Build log

build.log (text/plain), 15.04 KB, created by Willard Dawson on 2011-05-23 15:58:33 UTC

[32;01m * [39;49;00mPackage:    sci-biology/hmmer-3.0
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        amd64 elibc_glibc kernel_linux mpi selinux threads userland_GNU
[32;01m * [39;49;00mFEATURES:   sandbox selinux sesandbox
>>> Unpacking source...
>>> Unpacking hmmer-3.0.tar.gz to /var/tmp/portage/sci-biology/hmmer-3.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/hmmer-3.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0 ...
 [32;01m*[0m Applying hmmer-3.0-fix_tests.patch ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0 ...
 * econf: updating hmmer-3.0/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating hmmer-3.0/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating hmmer-3.0/easel/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating hmmer-3.0/easel/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-sse --enable-mpi --enable-threads --without-gsl
configure: Configuring HMMER for your system.
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
configure: Full HMMER source distribution - using full configuration
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... x86_64-pc-linux-gnu-gcc
configure: WARNING: You disabled the SSE implementation: I'll use the dummy impl instead.
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking for mpicc... mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
checking how to run the C preprocessor... mpicc -E
checking for C compiler vendor... (cached) gnu
checking for mpicc option to accept ISO C99... -std=gnu99
checking for mpicc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for ar... /usr/bin/ar
checking whether your make is GNU make... yes, it is.
configure: Activating "dummy" implementation
checking compiler support --start-group... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for sys/types.h... (cached) yes
checking sys/sysctl.h usability... yes
checking sys/sysctl.h presence... yes
checking for sys/sysctl.h... yes
checking for unistd.h... (cached) yes
checking for stdint.h... (cached) yes
checking for inttypes.h... (cached) yes
checking endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking whether byte ordering is bigendian... no
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for off_t... yes
checking for mkstemp... yes
checking for popen... yes
checking for strcasecmp... yes
checking for times... yes
checking for getpid... yes
checking for sysctl... yes
checking for sysconf... yes
checking for ntohs... yes
checking for ntohl... yes
checking for htons... yes
checking for htonl... yes
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating profmark/Makefile
config.status: creating src/impl_dummy/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/Makefile
config.status: creating Makefile
config.status: creating src/p7_config.h
config.status: creating easel/esl_config.h
config.status: linking src/impl_dummy to src/impl


HMMER configuration:

     compiler:             mpicc -std=gnu99 -march=native -O2 -pipe  -pthread
     linker:               -Wl,-O1 -Wl,--as-needed
     libraries:              
     DP implementation:    dummy

