=> Bootstrap dependency digest>=20010302: found digest-20080510 => Bootstrap dependency fetch-[0-9]*: found fetch-1.7 WARNING: [license.mk] Every package should define a LICENSE. ===> Building for mummer-3.20 cd /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz; /usr/bin/make mummer cd /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/tigr; /usr/bin/make all cd /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts; /usr/bin/make all make[1]: Entering directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz' cd libbasedir; /usr/bin/make libbase.a make[1]: Entering directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/tigr' g++ tigrinc.cc -c -o tigrinc.o g++ delta.cc -c -o delta.o g++ sw_align.cc -c -o sw_align.o make[1]: Entering directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts' /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__CSH_PATH?/usr/pkg/bin/tcsh?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ -e 's?__SCRIPT_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts?g' \ exact-tandems.csh > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/exact-tandems make[2]: Entering directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz/libbasedir' gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o cleanMUMcand.o cleanMUMcand.c chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/exact-tandems /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts?g' \ mapview.pl > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mapview chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mapview /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ mummerplot.pl > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mummerplot chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mummerplot /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__AUX_BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ nucmer.pl > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/nucmer chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/nucmer /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__AUX_BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ promer.pl > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/promer chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/promer /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__CSH_PATH?/usr/pkg/bin/tcsh?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ run-mummer1.csh > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/run-mummer1 chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/run-mummer1 /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__CSH_PATH?/usr/pkg/bin/tcsh?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ run-mummer3.csh > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/run-mummer3 chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/run-mummer3 /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ nucmer2xfig.pl > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/nucmer2xfig chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/nucmer2xfig /tmp/pkgsrc/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__BIN_DIR?/tmp/pkgsrc/biology/mummer/work/MUMmer3.20?g' \ dnadiff.pl > /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/dnadiff chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/dnadiff make[1]: Leaving directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/scripts' gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o clock.o clock.c gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o mapfile.o mapfile.c g++ translate.cc -c -o translate.o g++ prenuc.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/prenuc; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/prenuc gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o multiseq.o multiseq.c gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o procopt.o procopt.c g++ repeat-match.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/repeat-match; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/repeat-match gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o safescpy.o safescpy.c g++ annotate.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/annotate; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/annotate g++ combineMUMs.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/combineMUMs; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/combineMUMs gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o seterror.o seterror.c gcc -O3 -pipe -fstack-protector -Wno-format -fno-builtin -c -o space.o space.c g++ gaps.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/gaps; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/gaps g++ mgaps.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mgaps; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mgaps 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*' 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*' ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o safescpy.o seterror.o space.o g++ postnuc.cc tigrinc.o sw_align.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/postnuc; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/postnuc 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 `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz/libbasedir' cd streesrc; /usr/bin/make libstree.a make[2]: Entering directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz/streesrc' gcc -I../libbasedir -DSTREEHUGE -c -o construct.o construct.c gcc -I../libbasedir -DSTREEHUGE -c -o access.o access.c gcc -I../libbasedir -DSTREEHUGE -c -o scanpref.o scanpref.c g++ postpro.cc tigrinc.o sw_align.o translate.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/postpro; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/postpro g++ prepro.cc tigrinc.o translate.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/prepro; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/aux_bin/prepro gcc -I../libbasedir -DSTREEHUGE -c -o linkloc.o linkloc.c gcc -I../libbasedir -DSTREEHUGE -c -o depthtab.o depthtab.c gcc -I../libbasedir -DSTREEHUGE -c -o ex2leav.o ex2leav.c gcc -I../libbasedir -DSTREEHUGE -c -o dfs.o dfs.c gcc -I../libbasedir -DSTREEHUGE -c -o overmax.o overmax.c gcc -I../libbasedir -DSTREEHUGE -c -o oversucc.o oversucc.c gcc -I../libbasedir -DSTREEHUGE -c -o addleafcount.o addleafcount.c g++ delta-filter.cc tigrinc.o delta.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/delta-filter; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/delta-filter g++ show-aligns.cc tigrinc.o translate.o delta.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-aligns; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-aligns gcc -I../libbasedir -DSTREEHUGE -c -o iterator.o iterator.c 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 `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz/streesrc' cd mm3src; /usr/bin/make mummer make[2]: Entering directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz/mm3src' gcc -I../libbasedir -I../streesrc -c -o maxmat3.o maxmat3.c gcc -I../libbasedir -I../streesrc -c -o maxmatopt.o maxmatopt.c gcc -I../libbasedir -I../streesrc -c -o maxmatinp.o maxmatinp.c gcc -I../libbasedir -I../streesrc -c -o findmumcand.o findmumcand.c gcc -I../libbasedir -I../streesrc -c -o findmaxmat.o findmaxmat.c g++ show-coords.cc tigrinc.o delta.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-coords; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-coords gcc -I../libbasedir -I../streesrc -c -o procmaxmat.o procmaxmat.c g++ show-tiling.cc tigrinc.o delta.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-tiling; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-tiling gcc -Wl,-R/usr/pkg/lib maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \ -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mummer; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mummer g++ show-snps.cc tigrinc.o translate.o delta.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-snps; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-snps make[2]: Leaving directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz/mm3src' make[1]: Leaving directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/kurtz' g++ show-diff.cc tigrinc.o delta.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-diff; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/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*' show-diff.cc: In function 'void PrintDiff(DeltaGraph_t&)': show-diff.cc:169:64: error: 'sort' was not declared in this scope show-diff.cc:265:64: error: 'sort' was not declared in this scope chmod: cannot access `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/show-diff': No such file or directory make[1]: *** [show-diff] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory `/tmp/pkgsrc/biology/mummer/work/MUMmer3.20/src/tigr' make: *** [tigr] Error 2 *** Error code 2 Stop. bmake: stopped in /usr/pkgsrc/biology/mummer *** Error code 1 Stop. bmake: stopped in /usr/pkgsrc/biology/mummer