>>> Unpacking source... >>> Unpacking lagan20.tar.gz to /var/tmp/portage/sci-biology/lagan-2.0/work * Applying lagan-2.0-gcc4.3.patch ...  [ ok ] >>> 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 * * ERROR: sci-biology/lagan-2.0 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 2361: Called _eapi0_src_compile * ebuild.sh, line 600: Called _eapi2_src_compile * ebuild.sh, line 634: Called die * The specific snippet of code: * emake || die "emake failed" * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-biology/lagan-2.0:20090613-085355.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/lagan-2.0/temp/environment'. *