[Bioperl-l] bl2seq parsing confusion?

[Guojun Yang]

Hi, all,
I posted about the bl2seq report parsing. I worked on my windows and not in linux. In fact, I figured out that because the two machines have diff. versions of bioperl. The linux has a later version. It seems in this version, -readme can not be set to BPLite because it gave me an error saying "unallowed". But in the documentation, I can find many places talking about using next_feature, which doesn't seem to be functional in my situation. Is this really because of the later version use Bio::Tools::blast only?
Thanks,

Guojun



----- Original Message -----
From: Aaron J. Mackey <amackey at pcbi.upenn.edu>
To: Patrice Seyed <apseyed at bu.edu>
Cc: bioperl-l <bioperl-l at bioperl.org>
Sent: Mon,  7 Feb 2005 11:22:12 -0500
Subject: Re: [Bioperl-l] bioperl-ext make problems


>  From the CPAN prompt, type "look Bio::Ext::Align".  Then: "perl 
> Makefile.PL; make; make test" and see if you get more descriptive error 
> messages.  From your report we can't really figure out what's going on.
> 
> -Aaron
> 
> On Feb 7, 2005, at 10:01 AM, Patrice Seyed wrote:
> 
> > Hello,
> >
> > I'm getting error when trying to install bioperl-ext, wondering if you 
> > could
> > point me in the right direction. I run -eshell and -MCPAN, and then 
> > try to
> > install the module:
> >
> > CPAN.pm: Going to build B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
> >
> > Checking if your kit is complete...
> > Looks good
> > Writing Makefile for Bio::Ext::Align
> > ERROR from evaluation of
> > /root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't 
> > locate
> > Inline/MakeMaker.pm in @INC (@INC contains:
> > /usr/local/IT/perl-5.8.6/lib/5.8.6/i686-linux
> > /usr/local/IT/perl-5.8.6/lib/5.8.6
> > /usr/local/IT/perl-5.8.6/lib/site_perl/5.8.6/i686-linux
> > /usr/local/IT/perl-5.8.6/lib/site_perl/5.8.6
> > /usr/local/IT/perl-5.8.6/lib/site_perl 
> > /root/.cpan/build/bioperl-ext-1.4 .)
> > at ./Makefile.PL line 1.
> > BEGIN failed--compilation aborted at ./Makefile.PL line 1.
> > Running make test
> >   Make had some problems, maybe interrupted? Won't test
> > Running make install
> >   Make had some problems, maybe interrupted? Won't install
> >
> >
> > I then installed I/IN/INGY/Inline-0.44.tar.gz without complaint, and 
> > tried
> > again:
> >
> > cpan> install B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
> > Running make for B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
> >   Is already unwrapped into directory /root/.cpan/build/bioperl-ext-1.4
> >   Makefile.PL returned status 512
> > Running make test
> >   Make had some problems, maybe interrupted? Won't test
> > Running make install
> >   Make had some problems, maybe interrupted? Won't install
> >
> >
> > Another thing worth noting is that I had to do a force install for 
> > bioperl,
> > bioperl-run, bioperl-db, bioperl-microarray, and bioperl-gui, because 
> > of
> > make test errors for each one. I am running perl v5.8.6 and RHEL 3 
> > variant
> > with the 2.4.21-4.0.1.ELsmp kernel. Thanks in advance for any tips of 
> > this
> > problem or getting around this type of problem.
> >
> > Patrice
> >
> > Patrice Seyed
> > Linux System Administrator - LinGA
> > RHCE, SCSA
> > Boston University Medical Campus
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
> 
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