Build log

shrimp-2.0.1:20100809-040846.log (text/plain), 6.21 KB, created by Diego Elio Pettenò (RETIRED) on 2010-08-09 16:29:27 UTC

 * CPV:  sci-biology/shrimp-2.0.1
 * REPO: gentoo
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking SHRiMP_2_0_1.src.tar.gz to /var/tmp/portage/sci-biology/shrimp-2.0.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/shrimp-2.0.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/shrimp-2.0.1/work/SHRiMP_2_0_1 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/shrimp-2.0.1/work/SHRiMP_2_0_1 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/shrimp-2.0.1/work/SHRiMP_2_0_1 ...
make -j14 
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o gmapper/gmapper.o gmapper/gmapper.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/fasta.o common/fasta.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/util.o common/util.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/bitmap.o common/bitmap.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/sw-vector.o common/sw-vector.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/sw-gapless.o common/sw-gapless.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/sw-full-cs.o common/sw-full-cs.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/sw-full-ls.o common/sw-full-ls.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/output.o common/output.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/anchors.o common/anchors.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/input.o common/input.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o probcalc/probcalc.o probcalc/probcalc.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o common/dynhash.o common/dynhash.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o prettyprint/prettyprint.o prettyprint/prettyprint.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o probcalc_mp/probcalc_mp.o probcalc_mp/probcalc_mp.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o shrimp_var/shrimp_var.o shrimp_var/shrimp_var.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o shrimp2sam/shrimp2sam.o shrimp2sam/shrimp2sam.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -c -o utils/split-contigs.o utils/split-contigs.c
utils/split-contigs.c: In function ‘void read_contig_list_from_stdin()’:
utils/split-contigs.c:75:49: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o bin/shrimp_var shrimp_var/shrimp_var.o -lm -lz -lstdc++
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o bin/probcalc_mp probcalc_mp/probcalc_mp.o -lm -lz -lstdc++
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o bin/prettyprint prettyprint/prettyprint.o common/fasta.o common/dynhash.o common/sw-full-cs.o common/sw-full-ls.o common/input.o common/output.o common/util.o common/anchors.o -lm -lz -lstdc++
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o bin/shrimp2sam shrimp2sam/shrimp2sam.o common/fasta.o common/dynhash.o common/input.o common/output.o common/util.o common/anchors.o -lm -lz -lstdc++
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o utils/split-contigs utils/split-contigs.o common/fasta.o common/util.o -lm -lz -lstdc++
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o bin/probcalc probcalc/probcalc.o common/fasta.o common/dynhash.o common/input.o common/output.o common/util.o -lm -lz -lstdc++
ln -sf prettyprint bin/prettyprint-ls
ln -sf prettyprint bin/prettyprint-cs
ln -sf prettyprint bin/prettyprint-ls
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -fopenmp -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -o bin/gmapper gmapper/gmapper.o common/fasta.o common/util.o common/bitmap.o common/sw-vector.o common/sw-gapless.o common/sw-full-cs.o common/sw-full-ls.o common/output.o common/anchors.o common/input.o -lm -lz -lstdc++
ln -sf gmapper bin/gmapper-cs
ln -sf gmapper bin/gmapper-ls
>>> Source compiled.
>>> Test phase [none]: sci-biology/shrimp-2.0.1

>>> Install shrimp-2.0.1 into /var/tmp/portage/sci-biology/shrimp-2.0.1/image/ category sci-biology
>>> Completed installing shrimp-2.0.1 into /var/tmp/portage/sci-biology/shrimp-2.0.1/image/

 * Tinderbox QA Warning! ELF files in /usr/share
 TYPE   FILE 
ET_REL /var/tmp/portage/sci-biology/shrimp-2.0.1/image//usr/share/shrimp/utils/split-contigs.o 
ET_EXEC /var/tmp/portage/sci-biology/shrimp-2.0.1/image//usr/share/shrimp/utils/split-contigs 
 * Tinderbox QA Warning (end)! ELF files in /usr/share
strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/share/shrimp/utils/split-contigs.o
   usr/share/shrimp/utils/split-contigs
   usr/bin/gmapper
   usr/bin/prettyprint-cs
   usr/bin/shrimp_var
   usr/bin/gmapper-cs
   usr/bin/probcalc
   usr/bin/probcalc_mp
   usr/bin/shrimp2sam
   usr/bin/prettyprint-ls
   usr/bin/gmapper-ls
   usr/bin/prettyprint

 * QA Notice: Files built without respecting LDFLAGS have been detected
 *  Please include the following list of files in your report:
 * /usr/share/shrimp/utils/split-contigs
 * /usr/bin/gmapper
 * /usr/bin/prettyprint-cs
 * /usr/bin/shrimp_var
 * /usr/bin/gmapper-cs
 * /usr/bin/probcalc
 * /usr/bin/probcalc_mp
 * /usr/bin/shrimp2sam
 * /usr/bin/prettyprint-ls
 * /usr/bin/gmapper-ls
 * /usr/bin/prettyprint