[MUMmer-users] Getting started -- Looks like the build instructions are broken

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hello all,

I'm getting started with the coding portion of my summer research and the
MUMmer base package looks like the best piece of FOSS software and possibly
all software available to my needs.  I'm getting started, but it appears
that the current build  instructions at
http://mummer.sourceforge.net/manual/#compilation are incorrect or invalid
with the following output being generated

cd /ext/repo/MUMmer/MUMmer/src/kurtz; make mummer
make[1]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz'
cd libbasedir; make libbase.a
make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/libbasedir'
/usr/bin/gcc -O3   -c -o cleanMUMcand.o cleanMUMcand.c
/usr/bin/gcc -O3   -c -o clock.o clock.c
/usr/bin/gcc -O3   -c -o mapfile.o mapfile.c
/usr/bin/gcc -O3   -c -o multiseq.o multiseq.c
/usr/bin/gcc -O3   -c -o procopt.o procopt.c
/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
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 '/ext/repo/MUMmer/MUMmer/src/kurtz/libbasedir'
cd streesrc; make libstree.a
make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/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/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o dfs.o dfs.c
/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/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o addleafcount.o
addleafcount.c
/usr/bin/gcc -O3 -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 '/ext/repo/MUMmer/MUMmer/src/kurtz/streesrc'
cd mm3src; make mummer
make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/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  maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \
-o /ext/repo/MUMmer/MUMmer/mummer; chmod 755 /ext/repo/MUMmer/MUMmer/mummer
make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/mm3src'
make[1]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz'
cd /ext/repo/MUMmer/MUMmer/src/tigr; make all
make[1]: Entering directory '/ext/repo/MUMmer/MUMmer/src/tigr'
/usr/bin/g++ -O3 tigrinc.cc -c -o tigrinc.o
/usr/bin/g++ -O3 annotate.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/annotate;
chmod 755 /ext/repo/MUMmer/MUMmer/annotate
/usr/bin/g++ -O3 combineMUMs.cc tigrinc.o -o
/ext/repo/MUMmer/MUMmer/combineMUMs; chmod 755
/ext/repo/MUMmer/MUMmer/combineMUMs
combineMUMs.cc:26:38: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
 #define  DEFAULT_ERROR_FILE_NAME     "witherrors.gaps"
                                      ^
combineMUMs.cc:109:27: note: in expansion of macro ‘DEFAULT_ERROR_FILE_NAME’
 char  * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
                           ^
combineMUMs.cc:135:24: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
 char  * Query_Suffix = "Query";
                        ^
combineMUMs.cc:145:22: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
 char  * Ref_Suffix = "Ref";
                      ^
/usr/bin/g++ -O3 delta.cc -c -o delta.o
/usr/bin/g++ -O3 delta-filter.cc tigrinc.o delta.o -o
/ext/repo/MUMmer/MUMmer/delta-filter; chmod 755
/ext/repo/MUMmer/MUMmer/delta-filter
/usr/bin/g++ -O3 gaps.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/gaps; chmod
755 /ext/repo/MUMmer/MUMmer/gaps
/usr/bin/g++ -O3 mgaps.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/mgaps; chmod
755 /ext/repo/MUMmer/MUMmer/mgaps
mgaps.cc: In function ‘int Process_Cluster(Match_t*, int, char*)’:
mgaps.cc:533:18: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
            label = "#\n";
                  ^
mgaps.cc: In function ‘void Process_Matches(Match_t*, int, char*)’:
mgaps.cc:620:17: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
           label = "#\n";
                 ^
/usr/bin/g++ -O3 sw_align.cc -c -o sw_align.o
/usr/bin/g++ -O3 postnuc.cc tigrinc.o sw_align.o -o
/ext/repo/MUMmer/MUMmer/aux_bin/postnuc; chmod 755
/ext/repo/MUMmer/MUMmer/aux_bin/postnuc
/usr/bin/ld: cannot open output file
/ext/repo/MUMmer/MUMmer/aux_bin/postnuc: No such file or directory
collect2: error: ld returned 1 exit status
chmod: cannot access ‘/ext/repo/MUMmer/MUMmer/aux_bin/postnuc’: No such
file or directory
Makefile:69: recipe for target 'postnuc' failed
make[1]: *** [postnuc] Error 1
make[1]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/tigr'
Makefile:125: recipe for target 'tigr' failed
make: *** [tigr] Error 2

Before I go in and try to fix what shouldn't be fixed, has anyone else had
this issue and if so how was it resolved?  If not, when I get the fixes
made, what is the patch submission policy?

Thanks,
Josh Marshall