[Transdecoder-users] Two compilation errors Mac OSX

[Dorsey, B. <bd...@hu...>]

Hello decoders,

Sorry if this is a duplicate post, the first attempt was before subscribing to the list.

I got the following message when trying to compile transdecoder on Mac OSX 10.7.5:

sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make
make[3]: *** No targets specified and no makefile found.  Stop.
make[2]: *** [ext/fmemopen.o] Error 2
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2


The makefile in /ext is named "Makefile.osx", so I changed:  /transdecoder_rel16JAN2014/3rd_party/ffindex/src/Makefile.osx line 11 from "cd ext && make" to "cd ext && make -f Makefile.osx"

This fixed the first error but...

Then I get this error:

sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make -f Makefile.osx
cc -std=c99 -O3 -g -fPIC -Wall   -c -o fmemopen.o fmemopen.c
cc -std=c99 -O3 -g -fPIC -Wall -fnested-functions   -c -o ffindex.o ffindex.c
clang: warning: argument unused during compilation: '-fnested-functions'
ffindex.c:517:68: error: expected ';' at end of declaration
 void action(const void *node, const VISIT which, const int depth)
                                                                 						   ^
                                                                 						    ;
1 error generated.
make[2]: *** [ffindex.o] Error 1
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2


Below is the block in /transdecoder_rel16JAN2014/3rd_party/ffindex/src/ffindex.c referenced above:

int ffindex_tree_write(ffindex_index_t* index, FILE* index_file)
{
 int ret = EXIT_SUCCESS;
 void action(const void *node, const VISIT which, const int depth)
 {
   ffindex_entry_t *entry;
   switch (which)
   {
     case preorder:
       break;
     case endorder:
       break;
     case postorder:
     case leaf:
       entry = *(ffindex_entry_t **) node;
       if(fprintf(index_file, "%s\t%zd\t%zd\n", entry->name, entry->offset, entry->length) < 0)
         ret = EXIT_FAILURE;
       break;
   }                                        
 }
 twalk(index->tree_root, action);
 return ret;
}

This one I'm not comfortable trying to fix myself.
I know zero about c programming but it doesn't seem there should be a ';' at the end of this line.
However, should I put one there or is there another problem to address?

Thanks for any help,
Brian D.


~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brian Dorsey, Ph.D.
Post-Doctoral Research Associate
The Huntington Botanical Gardens
bd...@hu...