Date: Wed, 1 Oct 2014 02:35:15 GMT From: pkg-fallout@FreeBSD.org To: sunpoet@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 84amd64-default][science/pnetcdf] Failed for pnetcdf-1.5.0_5 in configure Message-ID: <201410010235.s912ZFF6049711@beefy2.isc.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: sunpoet@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/science/pnetcdf/Makefile 367888 2014-09-10 20:50:31Z gerald $ Log URL: http://beefy2.isc.freebsd.org/data/84amd64-default/2014-10-01_01h15m56s/logs/pnetcdf-1.5.0_5.log Build URL: http://beefy2.isc.freebsd.org/build.html?mastername=84amd64-default&build=2014-10-01_01h15m56s Log: ====>> Building science/pnetcdf build started at Wed Oct 1 02:34:49 UTC 2014 port directory: /usr/ports/science/pnetcdf building for: FreeBSD 84amd64-default-job-12 8.4-RELEASE-p14 FreeBSD 8.4-RELEASE-p14 amd64 maintained by: sunpoet@FreeBSD.org Makefile ident: $FreeBSD: head/science/pnetcdf/Makefile 367888 2014-09-10 20:50:31Z gerald $ Poudriere version: 3.1-pre Host OSVERSION: 1100027 Jail OSVERSION: 804000 ---Begin Environment--- OSVERSION=804000 UNAME_v=FreeBSD 8.4-RELEASE-p14 UNAME_r=8.4-RELEASE-p14 FTP_PASSIVE_MODE=YES BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/84amd64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=pnetcdf-1.5.0_5 OLDPWD=/root PWD=/usr/local/poudriere/data/.m/84amd64-default/ref/.p/pool MASTERNAME=84amd64-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for pnetcdf-1.5.0_5: DOCS=on: Build and/or install documentation ====> MPI (Message Passing Interface) support: you have to select exactly one of them OPENMPI=on: Parallel processing support via Open MPI MPICH2=off: Parallel processing support via MPICH2 ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --with-mpi=/usr/local/mpi/openmpi --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/pnetcdf/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/pnetcdf/work HOME=/wrkdirs/usr/ports/science/pnetcdf/work TMPDIR="/tmp" F77="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/pnetcdf/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/pnetcdf/work HOME=/wrkdirs/usr/ports/science/pnetcdf/work TMPDIR="/tmp" F77="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" 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="cc" CFLAGS="-O2 -pipe -fPIC -DPIC -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fPIC -DPIC -fno-strict -aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 0644" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=8.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.16.3 PERL_VER=5.16 PERL_ARCH=mach PERL5_MAN3=lib/perl5/5.16/man/man3 SITE_PERL=lib/perl5/site_perl/5.16 DOCSDIR="share/doc/pnetcdf" EXAMPLESDIR="share/examples/pnetcdf" DATADIR="share/pnetcdf" WWWDIR="www/pnetcdf" ETCDIR="etc/pnetcdf" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pnetcdf DOCSDIR=/usr/local/share/doc/pnetcdf EXAMPLESDIR=/usr/local/share/examples/pnetcdf WWWDIR=/usr/local/www/pnetcdf ETCDIR=/usr/local/etc/pnetcdf --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes #WITH_PKGNG=devel # clean-restricted ran via poudriere.conf NO_RESTRICTED #NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> pnetcdf-1.5.0_5 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.3.8_1.txz [84amd64-default-job-12] Installing pkg-1.3.8_1... done Message for pkg-1.3.8_1: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of pnetcdf-1.5.0_5 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by pnetcdf-1.5.0_5 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by pnetcdf-1.5.0_5 for building => SHA256 Checksum OK for parallel-netcdf-1.5.0.tar.bz2. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by pnetcdf-1.5.0_5 for building ===> Extracting for pnetcdf-1.5.0_5 => SHA256 Checksum OK for parallel-netcdf-1.5.0.tar.bz2. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for pnetcdf-1.5.0_5 ===> Applying FreeBSD patches for pnetcdf-1.5.0_5 =========================================================================== =======================<phase: build-depends >============================ ===> pnetcdf-1.5.0_5 depends on executable: gfortran48 - not found ===> Verifying install for gfortran48 in /usr/ports/lang/gcc ===> Installing existing package /packages/All/gcc-4.8.3_1.txz [84amd64-default-job-12] Installing indexinfo-0.2... done [84amd64-default-job-12] Installing libiconv-1.14_4... done [84amd64-default-job-12] Installing gettext-0.18.3.1_1... done [84amd64-default-job-12] Installing binutils-2.24_1... done [84amd64-default-job-12] Installing gcc-ecj-4.5... done [84amd64-default-job-12] Installing gmp-5.1.3_2... done [84amd64-default-job-12] Installing mpfr-3.1.2_2... done [84amd64-default-job-12] Installing mpc-1.0.2_1... done [84amd64-default-job-12] Installing gcc-4.8.3_1... done Message for gcc-4.8.3_1: 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. ===> Returning to build of pnetcdf-1.5.0_5 ===> pnetcdf-1.5.0_5 depends on executable: gmake - not found ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-3.82_1.txz [84amd64-default-job-12] Installing gmake-3.82_1... done ===> Returning to build of pnetcdf-1.5.0_5 ===> pnetcdf-1.5.0_5 depends on file: /usr/local/bin/as - found ===> pnetcdf-1.5.0_5 depends on file: /usr/local/bin/perl5.16.3 - not found ===> Verifying install for /usr/local/bin/perl5.16.3 in /usr/ports/lang/perl5.16 ===> Installing existing package /packages/All/perl5-5.16.3_11.txz [84amd64-default-job-12] Installing perl5-5.16.3_11... done ===> Returning to build