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

[Jim Nolan]

I sent the full list of test errors to Jason, but I got 29 errors 
looking for Staden::read when I tested Bioperl 1.2.3.
These were the tests that asked for it:
BioDBGFF, FootPrin, Genewise, Genpred, Index, LocusLin, Mutator, 
Perl, RepeatMa, SeqAnaly, SeqBuild, SeqFeatC, SeqFeatu, SeqIO, 
Sequence, Similari, StandAlo, Swiss, Tools, Variatio, ePCR, game, 
largefas, multiple, phd, primaryq, qual, scf, splicedseq

I think I get even more for the CVS version.
I guess it must be something specific to my machine, since nobody's 
heard of this one. When I saw the Staden::read errors, then I figured 
I had to have bioperl-ext.
Sorry I whined, I thought that it was just a new dependency that 
wasn't as much of a hassle for most machines as it is for mine.

If anyone has any clues as to what I did wrong, I'd be glad to hear them.

Thanks
Jim

>Jim,
>
>>  It would be great if there was a way to get rid of the dependency on
>installing bioperl-ext to get bioperl to work.
>
>This is odd. I've done 'make install' many, many times but I've never
>installed nor used the bioperl-ext library. Ever. Do you think you could
>have done something unconventional to see the behavior you're seeing?
>
>Brian O.
>
>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
>[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jim Nolan
>Sent: Friday, October 03, 2003 5:06 PM
>To: bioperl-l at portal.open-bio.org
>Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
>
>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
>--
>---------------------------------------------------------
>Jim Nolan                       email:JNolan at tulane.edu
>Department of Biochemistry SL43
>Tulane University Health Sciences Center
>1430 Tulane Ave.                Phone: (504)-584-2453
>New Orleans, LA 70112-2699      FAX:   (504)-584-2739
>http://www.tulane.edu/~biochem/faculty/nolan.htm
>http://phage.bioc.tulane.edu
>The requirements said: Windows 2000 or better.
>So I got a Macintosh.
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l


-- 
---------------------------------------------------------
Jim Nolan			email:JNolan at tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.