[Bioperl-l] [Gmod-gbrowse] GMOD PPM repository not working

Scott Cain cain at cshl.edu
Thu Jan 26 10:41:20 EST 2006


Hi Chris,

I still don't exactly know what the problem is, but this at least has
given me some insight on some messages in my error_log: I've been seeing
lots of messages about '/icon/somegif.gif' not found and haven't been
able to track down their source (not that I'd really tried, it was an
annoyance that hadn't risen to the level of serous debugging yet).  We
are using mod_rewrite, so that could be part of the problem.  I'll try
to fix it so that the icons display properly and that may have a side
effect of fixing ppm.

Scott


On Wed, 2006-01-25 at 21:34 -0600, Chris Fields wrote:
> Scott,
> 
> This popped up, for some reason, when I tried to install a perl module
> (Error.pm); maybe it has something to do with the reason PPM can't 'see'
> GMOD's repository.  It crashes PPM pretty nicely!  Looks like the home page
> for GMOD, so maybe Sourceforge is redirecting things and this messes with
> PPM?  
> 
> _____________________________________________
> C:\Perl\Scripts>ppm
> PPM - Programmer's Package Manager version 3.3.
> Copyright (c) 2001 ActiveState Corp. All Rights Reserved.
> ActiveState is a division of Sophos.
> 
> Entering interactive shell. Using Term::ReadLine::Perl as readline library.
> 
> Type 'help' to get started.
> 
> ppm> rep
> Repositories:
> [1] Bioperl
> [2] gmod
> [3] ActiveState PPM2 Repository
> [4] ActiveState Package Repository
> [ ] Bribes
> [ ] Kobes
> [ ] local
> ppm> install Error
> PPM::PPD::init: not a PPD and not a file:
> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
> 
> <head>
>   <title>The Generic Model Organism Database Project | GMOD</title>
>   <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
> <base href="http://www.gmod.org/" />
> <style type="text/css" media="all">@import "misc/drupal.css";</style>
>   <style type="text/css" media="all">@import
> "themes/bluemarine/style.css";</style>
>   <script type="text/javascript"> </script>
> </head>
> 
> <body>
> 
> <table border="0" cellpadding="0" cellspacing="0" id="header">
>   <tr>
>     <td id="logo">
> 
>       <a href="./" title="Home"><img src="files/bluemarine_logo.png"
> alt="Home" /></a>
> 
>       <h1 class='site-name'><a href="./" title="Home">GMOD</a></h1>
> 
>       <div class='site-slogan'>Generic Software Components for Model
> Organism Databases</div>
> 
> 
>     </td>
>     <td id="menu">
>       <div id="secondary"><a
> href="http://sourceforge.net/mail/?group_id=27707">Mailing lists</a> |
> <a
> href="http://sourceforge.net/tracker/?atid=391291&group_id=27707&func=browse
> ">Bug Reports</a> |
> <a
> href="http://sourceforge.net/tracker/?atid=391294&group_id=27707&func=browse
> ">Feature Requests</a> |
> <a href="/publications">Publications</a> |
> <a href="/meetings">Meetings</a> |
> 
> .... (lots of HTML removed)
> 
> 
> <center>This site is maintained by <a href="mailto:cain at cshl.edu">Scott
> Cain</a> | Powered by <a href="http://www.drupal.org">
> drupal</a></center>
> </div>
> </body>
> </html>
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 
> > -----Original Message-----
> > From: gmod-gbrowse-admin at lists.sourceforge.net [mailto:gmod-gbrowse-
> > admin at lists.sourceforge.net] On Behalf Of Scott Cain
> > Sent: Tuesday, January 24, 2006 10:16 AM
> > To: Chris Fields
> > Cc: 'Gbrowse (E-mail)'; bioperl-l at portal.open-bio.org
> > Subject: Re: [Gmod-gbrowse] GMOD PPM repository not working
> > 
> > Hi Chris,
> > 
> > Is it still misbehaving?  I'll do some testing today, but my ability to
> > do so is little hampered as I am traveling this week.
> > 
> > Thanks,
> > Scott
> > 
> > 
> > On Wed, 2006-01-18 at 10:51 -0600, Chris Fields wrote:
> > > Scott,
> > >
> > > I am trying to find the newest bioperl dev. Release (1.51) from PPM for
> > a
> > > quick write-up on installing bioperl-db on Windows.  I tried using the
> > GMOD
> > > repository:
> > >
> > > ppm> rep add gmod http://www.gmod.org/ggb/ppm
> > > Repositories:
> > > [1] gmod
> > > [ ] ActiveState Package Repository
> > > [ ] ActiveState PPM2 Repository
> > > [ ] Bioperl
> > > [ ] Bribes
> > > [ ] Kobes
> > > [ ] local
> > > ppm> search bioperl
> > > Searching in Active Repositories
> > > No matches for 'bioperl'; see 'help search'.
> > > ppm> search *
> > > Searching in Active Repositories
> > > No matches for '*'; see 'help search'.
> > > ppm>
> > >
> > >
> > > Any idea what's going on?  All other repositories work fine.  I can
> > download
> > > it and install locally w/o a problem.  I am running the newest
> > ActivePerl
> > > (5.8.7.815), WinXP.
> > >
> > > Christopher Fields
> > > Postdoctoral Researcher - Switzer Lab
> > > Dept. of Biochemistry
> > > University of Illinois Urbana-Champaign
> > >
> > >
> > >
> > >
> > > -------------------------------------------------------
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> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > Gmod-gbrowse at lists.sourceforge.net
> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                         cain at cshl.edu
> > GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> > Cold Spring Harbor Laboratory
> > 
> > 
> > 
> > -------------------------------------------------------
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> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> 
> _______________________________________________
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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