of pnetcdf-1.5.0_5 =========================================================================== =======================<phase: lib-depends >============================ ===> pnetcdf-1.5.0_5 depends on shared library: libmpi.so - not found ===> Verifying for libmpi.so in /usr/ports/net/openmpi ===> Installing existing package /packages/All/openmpi-1.8.2_1.txz [84amd64-default-job-12] Installing pciids-20140922... done [84amd64-default-job-12] Installing libpciaccess-0.13.2_2... done [84amd64-default-job-12] Installing libxml2-2.9.1_1... done [84amd64-default-job-12] Installing hwloc-1.9_1... done [84amd64-default-job-12] Installing libexecinfo-1.1_3... done [84amd64-default-job-12] Installing libltdl-2.4.2_3... done [84amd64-default-job-12] Installing openmpi-1.8.2_1... done ===> Returning to build of pnetcdf-1.5.0_5 =========================================================================== =======================<phase: configure >============================ ===> Configuring for pnetcdf-1.5.0_5 configure: loading site script /usr/ports/Templates/config.site checking for mpicc... no checking for mpcc_r... no checking for mpcc... no checking for mpixlc_r... no checking for mpixlc... no checking for blrts_xlc... no checking for mpxlc_r... no checking for mpxlc... no checking for cc... no checking for mpiicc... no checking for icc... no checking for mpicc... /usr/local/mpi/openmpi/bin/mpicc checking for gcc... /usr/local/mpi/openmpi/bin/mpicc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpicc accepts -g... yes checking for /usr/local/mpi/openmpi/bin/mpicc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking how to make dependencies... false checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for malloc.h... (cached) no checking for MPI_Comm_rank... yes checking for MPI_File_open... yes checking for mpicxx... no checking for mpic++... no checking for mpiCC... no checking for mpCC_r... no checking for mpCC... no checking for mpixlcxx_r... no checking for mpixlcxx... no checking for mpixlC_r... no checking for mpixlC... no checking for blrts_xlC... no checking for mpxlC_r... no checking for mpxlC... no checking for CC... no checking for mpiicpc... no checking for icpc... no checking for mpicxx... /usr/local/mpi/openmpi/bin/mpicxx checking whether we are using the GNU C++ compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpicxx accepts -g... yes checking for MPI_File_close... yes checking for mpif77... no checking for mpixlf77_r... no checking for mpixlf77... no checking for blrts_xlf... no checking for mpxlf_r... no checking for mpxlf... no checking for ftn... no checking for mpiifort... no checking for mpiifc... no checking for ifort... no checking for mpif77... /usr/local/mpi/openmpi/bin/mpif77 checking for mpif90... no checking for mpixlf90_r... no checking for mpixlf90... no checking for blrts_xlf90... no checking for mpxlf90_r... no checking for mpxlf90... no checking for mpxlf95_r... no checking for mpxlf95... no checking for ftn... no checking for mpiifort... no checking for mpiifc... no checking for ifort... no checking for mpif90... /usr/local/mpi/openmpi/bin/mpif90 checking whether we are using the GNU Fortran compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpif90 accepts -g... yes checking for Fortran flag to compile preprocessed .F files... none checking for Fortran flag to compile preprocessed .F90 files... none checking for Fortran flag to compile preprocessed .F files... (cached) none checking how to define symbols for preprocessed Fortran... -D checking for Fortran flag to compile .f90 files... none checking for Fortran flag needed to accept fixed-form source... -ffixed-form checking for Fortran flag to compile .f files... none checking whether we are using the GNU Fortran 77 compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpif77 accepts -g... yes checking for Fortran flag needed to accept free-form source... -ffree-form checking build system type... amd64-portbld-freebsd8.4 checking host system type... amd64-portbld-freebsd8.4 checking how to get verbose linking output from /usr/local/mpi/openmpi/bin/mpif90... -v checking for Fortran libraries of /usr/local/mpi/openmpi/bin/mpif90... -L/usr/local/lib/gcc48 -L/usr/local/mpi/openmpi/lib -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd8.4/4.8.3 -L/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd8.4/4.8.3/../../../../../x86_64-portbld-freebsd8.4/lib -L/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd8.4/4.8.3/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for C-equivalent to Fortran routine "SUB_A"... sub_a_ checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel checking for bison... no checking for byacc... byacc checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking for gawk... (cached) /usr/bin/awk checking whether ln -s works... yes checking whether gmake sets $(MAKE)... yes checking for egrep... (cached) /usr/bin/egrep checking for m4... m4 checking m4 flags... ./configure: 8694: Syntax error: Bad fd number ===> Script "configure" failed unexpectedly. Please report the problem to sunpoet@FreeBSD.org [maintainer] and attach the "/wrkdirs/usr/ports/science/pnetcdf/work/parallel-netcdf-1.5.0/config.log" including the output of the failure of your make command. Also, it might be a good idea to provide an overview of all packages installed on your system (e.g. a /usr/local/sbin/pkg-static info -g -Ea). *** Error code 1 Stop in /usr/ports/science/pnetcdf.
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