* CPV: sci-biology/infernal-1.0.2 * REPO: gentoo * Maintainer: weaver@gentoo.org sci-biology@gentoo.org * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking infernal-1.0.2.tar.gz to /var/tmp/portage/sci-biology/infernal-1.0.2/work >>> Source unpacked in /var/tmp/portage/sci-biology/infernal-1.0.2/work >>> Preparing source in /var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2 ... * econf: updating infernal-1.0.2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating infernal-1.0.2/easel/config.sub with /usr/share/gnuconfig/config.sub * econf: updating infernal-1.0.2/easel/config.guess with /usr/share/gnuconfig/config.guess * econf: updating infernal-1.0.2/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --prefix=/var/tmp/portage/sci-biology/infernal-1.0.2/image//usr --disable-mpi configure: Configuring Infernal for your system. checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu configure: Full Infernal source distribution - using full configuration checking for i686-pc-linux-gnu-gcc... i686-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 i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for C compiler vendor... gnu checking for i686-pc-linux-gnu-gcc option to accept ISO C99... -std=gnu99 checking for i686-pc-linux-gnu-gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99 checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... yes, it is. 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 emmintrin.h usability... no checking emmintrin.h presence... no checking for emmintrin.h... no checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking whether byte ordering is bigendian... no checking for int8_t... yes checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes 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 _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... 64 configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/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/config.h config.status: creating easel/esl_config.h >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2 ... make -j14 (cd easel; make CC="i686-pc-linux-gnu-gcc -std=gnu99" CFLAGS="-O2 -pipe"; make) make[1]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel' make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c easel.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_alphabet.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_cluster.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_dirichlet.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_distance.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_dmatrix.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_exponential.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_fileparser.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_gamma.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_getopts.c esl_getopts.c: In function ‘process_stdopt’: esl_getopts.c:1273:2: warning: format not a string literal and no format arguments esl_getopts.c:1273:2: warning: format not a string literal and no format arguments In file included from /usr/include/stdio.h:930:0, from esl_getopts.c:20: In function ‘snprintf’, inlined from ‘process_stdopt’ at esl_getopts.c:1273:2, inlined from ‘esl_opt_ProcessCmdline’ at esl_getopts.c:1116:5: /usr/include/bits/stdio2.h:65:3: warning: call to __builtin___snprintf_chk will always overflow destination buffer i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_gev.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_gumbel.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_histogram.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_hyperexp.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_keyhash.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_minimizer.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_mixgev.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_mpi.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_msa.c esl_msa.c: In function ‘esl_msa_CreateFromString’: esl_msa.c:3617:3: warning: format not a string literal and no format arguments i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_msacluster.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_msashuffle.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_msaweight.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_normal.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_paml.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_random.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_randomseq.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_ratematrix.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_regexp.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_rootfinder.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_scorematrix.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_sq.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_sqio.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_sse.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_ssi.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_stack.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_stats.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_stopwatch.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_stretchexp.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_swat.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_tree.c esl_tree.c: In function ‘esl_tree_CreateFromString’: esl_tree.c:152:3: warning: format not a string literal and no format arguments i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_vectorops.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_vmx.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -c esl_weibull.c i686-pc-linux-gnu-gcc -std=gnu99 -I. -O2 -pipe -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_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_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_swat.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.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_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_sse.o a - esl_ssi.o a - esl_stack.o a - esl_stats.o a - esl_stopwatch.o a - esl_stretchexp.o a - esl_swat.o a - esl_tree.o a - esl_vectorops.o a - esl_vmx.o a - esl_weibull.o a - esl_wuss.o i686-pc-linux-gnu-ranlib libeasel.a chmod 644 libeasel.a (cd miniapps; make) make[2]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel/miniapps' i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-afetch.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-afetch esl-afetch.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-alimanip.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-alimanip esl-alimanip.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-alimap.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-alimap esl-alimap.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-alistat.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-alistat esl-alistat.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-compalign.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-compalign esl-compalign.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-compstruct.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-compstruct esl-compstruct.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-construct.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-construct esl-construct.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-histplot.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-histplot esl-histplot.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-reformat.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-reformat esl-reformat.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-selectn.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-selectn esl-selectn.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-seqstat.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-seqstat esl-seqstat.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-sfetch.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-sfetch esl-sfetch.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-shuffle.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-shuffle esl-shuffle.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-ssdraw.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I.. -c esl-weight.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L.. -o esl-weight esl-weight.o -leasel -lm make[2]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel/miniapps' make[1]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel' make[1]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel' make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. (cd miniapps; make) make[2]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel/miniapps' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel/miniapps' make[1]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/easel' (cd src; make CC="i686-pc-linux-gnu-gcc -std=gnu99" CFLAGS="-O2 -pipe"; make module) make[1]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/src' make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmalign.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_dpalign.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_dpsearch.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_dpsmall.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_io.c cm_io.c: In function ‘write_binary_cm’: cm_io.c:1026:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result cm_io.c: In function ‘tagged_fwrite’: cm_io.c:1345:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result cm_io.c:1346:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result cm_io.c:1348:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result cm_io.c: In function ‘tagged_bin_string_read’: cm_io.c:1381:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result cm_io.c:1383:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result cm_io.c:1387:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result cm_io.c: In function ‘tagged_fread’: cm_io.c:1356:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result cm_io.c:1357:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result cm_io.c:1359:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_modelconfig.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_modelmaker.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_mx.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_parsetree.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_qdband.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cm_submodel.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cp9.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cp9_dp.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cp9_modelconfig.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cp9_modelmaker.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cp9_mx.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cp9_trace.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c alphabet.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c dispatch.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c display.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c eweight.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c errors.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c hmmband.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c hybridsearch.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c logsum.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c mpisupport.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c prior.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c rnamat.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c searchinfo.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c seqstoaln.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c stats.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c truncyk.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmalign cmalign.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmbuild.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmbuild cmbuild.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmcalibrate.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmcalibrate cmcalibrate.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmemit.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmemit cmemit.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmscore.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmscore cmscore.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmsearch.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmsearch cmsearch.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c cmstat.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o cmstat cmstat.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c trcyk.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o trcyk trcyk.