiler.c.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeTmp/testCCompiler.c Linking C executable cmTC_d890d /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_d890d.dir/link.txt --verbose=1 /usr/local/bin/gcc48 -O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing CMakeFiles/cmTC_d890d.dir/testCCompiler.c.o -o cmTC_d890d Process terminated due to timeout Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_d890d/fast" CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:45 (project) -- Configuring incomplete, errors occurred! See also "/wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeOutput.log". See also "/wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeError.log". *** Error code 1 Stop. make: stopped in /usr/ports/science/gromacs
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