[Transdecoder-users] Two compilation errors Mac OSX
Extracting likely coding regions from transcript sequences
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From: Dorsey, B. <bd...@hu...> - 2014-02-10 19:08:47
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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...
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