Re: [Transdecoder-users] Two compilation errors on OSX

[<Ale...@cs...>]

Sorry not a mac fan.

--
Alexie Papanicolaou
CSIRO Ecosystem Sciences

________________________________
From: Brian Haas
Sent: Monday, 17 February 2014 6:22:53 PM
To: Dorsey, Brian
Cc: tra...@li...; Papanicolaou, Alexie (CES, Black Mountain)
Subject: Re: [Transdecoder-users] Two compilation errors on OSX

Hi Brian,

I think it works well on linux, but I'm not sure it works 'out of the box' on mac.

Alexie might have more to say here.

best,

~b


On Fri, Feb 7, 2014 at 5:54 PM, Dorsey, Brian <bd...@hu...<mailto:bd...@hu...>> wrote:
Hello decoders,

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...<mailto:bd...@hu...>




------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
Transdecoder-users mailing list
Tra...@li...<mailto:Tra...@li...>
https://lists.sourceforge.net/lists/listinfo/transdecoder-users



--
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas