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

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Hi Josh,
Yes, the mummer build process is in need of an update, but it should still
work. Some helper binaries are compiled in the directory:

/ext/repo/MUMmer/MUMmer/aux_bin/

It appears to have trouble creating the first binary in this directory.
Does that aux_bin directory exist, and do you have write access to it?

Best,
-Adam

On Thu, Jul 9, 2015 at 6:33 PM, Joshua Marshall <jrm...@mt...> wrote:

> 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
>
>
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