Attachment 383993 Details for Bug 555450 – build.log

build.log

build.log (text/plain), 11.84 KB, created by FTBFS on 2010-01-14 17:25:32 UTC

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Creator: FTBFS

Created: 2010-01-14 17:25:32 UTC

Size: 11.84 KB

patch

obsolete

>Mock Version: 1.0.1
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-RScaLAPACK.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-RScaLAPACK-0.5.1-21.fc12.src.rpm/root/', None, 25200, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x1f69850>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-RScaLAPACK.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Wrote: /builddir/build/SRPMS/R-RScaLAPACK-0.5.1-21.fc13.src.rpm
>Child returncode was: 0
>LEAVE do --> 
>
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-RScaLAPACK.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-RScaLAPACK-0.5.1-21.fc12.src.rpm/root/', None, 25200, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x1f69850>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-RScaLAPACK.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.OL4TCQ
>+ umask 022
>+ cd /builddir/build/BUILD
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ cd /builddir/build/BUILD
>+ rm -rf RScaLAPACK
>+ /bin/mkdir -p RScaLAPACK
>+ cd RScaLAPACK
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/RScaLAPACK_0.5.1.tar.gz
>+ /bin/tar -xf -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ echo 'Patch #0 (R-RScaLAPACK-0.5.1-mpi-blacs.patch):'
>Patch #0 (R-RScaLAPACK-0.5.1-mpi-blacs.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-mpi-blacs.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ echo 'Patch #1 (R-RScaLAPACK-0.5.1-gcc4.patch):'
>Patch #1 (R-RScaLAPACK-0.5.1-gcc4.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-gcc4.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ echo 'Patch #3 (R-RScaLAPACK-0.5.1-configurefix.patch):'
>Patch #3 (R-RScaLAPACK-0.5.1-configurefix.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-configurefix.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ echo 'Patch #4 (R-RScaLAPACK-0.5.1-blacsfix.patch):'
>Patch #4 (R-RScaLAPACK-0.5.1-blacsfix.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-blacsfix.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ echo 'Patch #5 (R-RScaLAPACK-0.5.1-mpi_comm_create_.patch):'
>Patch #5 (R-RScaLAPACK-0.5.1-mpi_comm_create_.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-mpi_comm_create_.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ echo 'Patch #6 (R-RScaLAPACK-0.5.1-mpicc.patch):'
>Patch #6 (R-RScaLAPACK-0.5.1-mpicc.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-mpicc.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ echo 'Patch #7 (R-RScaLAPACK-0.5.1-openmpi.patch):'
>Patch #7 (R-RScaLAPACK-0.5.1-openmpi.patch):
>+ /bin/cat /builddir/build/SOURCES/R-RScaLAPACK-0.5.1-openmpi.patch
>+ /usr/bin/patch -s -p1 --fuzz=0
>+ cd RScaLAPACK
>++ R CMD config CC
>+ R_CC='gcc -m64 -std=gnu99'
>++ R CMD config F77
>+ R_F77='gfortran -m64'
>++ R CMD config SHLIB_LD
>+ R_SHLIB_LD='gcc -m64 -std=gnu99'
>++ echo gcc -m64 -std=gnu99
>++ sed 's|gcc|mpicc|'
>+ MPICC='mpicc -m64 -std=gnu99'
>++ echo gfortran -m64
>++ sed 's|gfortran|mpif77|'
>+ MPIF77='mpif77 -m64'
>++ echo gcc -m64 -std=gnu99
>++ sed 's|gcc|mpicc|'
>+ MPISHLIB_LD='mpicc -m64 -std=gnu99'
>+ sed -i 's|@MPICC@|mpicc -m64 -std=gnu99|g' configure.in
>+ sed -i 's|@MPIF77@|mpif77 -m64|g' configure.in
>+ sed -i 's|@MPICC@|mpicc -m64 -std=gnu99|g' src/Makefile.in
>+ sed -i 's|@MPISHLIB_LD@|mpicc -m64 -std=gnu99|' src/Makefile.in
>+ aclocal
>+ autoconf
>+ exit 0
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.RdSCol
