Build log

lagan-2.0-r1:20100828-095043.log (text/plain), 14.03 KB, created by Diego Elio Pettenò (RETIRED) on 2010-08-28 10:13:01 UTC

 * CPV:  sci-biology/lagan-2.0-r1
 * REPO: gentoo
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking lagan20.tar.gz to /var/tmp/portage/sci-biology/lagan-2.0-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/lagan-2.0-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20 ...
 * Applying lagan-2.0-gcc4.3.patch ...
  [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20 ...
make -j14 
(cd src; make)
make[1]: Entering directory `/var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20/src'
gcc -O3  -o ../anchors anchors.c skiplist.c
gcc -O3  -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
gcc -O3  -o ../order order.c diagmatrix.c filebuffer.c
gcc -O3  -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
gcc -O3  -o ../utils/bin2mf utils/bin2mf.c
gcc -O3  -o ../utils/bin2bl utils/bin2bl.c
gcc -O3  -o ../utils/cextract utils/cextract.c
gcc -O3  -o ../utils/cstat utils/cstat.c
gcc -O3  -o ../utils/contigorder utils/contigorder.c
gcc -O3  -o ../utils/getbounds utils/getbounds.c
gcc -O3  -o ../utils/getlength utils/getlength.c
gcc -O3  -o ../utils/getoverlap utils/getoverlap.c
anchors.c: In function ‘my_getline’:
anchors.c:232:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
gcc -O3  -o ../utils/rc utils/rc.c
gcc -O3  -o ../utils/seqmerge utils/seqmerge.c
utils/contigorder.c: In function ‘getFileInfo’:
utils/contigorder.c:15:5: warning: too few arguments for format
utils/contigorder.c:26:2: warning: unknown conversion type character ‘&’ in format
utils/contigorder.c: In function ‘getScores’:
utils/contigorder.c:52:5: warning: too few arguments for format
utils/cstat.c: In function ‘readseq’:
utils/cstat.c:67:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/cstat.c: In function ‘cntlets’:
utils/cstat.c:44:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/cextract.c: In function ‘readfile’:
utils/cextract.c:41:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/getbounds.c: In function ‘getLength’:
utils/getbounds.c:18:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/cextract.c: In function ‘getLength’:
utils/cextract.c:16:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/contigorder.c:56:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/contigorder.c:57:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/contigorder.c:63:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/contigorder.c: In function ‘getFileInfo’:
utils/contigorder.c:19:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/contigorder.c:20:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/contigorder.c:26:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/getlength.c: In function ‘main’:
utils/getlength.c:20:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
fchaos.c: In function ‘readSubstMatrix’:
fchaos.c:622:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
fchaos.c:627:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
fchaos.c:628:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
fchaos.c: In function ‘readfile’:
fchaos.c:344:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/rc.c: In function ‘main’:
utils/rc.c:39:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
order.c: In function ‘readSubstMatrix’:
order.c:145:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
order.c:149:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
order.c:150:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
order.c: In function ‘readfile’:
order.c:61:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
mlagan.c: In function ‘readfile’:
mlagan.c:79:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/seqmerge.c: In function ‘main’:
utils/seqmerge.c:19:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
gcc -O3  -o ../utils/scorealign utils/scorealign.c -lm
gcc -O3  -o ../utils/scorecontigs utils/scorecontigs.c -lm
gcc -O3  -o ../utils/getcontigpos utils/getcontigpos.c
gcc -O3  -o ../utils/fa2xfa utils/fa2xfa.c
g++ -O3  -o ../utils/Glue utils/Glue.cpp
utils/scorealign.c: In function ‘readScoreMatrix’:
utils/scorealign.c:415:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/scorealign.c:423:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/scorealign.c:425:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/scorealign.c:430:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
utils/scorealign.c: In function ‘getSequence’:
utils/scorealign.c:266:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/scorecontigs.c: In function ‘main’:
utils/scorecontigs.c:384:5: warning: format ‘%s’ expects type ‘char *’, but argument 6 has type ‘char (*)[1024]’
utils/scorecontigs.c: In function ‘readseq’:
utils/scorecontigs.c:81:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/scorecontigs.c: In function ‘cntlets’:
utils/scorecontigs.c:55:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
g++ -O3  -o ../utils/dotplot utils/dotplot.cpp
utils/getcontigpos.c: In function ‘readfile’:
utils/getcontigpos.c:41:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/getcontigpos.c: In function ‘getLength’:
utils/getcontigpos.c:16:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
gcc -O3  -o ../utils/overlay utils/overlay.c
utils/fa2xfa.c: In function ‘readfile’:
utils/fa2xfa.c:55:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/fa2xfa.c: In function ‘getLength’:
utils/fa2xfa.c:30:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/dotplot.cpp: In function ‘int main(int, char**)’:
utils/dotplot.cpp:37:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
utils/dotplot.cpp:74:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
utils/dotplot.cpp:97:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
skiplist.c: In function ‘printSLE’:
skiplist.c:12:3: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘void *’
utils/overlay.c: In function ‘read_align’:
utils/overlay.c:109:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’:
utils/Glue.cpp:64:17: warning: deprecated conversion from string constant to ‘char*’
utils/Glue.cpp:72:44: warning: deprecated conversion from string constant to ‘char*’
utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’:
utils/Glue.cpp:44:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
utils/Glue.cpp:52:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result
utils/Glue.cpp:54:30: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result
utils/Glue.cpp:59:44: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result
multial.c: In function ‘readSubstMatrix’:
multial.c:478:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
multial.c:486:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
multial.c:487:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
skiplist.c: In function ‘printSLE’:
skiplist.c:12:3: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘void *’
skiplist.c: In function ‘printSLE’:
skiplist.c:12:3: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘void *’
(cd glocal; make)
make[2]: Entering directory `/var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20/src/glocal'
g++ -Wno-deprecated  -O3 -I./ -c glocal.cpp
g++ -Wno-deprecated  -O3 -I./ -c io.cpp
g++ -Wno-deprecated  -O3 -I./ -c rightinfluence.cpp
g++ -Wno-deprecated  -O3 -I./ -c leftinfluence.cpp
g++ -Wno-deprecated  -O3 -I./ -c score.cpp
io.cpp: In function ‘long long int my_getline(FILE*, hll*)’:
io.cpp:60:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
g++   glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm
make[2]: Leaving directory `/var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20/src/glocal'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/lagan-2.0-r1/work/lagan20/src'
>>> Source compiled.
>>> Test phase [none]: sci-biology/lagan-2.0-r1

