* Package: sci-biology/hmmer-3.0  * Repository: gentoo  * Maintainer: sci-biology@gentoo.org  * USE: amd64 elibc_glibc kernel_linux mpi selinux threads userland_GNU  * FEATURES: 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 ... * Applying hmmer-3.0-fix_tests.patch ...  [ ok ] >>> 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 * ERROR: sci-biology/hmmer-3.0 failed (compile phase): * emake failed * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2172: Called _eapi2_src_compile * ebuild.sh, line 665: Called die * The specific snippet of code: * emake || die "emake failed" * * If you need support, post the output of 'emerge --info =sci-biology/hmmer-3.0', * the complete build log and the output of 'emerge -pqv =sci-biology/hmmer-3.0'. * The complete build log is located at '/var/tmp/portage/sci-biology/hmmer-3.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/hmmer-3.0/temp/environment'. * S: '/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0'