Attachment 248142 Details for Bug 338177 – Build log

Build log

infernal-1.0.2:20100918-192556.log (text/plain), 30.75 KB, created by Diego Elio Pettenò (RETIRED) on 2010-09-20 11:45:11 UTC

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Creator: Diego Elio Pettenò (RETIRED)

Created: 2010-09-20 11:45:11 UTC

Size: 30.75 KB

patch

obsolete

> * 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 âprocess_stdoptâ:
>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 âsnprintfâ,
>    inlined from âprocess_stdoptâ at esl_getopts.c:1273:2,
>    inlined from âesl_opt_ProcessCmdlineâ 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 âesl_msa_CreateFromStringâ:
>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 âesl_tree_CreateFromStringâ:
>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 âwrite_binary_cmâ:
>cm_io.c:1026:9: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result
>cm_io.c: In function âtagged_fwriteâ:
>cm_io.c:1345:9: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result
>cm_io.c:1346:9: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result
>cm_io.c:1348:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result
>cm_io.c: In function âtagged_bin_string_readâ:
>cm_io.c:1381:8: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result
>cm_io.c:1383:8: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result
>cm_io.c:1387:10: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result
>cm_io.c: In function âtagged_freadâ:
>cm_io.c:1356:8: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result
>cm_io.c:1357:8: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result
>cm_io.c:1359:10: warning: ignoring return value of âfreadâ, 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/

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Attachments on bug 338177: 248142