[Bioperl-l] OS X bioperl, staden/read, install problems
Jason Stajich
jason at cgt.duhs.duke.edu
Sat Oct 4 08:55:51 EDT 2003
I would try to get things back to a simple state.
Are you using the system installed perl 5.6.0?
Hopefully you've made your changes on your system by adding things to
PERL5LIB so you can just reset it to a simple state. If not, you'll be
picking out files and dirs from /Library/Perl I guess
Get rid of any of the bioperl-ext stuff from your paths, you don't need
them.
At a very minimum look at Bio::SeqIO.pm - you can comment out the
following lines and see if your warnings go away.
#sub BEGIN {
# eval { require Bio::SeqIO::staden::read; };
#}
We've managed to have so many problems with this - I would just suggest
people comment it out from their local installs if they have problems
until Aaron or someone can get detailed, reproduceable problem reports
from folks.
I would really try and whittle things down to a bare minimum and then
try and run the tests. You can always run a specific test by saying
% make test_FootPrinter
or
% perl -I. -w t/FootPrinter.t
to see more details and when the error is occuring.
-jason
On Fri, 3 Oct 2003, Jim Nolan wrote:
> 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
>
>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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