* CPV: sci-biology/mummer-3.22 * REPO: gentoo * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking MUMmer3.22.tar.gz to /var/tmp/portage/sci-biology/mummer-3.22/work >>> Source unpacked in /var/tmp/portage/sci-biology/mummer-3.22/work >>> Preparing source in /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22 ... make -j14 cd /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz; make mummer cd /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/tigr; make all cd /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts; make all make[1]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz' cd libbasedir; make libbase.a make[1]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/tigr' /usr/bin/g++ -O3 tigrinc.cc -c -o tigrinc.o make[2]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/libbasedir' /usr/bin/gcc -O3 -c -o cleanMUMcand.o cleanMUMcand.c /usr/bin/g++ -O3 delta.cc -c -o delta.o make[1]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts' /bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ exact-tandems.csh > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/exact-tandems /bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ mapview.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mapview /usr/bin/g++ -O3 sw_align.cc -c -o sw_align.o /usr/bin/g++ -O3 translate.cc -c -o translate.o /bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ mummerplot.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummerplot /bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ -e 's?__AUX_BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ nucmer.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer /bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ -e 's?__AUX_BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ promer.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/promer /bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ run-mummer1.csh > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer1 chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/exact-tandems /usr/bin/gcc -O3 -c -o clock.o clock.c /usr/bin/gcc -O3 -c -o mapfile.o mapfile.c /bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ run-mummer3.csh > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer3 chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mapview chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummerplot chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/promer chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer1 /usr/bin/gcc -O3 -c -o multiseq.o multiseq.c /bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ nucmer2xfig.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer2xfig /usr/bin/gcc -O3 -c -o procopt.o procopt.c /bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ dnadiff.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/dnadiff chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer3 /usr/bin/gcc -O3 -c -o safescpy.o safescpy.c /usr/bin/gcc -O3 -c -o seterror.o seterror.c /usr/bin/gcc -O3 -c -o space.o space.c chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/dnadiff chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer2xfig make[1]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts' tigrinc.cc: In function ‘int Read_String(FILE*, char*&, long int&, char*, int)’: tigrinc.cc:335:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o safescpy.o seterror.o space.o ar: creating libbase.a a - cleanMUMcand.o a - clock.o a - mapfile.o a - multiseq.o a - procopt.o a - safescpy.o a - seterror.o a - space.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/libbasedir' cd streesrc; make libstree.a make[2]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/streesrc' /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o construct.o construct.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o access.o access.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o scanpref.o scanpref.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o linkloc.o linkloc.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o depthtab.o depthtab.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o ex2leav.o ex2leav.c /usr/bin/g++ -O3 annotate.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/annotate; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/annotate /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o dfs.o dfs.c /usr/bin/g++ -O3 combineMUMs.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/combineMUMs; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/combineMUMs /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o overmax.o overmax.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o oversucc.o oversucc.c /usr/bin/g++ -O3 gaps.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/gaps; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/gaps /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o addleafcount.o addleafcount.c /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o iterator.o iterator.c /usr/bin/g++ -O3 mgaps.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mgaps; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mgaps /usr/bin/g++ -O3 prenuc.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prenuc; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prenuc /usr/bin/g++ -O3 prepro.cc tigrinc.o translate.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prepro; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prepro combineMUMs.cc:109:27: warning: deprecated conversion from string constant to ‘char*’ combineMUMs.cc:135:24: warning: deprecated conversion from string constant to ‘char*’ combineMUMs.cc:145:22: warning: deprecated conversion from string constant to ‘char*’ combineMUMs.cc: In function ‘int Read_String(FILE*, char**, long int*, char*)’: combineMUMs.cc:1481:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /usr/bin/g++ -O3 repeat-match.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/repeat-match; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/repeat-match mgaps.cc: In function ‘int Process_Cluster(Match_t*, int, char*)’: mgaps.cc:533:20: warning: deprecated conversion from string constant to ‘char*’ mgaps.cc: In function ‘void Process_Matches(Match_t*, int, char*)’: mgaps.cc:620:19: warning: deprecated conversion from string constant to ‘char*’ /usr/bin/g++ -O3 postnuc.cc tigrinc.o sw_align.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postnuc; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postnuc /usr/bin/g++ -O3 postpro.cc tigrinc.o sw_align.o translate.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postpro; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postpro ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o ar: creating libstree.a a - construct.o a - access.o a - scanpref.o a - linkloc.o a - depthtab.o a - ex2leav.o a - dfs.o a - overmax.o a - oversucc.o a - addleafcount.o a - iterator.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/streesrc' cd mm3src; make mummer make[2]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/mm3src' /usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o maxmat3.o maxmat3.c /usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o maxmatopt.o maxmatopt.c /usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o maxmatinp.o maxmatinp.c /usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o findmumcand.o findmumcand.c /usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o findmaxmat.o findmaxmat.c /usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o procmaxmat.o procmaxmat.c /usr/bin/gcc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \ -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummer; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummer make[2]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/mm3src' make[1]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz' /usr/bin/g++ -O3 delta-filter.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/delta-filter; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/delta-filter /usr/bin/g++ -O3 show-aligns.cc tigrinc.o translate.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-aligns; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-aligns /usr/bin/g++ -O3 show-coords.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-coords; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-coords /usr/bin/g++ -O3 show-tiling.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-tiling; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-tiling /usr/bin/g++ -O3 show-snps.cc tigrinc.o translate.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-snps; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-snps /usr/bin/g++ -O3 show-diff.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-diff; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-diff show-coords.cc: In function ‘void printBtab(std::vector)’: show-coords.cc:799:12: warning: deprecated conversion from string constant to ‘char*’ show-coords.cc:801:12: warning: deprecated conversion from string constant to ‘char*’ show-coords.cc:803:12: warning: deprecated conversion from string constant to ‘char*’ make[1]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/tigr' >>> Source compiled. >>> Test phase [check]: sci-biology/mummer-3.22 make -j14 -j1 check check complete >>> Install mummer-3.22 into /var/tmp/portage/sci-biology/mummer-3.22/image/ category sci-biology >>> Completed installing mummer-3.22 into /var/tmp/portage/sci-biology/mummer-3.22/image/ strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/bin/repeat-match usr/bin/gaps usr/bin/show-tiling usr/bin/show-coords usr/bin/prenuc usr/bin/combineMUMs usr/bin/mgaps usr/bin/show-snps usr/bin/mummer usr/bin/mummer-annotate usr/bin/show-aligns usr/bin/show-diff usr/bin/postpro usr/bin/postnuc usr/bin/delta-filter usr/bin/prepro  * QA Notice: Files built without respecting LDFLAGS have been detected * Please include the following list of files in your report: * /usr/bin/repeat-match * /usr/bin/gaps * /usr/bin/show-tiling * /usr/bin/show-coords * /usr/bin/prenuc * /usr/bin/combineMUMs * /usr/bin/mgaps * /usr/bin/show-snps * /usr/bin/mummer-annotate * /usr/bin/show-aligns * /usr/bin/show-diff * /usr/bin/postpro * /usr/bin/postnuc * /usr/bin/delta-filter * /usr/bin/prepro  * Gentoo contact information ... herds: sci-biology maintainers: weaver@gentoo.org