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd RScaLAPACK
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ exit 0
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.rf31aQ
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64
>++ dirname /builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64
>+ cd RScaLAPACK
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ mkdir -p /builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64/usr/lib64/R/library
>+ export MPI_COMPILER=openmpi
>+ MPI_COMPILER=openmpi
>+ . /etc/profile.d/modules.sh
>++++ /bin/ps -p 1801 -ocomm=
>+++ /bin/basename sh
>++ shell=sh
>++ '[' -f /usr/share/Modules/init/sh ']'
>++ . /usr/share/Modules/init/sh
>+++ MODULESHOME=/usr/share/Modules
>+++ export MODULESHOME
>+++ '[' '' = '' ']'
>+++ LOADEDMODULES=
>+++ export LOADEDMODULES
>+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
>+ module load openmpi-x86_64
>++ /usr/bin/modulecmd sh load openmpi-x86_64
>+ eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=openmpi-x86_64' ';export' 'LOADEDMODULES;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64%\{_cc_name_suffix\}' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi@' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/bin:/usr/local/sbin:/builddir/bin' ';export' 'PATH;_LMFILES_=/etc/modulefiles/openmpi-x86_64' ';export' '_LMFILES_;'
>++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib
>++ export LD_LIBRARY_PATH
>++ LOADEDMODULES=openmpi-x86_64
>++ export LOADEDMODULES
>++ MPI_BIN=/usr/lib64/openmpi/bin
>++ export MPI_BIN
>++ MPI_COMPILER='openmpi-x86_64%{_cc_name_suffix}'
>++ export MPI_COMPILER
>++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64
>++ export MPI_FORTRAN_MOD_DIR
>++ MPI_HOME=/usr/lib64/openmpi@
>++ export MPI_HOME
>++ MPI_INCLUDE=/usr/include/openmpi-x86_64
>++ export MPI_INCLUDE
>++ MPI_LIB=/usr/lib64/openmpi/lib
>++ export MPI_LIB
>++ MPI_MAN=/usr/share/man/openmpi-x86_64
>++ export MPI_MAN
>++ MPI_PYTHON_SITEARCH=/openmpi
>++ export MPI_PYTHON_SITEARCH
>++ MPI_SUFFIX=_openmpi
>++ export MPI_SUFFIX
>++ MPI_SYSCONFIG=/etc/openmpi-x86_64
>++ export MPI_SYSCONFIG
>++ PATH=/usr/lib64/openmpi/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/bin:/usr/local/sbin:/builddir/bin
>++ export PATH
>++ _LMFILES_=/etc/modulefiles/openmpi-x86_64
>++ export _LMFILES_
>+ export CFLAGS=
>+ CFLAGS=
>+ OPENMPICFLAGS=
>+ OPENMPILDFLAGS=
>+ . /etc/profile.d/modules.sh
>++++ /bin/ps -p 1801 -ocomm=
>+++ /bin/basename sh
>++ shell=sh
>++ '[' -f /usr/share/Modules/init/sh ']'
>++ . /usr/share/Modules/init/sh
>+++ MODULESHOME=/usr/share/Modules
>+++ export MODULESHOME
>+++ '[' openmpi-x86_64 = '' ']'
>+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
>+ module load blacs-openmpi-x86_64
>++ /usr/bin/modulecmd sh load blacs-openmpi-x86_64
>+ eval LDFLAGS=-L/usr/lib64/blacs-openmpi ';export' 'LDFLAGS;LD_LIBRARY_PATH=/usr/lib64/blacs-openmpi:/usr/lib64/openmpi/lib' ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=openmpi-x86_64:blacs-openmpi-x86_64' ';export' 'LOADEDMODULES;_LMFILES_=/etc/modulefiles/openmpi-x86_64:/usr/share/Modules/modulefiles/blacs-openmpi-x86_64' ';export' '_LMFILES_;'
>++ LDFLAGS=-L/usr/lib64/blacs-openmpi
>++ export LDFLAGS
>++ LD_LIBRARY_PATH=/usr/lib64/blacs-openmpi:/usr/lib64/openmpi/lib
>++ export LD_LIBRARY_PATH
>++ LOADEDMODULES=openmpi-x86_64:blacs-openmpi-x86_64
>++ export LOADEDMODULES
>++ _LMFILES_=/etc/modulefiles/openmpi-x86_64:/usr/share/Modules/modulefiles/blacs-openmpi-x86_64
>++ export _LMFILES_
>+ export CFLAGS=
>+ CFLAGS=
>+ BLACSCFLAGS=
>+ BLACSLDFLAGS=-L/usr/lib64/blacs-openmpi
>+ . /etc/profile.d/modules.sh
>++++ /bin/ps -p 1801 -ocomm=
>+++ /bin/basename sh
>++ shell=sh
>++ '[' -f /usr/share/Modules/init/sh ']'
