Build log

shrimp-1.3.0:20091126-200304.log (text/plain), 5.78 KB, created by Diego Elio Pettenò (RETIRED) on 2009-11-27 11:46:58 UTC

>>> Unpacking source...
>>> Unpacking SHRiMP_1_3_0.src.tar.gz to /var/tmp/portage/sci-biology/shrimp-1.3.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/shrimp-1.3.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/shrimp-1.3.0/work/SHRiMP_1_3_0 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/shrimp-1.3.0/work/SHRiMP_1_3_0 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/shrimp-1.3.0/work/SHRiMP_1_3_0 ...
make -j14 
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o rmapper/rmapper.o rmapper/rmapper.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/fasta.o common/fasta.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/dag_align.o common/dag_align.cpp
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/dag_glue.o common/dag_glue.cpp
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/dag_kmers.o common/dag_kmers.cpp
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/sw-vector.o common/sw-vector.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/sw-full-cs.o common/sw-full-cs.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/sw-full-ls.o common/sw-full-ls.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/input.o common/input.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/output.o common/output.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/util.o common/util.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/anchors.o common/anchors.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/bitmap.o common/bitmap.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o probcalc/probcalc.o probcalc/probcalc.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o common/dynhash.o common/dynhash.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o prettyprint/prettyprint.o prettyprint/prettyprint.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o mergehits/mergehits.o mergehits/mergehits.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o probcalc_mp/probcalc_mp.o probcalc_mp/probcalc_mp.c
g++ -O2 -pipe -O3 -mmmx -msse -msse2 -DNDEBUG -DEXTRA_STATS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DSHRIMP_BUGS=OFF  -c -o shrimp_var/shrimp_var.o shrimp_var/shrimp_var.c
In file included from common/dag_glue.cpp:14:
common/../common/dag_glue.h:24: error: 'uint64_t' does not name a type
common/../common/dag_glue.h:25: error: 'uint64_t' does not name a type
common/../common/dag_glue.h:26: error: 'uint64_t' does not name a type
In file included from common/../common/util.h:23,
                 from common/dag_glue.cpp:16:
common/../common/../common/fasta.h:55: error: 'uint64_t' does not name a type
common/../common/../common/fasta.h:62: error: expected constructor, destructor, or type conversion before '*' token
common/../common/../common/fasta.h:63: error: expected constructor, destructor, or type conversion before '*' token
common/dag_glue.cpp: In function 'dag_statistics* dag_get_statistics()':
common/dag_glue.cpp:196: error: 'struct dag_statistics' has no member named 'aligner_invocations'
common/dag_glue.cpp:198: error: 'struct dag_statistics' has no member named 'kmers_invocations'
common/dag_glue.cpp:199: error: 'struct dag_statistics' has no member named 'kmers_total_kmers'
make: *** [common/dag_glue.o] Error 1
make: *** Waiting for unfinished jobs....
shrimp_var/shrimp_var.c: In function 'void editstr_to_stats(char*, long int, int)':
shrimp_var/shrimp_var.c:476: warning: format not a string literal and no format arguments
 [31;01m*[0m ERROR: sci-biology/shrimp-1.3.0 failed:
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line  55:  Called src_compile
 [31;01m*[0m   environment, line 339:  Called _eapi2_src_compile
 [31;01m*[0m     ebuild.sh, line 635:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		emake || die "emake failed"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/shrimp-1.3.0',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/shrimp-1.3.0'.
 [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-biology/shrimp-1.3.0:20091126-200304.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/shrimp-1.3.0/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/shrimp-1.3.0/work/SHRiMP_1_3_0'