[Bioperl-l] Failed to load module Bio::SeqIO::swiss

Chaogu Zheng cgzheng86 at gmail.com
Thu Oct 21 13:57:06 EDT 2010


Maybe my reason for this is silly. I am using the Mac OS X 10.6, which
has the pre-installed perl 5.10.0. Fink only has the unstable bioperl
1.6.1 for Mac OS X 10.6. If I want to install bioperl-pm588 that is
the fink-stable 1.5.1 version, I guess I have to install an earlier
version of perl 5.8.8. I did not bother to do that.

So, do you think I really need to uninstall bioperl-pm5100 and get
perl 5.8.8 to try the fink-stable one?

Ryan

On Oct 21, 11:05 am, Chris Fields <cjfie... at illinois.edu> wrote:
> Like the error message says, you need to install Data::Stag (so, for some reason, this way left off).  However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.
>
> chris
>
> On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:
>
>
>
>
>
> > I am extremely new to Bioperl and got a problem immediately after I
> > installed it.
>
> > I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> > Everything seems to be fine. However, when I tried to retrieve some
> > sequences from swissprot, I found the following errors.
>
> > It seems the module Bio::SeqIO::swiss can not be loaded, though I
> > indeed found it under the correct directory. By the way, if I change
> > 'swiss' to 'genbank' I can successfully run the program.
>
> > I don't know how to fix it. Anyone can help me?
>
> > Ryan
>
> > Bio::SeqIO: swiss cannot be found
> > Exception
> > ------------- EXCEPTION -------------
> > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> > Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> > multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> > multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> > 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> > Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> > 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> > 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> > Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> > Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> > 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> > Annotation/TagTree.pm line 123.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> > line 439.
>
> > STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> > Root.pm:441
> > STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> > STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> > SeqIO.pm:569
> > STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> > STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:472
> > STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> > DB/WebDBSeqI.pm:314
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:186
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
>
> > For more information about the SeqIO system please see the SeqIO docs.
> > This includes ways of checking for formats at compile time, not run
> > time
>
> > ------------- EXCEPTION -------------
> > MSG: acc P11217 does not exist
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:187
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
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