* 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: weaver@gentoo.org