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel -c truncyk_check.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -L../easel -o truncyk_check truncyk_check.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm make[1]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/src' make[1]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/src' make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. /usr/bin/ar rcv libinfernal.a cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o a - cm.o a - cm_dpalign.o a - cm_dpsearch.o a - cm_dpsmall.o a - cm_io.o a - cm_modelconfig.o a - cm_modelmaker.o a - cm_mx.o a - cm_parsetree.o a - cm_qdband.o a - cm_submodel.o a - cp9.o a - cp9_dp.o a - cp9_modelconfig.o a - cp9_modelmaker.o a - cp9_mx.o a - cp9_trace.o a - alphabet.o a - dispatch.o a - display.o a - eweight.o a - errors.o a - hmmband.o a - hybridsearch.o a - logsum.o a - mpisupport.o a - prior.o a - rnamat.o a - searchinfo.o a - seqstoaln.o a - stats.o a - truncyk.o i686-pc-linux-gnu-ranlib libinfernal.a chmod 644 libinfernal.a make[1]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/src' (cd testsuite; make CC="i686-pc-linux-gnu-gcc -std=gnu99" CFLAGS="-O2 -pipe") make[1]: Entering directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/testsuite' make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel/ -I../src -c bandcyk-montecarlo-test.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -DHAVE_CONFIG_H -L../easel/ -L../src -o bandcyk-montecarlo-test bandcyk-montecarlo-test.o -linfernal -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel/ -I../src -c bandcyk-truncation-test.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -DHAVE_CONFIG_H -L../easel/ -L../src -o bandcyk-truncation-test bandcyk-truncation-test.o -linfernal -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel/ -I../src -c cp9-test.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -DHAVE_CONFIG_H -L../easel/ -L../src -o cp9-test cp9-test.o -linfernal -leasel -lm i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -DHAVE_CONFIG_H -I../easel/ -I../src -c sub_cm-test.c i686-pc-linux-gnu-gcc -std=gnu99 -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -DHAVE_CONFIG_H -L../easel/ -L../src -o sub_cm-test sub_cm-test.o -linfernal -leasel -lm make[1]: Leaving directory `/var/tmp/portage/sci-biology/infernal-1.0.2/work/infernal-1.0.2/testsuite' >>> Source compiled. >>> Test phase [check]: sci-biology/infernal-1.0.2 make -j14 -j1 check (cd testsuite; ./sqc -p ../easel/miniapps 4 exercises.sqc . ../src) exercise 1 [ cmalign:help/1] ... ok. exercise 2 [ cmalign:help/2] ... ok. exercise 3 [ cmalign:trna/1] ... ok. exercise 4 [ cmalign:trna/2] ... ok. exercise 5 [ cmalign:vault/1] ... ok. exercise 6 [ cmalign:vault/2] ... ok. exercise 7 [ cmbuild:help/1] ... ok. exercise 8 [ cmbuild:help/2] ... ok. exercise 9 [ cmbuild/rf/trna] ... ok. exercise 10 [ cmbuild/trna] ... ok. exercise 11 [ cmbuild/rf/RNaseP] ... ok. exercise 12 [ cmbuild/RNaseP] ... ok. exercise 13 [ cmbuild/SRP] ... ok. exercise 14 [ cmcalibrate:help/1] ... ok. exercise 15 [ cmcalibrate:help/2] ... ok. exercise 16 [ cmcalibrate:trna] ... ok. exercise 17 [ cmscore:help/1] ... ok. exercise 18 [ cmscore:help/2] ... ok. exercise 19 [ cmscore/trna1] ... ok. exercise 20 [ cmscore/trna2] ... ok. exercise 21 [ cmscore/local/trna1] ... ok. exercise 22 [ cmscore/local/trna2] ... ok. exercise 23 [ trna1/rand50] ... ok. exercise 24 [ trna2/rand50] ... ok. exercise 25 [ trna1/rand50/local] ... ok. exercise 26 [ trna2/rand50/local] ... ok. exercise 27 [ rnaseP/bsu] ... ok. exercise 28 [ rnaseP/bsu/local] ... ok. exercise 29 [ srp/ffs] ... ok. exercise 30 [ rnaseP/rand] ... ok. exercise 31 [ rnaseP/rand/local] ... ok. exercise 32 [ cmsearch:help/1] ... ok. exercise 33 [ cmsearch:help/2] ... ok. exercise 34 [ trna/search] ... ok. exercise 35 [ rnaseP/search] ... ok. exercise 36 [ srp/search] ... ok. exercise 37 [ cmemit:help/1] ... ok. exercise 38 [ cmemit:help/2] ... ok. exercise 39 [ trna/emit] ... ok. exercise 40 [ rnaseP/emit] ... ok. exercise 41 [ srp/emit] ... ok. exercise 42 [ cmstat:help/1] ... ok. exercise 43 [ trna/stat] ... ok. exercise 44 [ rnaseP/stat] ... ok. exercise 45 [ srp/stat] ... ok. exercise 46 [ bandcyk/mc/trna] ... ok. exercise 47 [ bandcyk/mc/rp] ... ok. exercise 48 [ bandcyk/mc/ssu] ... ok. exercise 49 [ bandcyk/trunc/trna] ... ok. exercise 50 [ bandcyk/trunc/rp] ... ok. exercise 51 [ bandcyk/trunc/ssu] ... ok. exercise 52 [ cp9/trna] ... ok. exercise 53 [ cp9/trna] ... ok. exercise 54 [ cp9/rp] ... ok. exercise 55 [ cp9/ssu] ... ok. exercise 56 [ sub/trna1] ... ok. exercise 57 [ sub/rp] ... ok. exercise 58 [ sub/ssu] ... ok. exercise 59 [ sub/trna2] ... ok. All 59 exercises at level <= 4 passed. System information: Sat Sep 18 21:31:27 CEST 2010 Linux tinderbox 2.6.35.4+ #19 SMP PREEMPT Fri Aug 27 12:02:06 CEST 2010 i686 Quad-Core AMD Opteron(tm) Processor 2350 AuthenticAMD GNU/Linux >>> Install infernal-1.0.2 into /var/tmp/portage/sci-biology/infernal-1.0.2/image/ category sci-biology make -j14 install mkdir -p /var/tmp/portage/sci-biology/infernal-1.0.2/image//usr/bin for file in cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat; do\ cp src/$file /var/tmp/portage/sci-biology/infernal-1.0.2/image//usr/bin/;\ done >>> Completed installing infernal-1.0.2 into /var/tmp/portage/sci-biology/infernal-1.0.2/image/ * QA Notice: make jobserver unavailable: * * make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. * make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. * make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. * make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. * make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/bin/cmsearch usr/bin/cmstat usr/bin/cmcalibrate usr/bin/cmalign usr/bin/cmemit usr/bin/cmscore usr/bin/cmbuild * QA Notice: Files built without respecting LDFLAGS have been detected * Please include the following list of files in your report: * /usr/bin/cmsearch * /usr/bin/cmstat * /usr/bin/cmcalibrate * /usr/bin/cmalign * /usr/bin/cmemit * /usr/bin/cmscore * /usr/bin/cmbuild * QA Notice: Package has poor programming practices which may compile * fine but exhibit random runtime failures. * /usr/include/bits/stdio2.h:65:3: warning: call to __builtin___snprintf_chk will always overflow destination buffer * Please do not file a Gentoo bug and instead report the above QA * issues directly to the upstream developers of this software. * Homepage: http://infernal.janelia.org/