[package - 84i386-default][science/pnetcdf] Failed for pnetcdf-1.5.0_2 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Aug 27 04:48:27 UTC 2014
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 at FreeBSD.org
Last committer: tijl at FreeBSD.org
Ident: $FreeBSD: head/science/pnetcdf/Makefile 361800 2014-07-14 16:51:44Z tijl $
Log URL: http://beefy1.isc.freebsd.org/data/84i386-default/2014-08-27_04h26m48s/logs/pnetcdf-1.5.0_2.log
Build URL: http://beefy1.isc.freebsd.org/build.html?mastername=84i386-default&build=2014-08-27_04h26m48s
Log:
====>> Building science/pnetcdf
build started at Wed Aug 27 04:48:04 UTC 2014
port directory: /usr/ports/science/pnetcdf
building for: FreeBSD 84i386-default-job-19 8.4-RELEASE-p14 FreeBSD 8.4-RELEASE-p14 i386
maintained by: sunpoet at FreeBSD.org
Makefile ident: $FreeBSD: head/science/pnetcdf/Makefile 361800 2014-07-14 16:51:44Z tijl $
Poudriere version: 3.1-pre
Host OSVERSION: 1100027
Jail OSVERSION: 804000
---Begin Environment---
UNAME_m=i386
UNAME_p=i386
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/84i386-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_2
OLDPWD=/usr/local/poudriere/data/logs/bulk
PWD=/usr/local/poudriere/data/.m/84i386-default/ref/.p/pool
MASTERNAME=84i386-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_2:
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="gfortran47" FC="gfortran47" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc47" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc47" 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="gfortran47" FC="gfortran47" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc47" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc47" 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/gcc47 -L/usr/local/lib/gcc47 -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 444" 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=""
PORTDATA=""
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---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
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 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_2 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-1.3.7.txz
[84i386-default-job-19] Installing pkg-1.3.7... done
Message for pkg-1.3.7:
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of pnetcdf-1.5.0_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by pnetcdf-1.5.0_2 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by pnetcdf-1.5.0_2 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_2 for building
===> Extracting for pnetcdf-1.5.0_2
=> SHA256 Checksum OK for parallel-netcdf-1.5.0.tar.bz2.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for pnetcdf-1.5.0_2
===> Applying FreeBSD patches for pnetcdf-1.5.0_2
===========================================================================
=======================<phase: build-depends >============================
===> pnetcdf-1.5.0_2 depends on executable: gfortran47 - not found
===> Verifying install for gfortran47 in /usr/ports/lang/gcc
===> Installing existing package /packages/All/gcc-4.7.4.txz
[84i386-default-job-19] Installing indexinfo-0.2... done
[84i386-default-job-19] Installing libiconv-1.14_3... done
[84i386-default-job-19] Installing gettext-0.18.3.1_1... done
[84i386-default-job-19] Installing binutils-2.24... done
[84i386-default-job-19] Installing gcc-ecj-4.5... done
[84i386-default-job-19] Installing gmp-5.1.3_2... done
[84i386-default-job-19] Installing mpfr-3.1.2_2... done
[84i386-default-job-19] Installing mpc-1.0.2... done
[84i386-default-job-19] Installing gcc-4.7.4... done
Message for gcc-4.7.4:
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/gcc47
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> Returning to build of pnetcdf-1.5.0_2
===> pnetcdf-1.5.0_2 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
[84i386-default-job-19] Installing gmake-3.82_1... done
===> Returning to build of pnetcdf-1.5.0_2
===> pnetcdf-1.5.0_2 depends on file: /usr/local/bin/as - found
===> pnetcdf-1.5.0_2 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
[84i386-default-job-19] Installing perl5-5.16.3_11... done
===> Returning to build of pnetcdf-1.5.0_2
===========================================================================
=======================<phase: lib-depends >============================
===> pnetcdf-1.5.0_2 depends on shared library: libmpi.so - not found
===> Verifying for libmpi.so in /usr/ports/net/openmpi
===> Installing existing package /packages/All/openmpi-1.8.1_2.txz
[84i386-default-job-19] Installing pciids-20140810... done
[84i386-default-job-19] Installing libpciaccess-0.13.2_2... done
[84i386-default-job-19] Installing libxml2-2.9.1_1... done
[84i386-default-job-19] Installing hwloc-1.9_1... done
[84i386-default-job-19] Installing libexecinfo-1.1_3... done
[84i386-default-job-19] Installing libltdl-2.4.2_3... done
[84i386-default-job-19] Installing openmpi-1.8.1_2... done
===> Returning to build of pnetcdf-1.5.0_2
===========================================================================
=======================<phase: configure >============================
===> Configuring for pnetcdf-1.5.0_2
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... i386-portbld-freebsd8.4
checking host system type... i386-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/gcc47 -L/usr/local/mpi/openmpi/lib -L/usr/local/bin -L/usr/local/lib/gcc47/gcc/i386-portbld-freebsd8.4/4.7.4 -L/usr/local/lib/gcc47/gcc/i386-portbld-freebsd8.4/4.7.4/../../../../../i386-portbld-freebsd8.4/lib -L/usr/local/lib/gcc47/gcc/i386-portbld-freebsd8.4/4.7.4/../../.. -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 at 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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