Build log

lagan-2.0:20090613-085355.log (text/plain), 7.93 KB, created by Diego Elio Pettenò (RETIRED) on 2009-06-13 12:04:41 UTC

>>> Unpacking source...
>>> Unpacking lagan20.tar.gz to /var/tmp/portage/sci-biology/lagan-2.0/work
 [32;01m*[0m Applying lagan-2.0-gcc4.3.patch ...
[A[72C  [34;01m[ [32;01mok[34;01m ][0m
>>> Source unpacked in /var/tmp/portage/sci-biology/lagan-2.0/work
>>> Compiling source in /var/tmp/portage/sci-biology/lagan-2.0/work/lagan20 ...
make -j14 
(cd src; make)
make[1]: Entering directory `/var/tmp/portage/sci-biology/lagan-2.0/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:228: error: conflicting types for 'getline'
/usr/include/stdio.h:651: note: previous declaration of 'getline' was here
anchors.c: In function 'getline':
anchors.c:232: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/getlength.c: In function 'main':
utils/getlength.c:20: 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: warning: too few arguments for format
utils/contigorder.c:26: warning: unknown conversion type character '&' in format
utils/contigorder.c:19: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/contigorder.c:20: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/contigorder.c:26: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/contigorder.c: In function 'getScores':
utils/contigorder.c:52: warning: too few arguments for format
utils/contigorder.c:56: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/contigorder.c:57: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/contigorder.c:63: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/getbounds.c: In function 'getLength':
utils/getbounds.c:18: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
order.c: In function 'readfile':
order.c:61: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/cextract.c: In function 'getLength':
utils/cextract.c:16: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
order.c: In function 'readSubstMatrix':
order.c:145: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
order.c:149: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
order.c:150: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
fchaos.c: In function 'readfile':
fchaos.c:344: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/cextract.c: In function 'readfile':
utils/cextract.c:41: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
fchaos.c: In function 'readSubstMatrix':
fchaos.c:622: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
fchaos.c:627: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
fchaos.c:628: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/cstat.c: In function 'cntlets':
utils/cstat.c:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/cstat.c: In function 'readseq':
utils/cstat.c:67: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
mlagan.c: In function 'readfile':
mlagan.c:79: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
skiplist.c: In function 'printSLE':
skiplist.c:12: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'void *'
gcc -O3  -o ../utils/scorealign utils/scorealign.c -lm
utils/rc.c: In function 'main':
utils/rc.c:39: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
gcc -O3  -o ../utils/scorecontigs utils/scorecontigs.c -lm
utils/seqmerge.c: In function 'main':
utils/seqmerge.c:19: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/scorecontigs.c: In function 'cntlets':
utils/scorecontigs.c:55: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/scorecontigs.c: In function 'readseq':
utils/scorecontigs.c:81: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/scorecontigs.c: In function 'main':
utils/scorecontigs.c:384: warning: format '%s' expects type 'char *', but argument 6 has type 'char (*)[1024]'
gcc -O3  -o ../utils/getcontigpos utils/getcontigpos.c
make[1]: *** [../anchors] Error 1
make[1]: *** Waiting for unfinished jobs....
utils/scorealign.c: In function 'getSequence':
utils/scorealign.c:266: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/scorealign.c: In function 'readScoreMatrix':
utils/scorealign.c:415: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/scorealign.c:423: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/scorealign.c:425: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/scorealign.c:430: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
utils/getcontigpos.c: In function 'getLength':
utils/getcontigpos.c:16: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
utils/getcontigpos.c: In function 'readfile':
utils/getcontigpos.c:41: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
multial.c: In function 'readSubstMatrix':
multial.c:478: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
multial.c:486: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
multial.c:487: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result
skiplist.c: In function 'printSLE':
skiplist.c:12: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'void *'
skiplist.c: In function 'printSLE':
skiplist.c:12: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'void *'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/lagan-2.0/work/lagan20/src'
make: *** [all] Error 2
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-biology/lagan-2.0 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_compile
 [31;01m*[0m             environment, line 2361:  Called _eapi0_src_compile
 [31;01m*[0m               ebuild.sh, line  600:  Called _eapi2_src_compile
 [31;01m*[0m               ebuild.sh, line  634:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		emake || die "emake failed"
 [31;01m*[0m  The die message:
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
 [31;01m*[0m A complete build log is located at '/var/log/portage/sci-biology/lagan-2.0:20090613-085355.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/lagan-2.0/temp/environment'.
 [31;01m*[0m