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

[Brian Osborne]

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.
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