[Bioperl-l] OS X bioperl, staden/read, install problems

[Jason Stajich]

And you've tried with bioperl 1.2.3?

But I'm a little confused -

 a) you do not need bioperl-ext unless you want to use the specialized
    stuff in there (c-extensions to bioperl modules).

 b) What test is giving you the warnings about IO::Staden - I can
    find no reference to it in any of the tests.  Very weird error
    t/FootPrinter.t has nothing to do with Staden.

We have tried very hard (or at least I advocate it very strongly) not to
have a lot of dependancies, I think we are using a bare minimum of them,
IO::String being one of the most essential. Lincoln even wrote
his own socket based HTTP access to begin to remove LWP as a dependancy.

What people need to remember is when it warns you about extra modules when
you run perl Makefile.PL you don't HAVE To install all of those things,
only those which are dependancies for functionality you want.


-jason
On Fri, 3 Oct 2003, Jim Nolan wrote:

> I have been unable to install bioperl versions later than 1.2.1 on
> Mac OS X. The first error I get is during 'make test':
> "The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
>    '/Library/Perl'
> If this is a CPAN/distributed module, you may need to reinstall it on your
> system.
> To allow Inline to compile the module in a temporary cache, simply remove the
> Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>   at t/FootPrinter.t line 0"
> and numerous other tests.
>
> So I attempted to install bioperl-ext, which meant instaling the
> Staden io_lib, though I don't use Staden. This had the difficulty of
> errors caused by the locations of os.h and config.h
> (http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
> I proceeded with the bioperl-ext install, using the directions at
> http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
> (which worked great until recently) I did the -fPIC edit, I did the
> ranlib, but on make test for bioper-ext, I get:
> /usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
> /System/Library/Perl/ExtUtils/xsubpp  -typemap
> /System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
> read.xsc read.c
> cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
> -I/usr/local/include/io_lib -g -pipe -pipe -fno-common
> -no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
> -fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
> -I/System/Library/Perl/darwin/CORE  read.c
> In file included from /usr/local/include/io_lib/os.h:4,
>                   from /usr/local/include/io_lib/Read.h:43,
>                   from read.xs:5:
> /usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
> read.c:1:1: warning: this is the location of the previous definition
> In file included from /usr/local/include/io_lib/translate.h:20,
>                   from /usr/local/include/io_lib/Read.h:227,
>                   from read.xs:5:
> /usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
> /usr/local/include/io_lib/expFileIO.h:42: warning: data definition
> has no type o"
> and lots of similar warnings.
>
> So it seems like there is still a problem with these libraries,
> though I copied them where the compiler seems to be looking for them.
>
> Can someone point me in the right direction?
>
>
> It would be great if there was a way to get rid of the dependency on
> installing bioperl-ext to get bioperl to work. Even if the solution
> for my particular problem is simple, the need to install additional
> layers of dependencies takes a lot of the fun out of it for us lame
> biological types ;-)
> .
>
> Thanks.
> Jim
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu