[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;'
t/*.t
t/DB.........................ok
1/78 skipped:
t/SeqIO......................ok
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/StandAloneBlast............ok
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.
t/game.......................ok
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.
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
--
---------------------------------------------------------
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.
More information about the Bioperl-l
mailing list