>>> Install lagan-2.0-r1 into /var/tmp/portage/sci-biology/lagan-2.0-r1/image/ category sci-biology
>>> Completed installing lagan-2.0-r1 into /var/tmp/portage/sci-biology/lagan-2.0-r1/image/

 * Tinderbox QA Warning! ELF files in /usr/share
 TYPE   FILE 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/scorecontigs 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/scorealign 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/contigorder 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/getlength 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/bin2bl 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/overlay 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/cstat 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/getoverlap 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/getcontigpos 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/cextract 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/getbounds 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/dotplot 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/seqmerge 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/bin2mf 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/rc 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/Glue 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/utils/fa2xfa 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/chaos 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/order 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/anchors 
ET_EXEC /var/tmp/portage/sci-biology/lagan-2.0-r1/image//usr/share/lagan/glocal 
 * Tinderbox QA Warning (end)! ELF files in /usr/share
strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/share/lagan/utils/scorecontigs
   usr/share/lagan/utils/scorealign
   usr/share/lagan/utils/contigorder
   usr/share/lagan/utils/getlength
   usr/share/lagan/utils/bin2bl
   usr/share/lagan/utils/overlay
   usr/share/lagan/utils/cstat
   usr/share/lagan/utils/getoverlap
   usr/share/lagan/utils/getcontigpos
   usr/share/lagan/utils/cextract
   usr/share/lagan/utils/getbounds
   usr/share/lagan/utils/dotplot
   usr/share/lagan/utils/seqmerge
   usr/share/lagan/utils/bin2mf
   usr/share/lagan/utils/rc
   usr/share/lagan/utils/Glue
   usr/share/lagan/utils/fa2xfa
   usr/share/lagan/chaos
   usr/share/lagan/order
   usr/share/lagan/anchors
   usr/share/lagan/glocal
   usr/bin/mlagan

 * QA Notice: Files built without respecting LDFLAGS have been detected
 *  Please include the following list of files in your report:
 * /usr/share/lagan/utils/scorecontigs
 * /usr/share/lagan/utils/scorealign
 * /usr/share/lagan/utils/contigorder
 * /usr/share/lagan/utils/getlength
 * /usr/share/lagan/utils/bin2bl
 * /usr/share/lagan/utils/overlay
 * /usr/share/lagan/utils/cstat
 * /usr/share/lagan/utils/getoverlap
 * /usr/share/lagan/utils/getcontigpos
 * /usr/share/lagan/utils/cextract
 * /usr/share/lagan/utils/getbounds
 * /usr/share/lagan/utils/dotplot
 * /usr/share/lagan/utils/seqmerge
 * /usr/share/lagan/utils/bin2mf
 * /usr/share/lagan/utils/rc
 * /usr/share/lagan/utils/Glue
 * /usr/share/lagan/utils/fa2xfa
 * /usr/share/lagan/chaos
 * /usr/share/lagan/order
 * /usr/share/lagan/anchors
 * /usr/share/lagan/glocal
 * /usr/bin/mlagan

 * Gentoo contact information ...
herds:
    sci-biology
maintainers:
    [e-mail]