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

Mon Oct 6 10:52:28 EDT 2003

> Thanks for your help. I would like to reinstate my whine about adding
> new dependencies, though ;-).

Noted - it is always a trade-off, feel free to pipe up when we debate
on-list about whether or not add another dependancy.

>
> I would be happy to provide feedback on errors in installing
> bioperl-ext on OS X if needed.

When I get together with Aaron at the end of the month I will try and go
through it with him so I understand what is supposed to happen and/or how
we might reorg bioperl-ext to be less problematic.

>
> Thanks again.
> Jim
>
> At 8:55 AM -0400 10/4/03, Jason Stajich wrote:
> >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
>
>
>

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