configure: WARNING: The "dummy" implementation is a portable ANSI C reference implementation.
configure: WARNING: It is slow, and is not intended for production use.
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0 ...
make 
cd easel;  make libeasel.a
make[1]: Entering directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/easel'
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o easel.o -c easel.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_alphabet.o -c esl_alphabet.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_cluster.o -c esl_cluster.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_dirichlet.o -c esl_dirichlet.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_distance.o -c esl_distance.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_dmatrix.o -c esl_dmatrix.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_exponential.o -c esl_exponential.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_fileparser.o -c esl_fileparser.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_gamma.o -c esl_gamma.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_getopts.o -c esl_getopts.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_gev.o -c esl_gev.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_gumbel.o -c esl_gumbel.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_histogram.o -c esl_histogram.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_hmm.o -c esl_hmm.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_hyperexp.o -c esl_hyperexp.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_keyhash.o -c esl_keyhash.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_minimizer.o -c esl_minimizer.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_mixgev.o -c esl_mixgev.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_mpi.o -c esl_mpi.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_msa.o -c esl_msa.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_msacluster.o -c esl_msacluster.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_msashuffle.o -c esl_msashuffle.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_msaweight.o -c esl_msaweight.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_normal.o -c esl_normal.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_paml.o -c esl_paml.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_random.o -c esl_random.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_randomseq.o -c esl_randomseq.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_ratematrix.o -c esl_ratematrix.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_regexp.o -c esl_regexp.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_rootfinder.o -c esl_rootfinder.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_scorematrix.o -c esl_scorematrix.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_sq.o -c esl_sq.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_sqio.o -c esl_sqio.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_sqio_ascii.o -c esl_sqio_ascii.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_sqio_ncbi.o -c esl_sqio_ncbi.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_sse.o -c esl_sse.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_ssi.o -c esl_ssi.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_stack.o -c esl_stack.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_stats.o -c esl_stats.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_stopwatch.o -c esl_stopwatch.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_stretchexp.o -c esl_stretchexp.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_threads.o -c esl_threads.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_tree.o -c esl_tree.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_vectorops.o -c esl_vectorops.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_vmx.o -c esl_vmx.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_weibull.o -c esl_weibull.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_workqueue.o -c esl_workqueue.c		
mpicc -std=gnu99 -I. -I. -march=native -O2 -pipe -pthread   -o esl_wuss.o -c esl_wuss.c		
/usr/bin/ar rcv libeasel.a easel.o esl_alphabet.o esl_cluster.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hmm.o esl_hyperexp.o esl_keyhash.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_threads.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_workqueue.o esl_wuss.o
a - easel.o
a - esl_alphabet.o
a - esl_cluster.o
a - esl_dirichlet.o
a - esl_distance.o
a - esl_dmatrix.o
a - esl_exponential.o
a - esl_fileparser.o
a - esl_gamma.o
a - esl_getopts.o
a - esl_gev.o
a - esl_gumbel.o
a - esl_histogram.o
a - esl_hmm.o
a - esl_hyperexp.o
a - esl_keyhash.o
a - esl_minimizer.o
a - esl_mixgev.o
a - esl_mpi.o
a - esl_msa.o
a - esl_msacluster.o
a - esl_msashuffle.o
a - esl_msaweight.o
a - esl_normal.o
a - esl_paml.o
a - esl_random.o
a - esl_randomseq.o
a - esl_ratematrix.o
a - esl_regexp.o
a - esl_rootfinder.o
a - esl_scorematrix.o
a - esl_sq.o
a - esl_sqio.o
a - esl_sqio_ascii.o
a - esl_sqio_ncbi.o
a - esl_sse.o
a - esl_ssi.o
a - esl_stack.o
a - esl_stats.o
a - esl_stopwatch.o
a - esl_stretchexp.o
a - esl_threads.o
a - esl_tree.o
a - esl_vectorops.o
a - esl_vmx.o
a - esl_weibull.o
a - esl_workqueue.o
a - esl_wuss.o
x86_64-pc-linux-gnu-ranlib libeasel.a
chmod 644 libeasel.a
make[1]: Leaving directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/easel'
cd src/impl_dummy; make libhmmerimpl.a
make[1]: Entering directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/src/impl_dummy'
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c decoding.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c fwdback.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c io.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c msvfilter.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c null2.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c optacc.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c stotrace.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c vitfilter.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c p7_omx.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c p7_oprofile.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c mpi.c
mpi.c:27:23: error: impl_dummy.: No such file or directory
mpi.c: In function 'p7_oprofile_MPIRecv':
mpi.c:133: warning: passing argument 4 of 'p7_profile_MPIRecv' from incompatible pointer type
../hmmer.h:931: note: expected 'const struct ESL_ALPHABET *' but argument is of type 'struct ESL_ALPHABET **'
make[1]: *** [mpi.o] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/src/impl_dummy'
make: *** [impl_lib] Error 2
emake failed
 [31;01m*[0m ERROR: sci-biology/hmmer-3.0 failed (compile phase):
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   56:  Called src_compile
 [31;01m*[0m   environment, line 2172:  Called _eapi2_src_compile
 [31;01m*[0m     ebuild.sh, line  665:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		emake || die "emake failed"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/hmmer-3.0',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/hmmer-3.0'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/hmmer-3.0/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/hmmer-3.0/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0'