>++ . /usr/share/Modules/init/sh
>+++ MODULESHOME=/usr/share/Modules
>+++ export MODULESHOME
>+++ '[' openmpi-x86_64:blacs-openmpi-x86_64 = '' ']'
>+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
>+ module load scalapack-openmpi-x86_64
>++ /usr/bin/modulecmd sh load scalapack-openmpi-x86_64
>+ eval LDFLAGS=-L/usr/lib64/scalapack-openmpi ';export' 'LDFLAGS;LD_LIBRARY_PATH=/usr/lib64/scalapack-openmpi:/usr/lib64/blacs-openmpi:/usr/lib64/openmpi/lib' ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=openmpi-x86_64:blacs-openmpi-x86_64:scalapack-openmpi-x86_64' ';export' 'LOADEDMODULES;_LMFILES_=/etc/modulefiles/openmpi-x86_64:/usr/share/Modules/modulefiles/blacs-openmpi-x86_64:/usr/share/Modules/modulefiles/scalapack-openmpi-x86_64' ';export' '_LMFILES_;'
>++ LDFLAGS=-L/usr/lib64/scalapack-openmpi
>++ export LDFLAGS
>++ LD_LIBRARY_PATH=/usr/lib64/scalapack-openmpi:/usr/lib64/blacs-openmpi:/usr/lib64/openmpi/lib
>++ export LD_LIBRARY_PATH
>++ LOADEDMODULES=openmpi-x86_64:blacs-openmpi-x86_64:scalapack-openmpi-x86_64
>++ export LOADEDMODULES
>++ _LMFILES_=/etc/modulefiles/openmpi-x86_64:/usr/share/Modules/modulefiles/blacs-openmpi-x86_64:/usr/share/Modules/modulefiles/scalapack-openmpi-x86_64
>++ export _LMFILES_
>+ export CFLAGS=
>+ CFLAGS=
>+ RPM_OPT_FLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
>+ /usr/bin/R CMD INSTALL '--configure-args=--with-blas=/usr/lib64 CC='\''mpicc'\'' F77='\''mpif77'\'' CFLAGS='\'' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -L/usr/lib64/scalapack-openmpi -L/usr/lib64/blacs-openmpi  -lutil -lmpiblacsCinit -lmpiblacs -lmpi -llapack'\'' FFLAGS='\'' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -L/usr/lib64/scalapack-openmpi -L/usr/lib64/blacs-openmpi  -lutil -llapack -lmpi'\''' -l /builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64/usr/lib64/R/library RScaLAPACK
>WARNING: unknown gui '-pipe', using X11
>* installing *source* package 'RScaLAPACK' ...
>configure: BLAS_LIB=/usr/lib64 .. is set
>checking for gcc... mpicc -m64 -std=gnu99
>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 mpicc -m64 -std=gnu99 accepts -g... yes
>checking for mpicc -m64 -std=gnu99 option to accept ISO C89... none needed
>checking for pthread_atfork in -lpthread... yes
>checking for LAM-MPI... checking LAM-MPI Libraries in the system... checking for library containing lam_rtrstore... no
>configure: Lam-Libraries not found ..
>checking for OPENMPI... checking for library containing MPI_Comm_spawn... none required
>checking for MPI_Intercomm_merge in -lmpi... yes
>checking for pmpi_comm_create__ in -lmpi_f77... yes
>configure: libatlas.a not found
>./configure: line 263: return: -1: invalid option
>return: usage: return [n]
>ERROR: configuration failed for package 'RScaLAPACK'
>* removing '/builddir/build/BUILDROOT/R-RScaLAPACK-0.5.1-21.fc13.x86_64/usr/lib64/R/library/RScaLAPACK'
>error: Bad exit status from /var/tmp/rpm-tmp.rf31aQ (%install)
>    Bad exit status from /var/tmp/rpm-tmp.rf31aQ (%install)
>RPM build errors:
>Child returncode was: 1
>EXCEPTION: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-RScaLAPACK.spec']
>Traceback (most recent call last):
>  File "/usr/lib/python2.6/site-packages/mock/trace_decorator.py", line 70, in trace
>    result = func(*args, **kw)
>  File "/usr/lib/python2.6/site-packages/mock/util.py", line 324, in do
>    raise mock.exception.Error, ("Command failed. See logs for output.\n # %s" % (command,), child.returncode)
>Error: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-RScaLAPACK.spec']
>LEAVE do --> EXCEPTION RAISED
>

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Attachments on bug 555450: 383989 | 383990 | 383991 | 383992 | 383993 | 383994