Build log

infernal-1.0.2:20100918-192556.log (text/plain), 30.75 KB, created by Diego Elio Pettenò (RETIRED) on 2010-09-20 11:45:35 UTC

 * CPV:  sci-biology/infernal-1.0.2
 * REPO: gentoo
 * Maintainer: [e-mail] [e-mail]
 * 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/