=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for mummer-3.20nb10 cd /pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz; /usr/pkg/bin/gmake mummer cd /pbulk/work/biology/mummer/work/MUMmer3.20/src/tigr; /usr/pkg/bin/gmake all cd /pbulk/work/biology/mummer/work/MUMmer3.20/scripts; /usr/pkg/bin/gmake all gmake[1]: Entering directory '/pbulk/work/biology/mummer/work/MUMmer3.20/scripts' gmake[1]: Entering directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/tigr' c++ tigrinc.cc -c -o tigrinc.o gmake[1]: Entering directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz' cd libbasedir; /usr/pkg/bin/gmake libbase.a c++ delta.cc -c -o delta.o /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ -e 's?__SCRIPT_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/scripts?g' \ exact-tandems.csh > /pbulk/work/biology/mummer/work/MUMmer3.20/exact-tandems /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/scripts?g' \ mapview.pl > /pbulk/work/biology/mummer/work/MUMmer3.20/mapview c++ sw_align.cc -c -o sw_align.o c++ translate.cc -c -o translate.o /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ mummerplot.pl > /pbulk/work/biology/mummer/work/MUMmer3.20/mummerplot chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/exact-tandems chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/mapview /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__AUX_BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ nucmer.pl > /pbulk/work/biology/mummer/work/MUMmer3.20/nucmer chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/mummerplot /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__AUX_BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ promer.pl > /pbulk/work/biology/mummer/work/MUMmer3.20/promer gmake[2]: Entering directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz/libbasedir' gcc -O2 -c -o cleanMUMcand.o cleanMUMcand.c /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ run-mummer1.csh > /pbulk/work/biology/mummer/work/MUMmer3.20/run-mummer1 chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/nucmer chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/promer gcc -O2 -c -o clock.o clock.c chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/run-mummer1 gcc -O2 -c -o mapfile.o mapfile.c /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ run-mummer3.csh > /pbulk/work/biology/mummer/work/MUMmer3.20/run-mummer3 chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/run-mummer3 /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ nucmer2xfig.pl > /pbulk/work/biology/mummer/work/MUMmer3.20/nucmer2xfig chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/nucmer2xfig /pbulk/work/biology/mummer/work/.tools/bin/sed -e 's?__PERL_PATH?/usr/pkg/bin/perl?g' \ -e 's?__SCRIPT_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20/scripts?g' \ -e 's?__BIN_DIR?/pbulk/work/biology/mummer/work/MUMmer3.20?g' \ dnadiff.pl > /pbulk/work/biology/mummer/work/MUMmer3.20/dnadiff chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/dnadiff gmake[1]: Leaving directory '/pbulk/work/biology/mummer/work/MUMmer3.20/scripts' gcc -O2 -c -o multiseq.o multiseq.c gcc -O2 -c -o procopt.o procopt.c gcc -O2 -c -o safescpy.o safescpy.c gcc -O2 -c -o seterror.o seterror.c gcc -O2 -c -o space.o space.c c++ annotate.cc tigrinc.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/annotate; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/annotate c++ combineMUMs.cc tigrinc.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/combineMUMs; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/combineMUMs c++ gaps.cc tigrinc.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/gaps; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/gaps c++ mgaps.cc tigrinc.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/mgaps; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/mgaps c++ prenuc.cc tigrinc.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/prenuc; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/prenuc 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 gmake[2]: Leaving directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz/libbasedir' cd streesrc; /usr/pkg/bin/gmake libstree.a gmake[2]: Entering directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz/streesrc' gcc -I../libbasedir -DSTREEHUGE -c -o construct.o construct.c c++ prepro.cc tigrinc.o translate.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/prepro; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/prepro mgaps.cc: In function 'int Process_Cluster(Match_t*, int, char*)': mgaps.cc:533:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 533 | label = "#\n"; | ^~~~~ mgaps.cc: In function 'void Process_Matches(Match_t*, int, char*)': mgaps.cc:620:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 620 | label = "#\n"; | ^~~~~ gcc -I../libbasedir -DSTREEHUGE -c -o access.o access.c c++ repeat-match.cc tigrinc.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/repeat-match; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/repeat-match gcc -I../libbasedir -DSTREEHUGE -c -o scanpref.o scanpref.c combineMUMs.cc:26:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 26 | #define DEFAULT_ERROR_FILE_NAME "witherrors.gaps" | ^~~~~~~~~~~~~~~~~ combineMUMs.cc:109:27: note: in expansion of macro 'DEFAULT_ERROR_FILE_NAME' 109 | char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; | ^~~~~~~~~~~~~~~~~~~~~~~ combineMUMs.cc:135:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | char * Query_Suffix = "Query"; | ^~~~~~~ combineMUMs.cc:145:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 145 | char * Ref_Suffix = "Ref"; | ^~~~~ c++ postnuc.cc tigrinc.o sw_align.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/postnuc; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/postnuc gcc -I../libbasedir -DSTREEHUGE -c -o linkloc.o linkloc.c c++ postpro.cc tigrinc.o sw_align.o translate.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/postpro; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/aux_bin/postpro 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 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 gmake[2]: Leaving directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz/streesrc' cd mm3src; /usr/pkg/bin/gmake mummer gmake[2]: Entering directory '/pbulk/work/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 gcc -I../libbasedir -I../streesrc -c -o procmaxmat.o procmaxmat.c gcc -Wl,-zrelro -Wl,-R/usr/pkg/lib maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \ -o /pbulk/work/biology/mummer/work/MUMmer3.20/mummer; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/mummer gmake[2]: Leaving directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz/mm3src' gmake[1]: Leaving directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/kurtz' c++ delta-filter.cc tigrinc.o delta.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/delta-filter; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/delta-filter c++ show-aligns.cc tigrinc.o translate.o delta.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/show-aligns; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/show-aligns c++ show-coords.cc tigrinc.o delta.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/show-coords; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/show-coords c++ show-tiling.cc tigrinc.o delta.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/show-tiling; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/show-tiling c++ show-snps.cc tigrinc.o translate.o delta.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/show-snps; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/show-snps c++ show-diff.cc tigrinc.o delta.o -o /pbulk/work/biology/mummer/work/MUMmer3.20/show-diff; chmod 755 /pbulk/work/biology/mummer/work/MUMmer3.20/show-diff show-coords.cc: In function 'void printBtab(std::vector)': show-coords.cc:799:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 799 | type = "NUCMER"; | ^~~~~~~~ show-coords.cc:801:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 801 | type = "PROMER"; | ^~~~~~~~ show-coords.cc:803:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 803 | type = "NULL"; | ^~~~~~ gmake[1]: Leaving directory '/pbulk/work/biology/mummer/work/MUMmer3.20/src/tigr'