=> Bootstrap dependency digest>=20010302: found digest-20111104
=> 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
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 procopt.o procopt.c
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
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*'
g++  mgaps.cc tigrinc.o -o /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mgaps; chmod 755 /tmp/pkgsrc/biology/mummer/work/MUMmer3.20/mgaps
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
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
gcc -I../libbasedir -DSTREEHUGE   -c -o linkloc.o linkloc.c
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
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 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
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
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
gcc -I../libbasedir -I../streesrc   -c -o procmaxmat.o procmaxmat.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 -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-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
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-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
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<AlignStats>)':
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