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

Jim Nolan jnolan at tulane.edu
Mon Oct 6 10:47:57 EDT 2003

All is right with the world. I rooted around and only found that 
SeqIO/staden/read had been installed, but not the rest of 
bioperl-ext, since I never passed all the tests. I commented the 
lines from SeqIO.pm which required staden/read and ran make test. 
Essentially all passed, with some minor errors.
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/System/Library/Perl/darwin -I/System/Library/Perl -e 'use 
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' 
         1/78 skipped:
         3/184 skipped:
t/StandAloneBlast............ok 4/10Blast Database swissprot not 
found at t/StandAloneBlast.t line 72.
Blast databases(s) not found, skipping remaining  tests at 
t/StandAloneBlast.t line 76.
t/game.......................ok 20/23Use of uninitialized value in 
pattern match (m//) at /Library/Perl/XML/Writer.pm line 307.
Use of uninitialized value in print at 
/System/Library/Perl/darwin/IO/Handle.pm line 379.
All tests successful, 4 subtests skipped.
Files=137, Tests=6319, 460 wallclock secs (93.89 cusr + 16.76 csys = 
110.65 CPU)

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

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

Thanks again.

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
>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
>% perl -I. -w t/FootPrinter.t
>to see more details and when the error is occuring.
>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

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
The requirements said: Windows 2000 or better.
So I got a Macintosh.

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