[Bioperl-l] Problems with installing bioperl using PPM3
cjfields at uiuc.edu
Thu Apr 8 15:40:03 EDT 2004
At 07:58 AM 4/8/2004, omid at rogers.com wrote:
>Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when
>using PPM3 I encountered a new set of problems.
>it seems that bioperl-1.4 does not work for for PPM3 on build 633 but I
>was able to install an ealier version of bioperl "Bioinformatics Toolkit".
>with build 635 it seems that ppm3 itself has problems installing some
>modules. some bioperl dependencies were able to be installed while others
>that worked with build 633 were not.
>Also, I encountered a problem installing "IO-String"
>with both versions. This module is one of the listed dependencies for bioperl.
What kind of problem? Are the ActiveState repositories turned 'on'?
The default repositories (ActiveState PPM2 and PPM3) both should have the
latest IO-String (v. 1.0.4). I checked using PPM3 on Perl 5.8.3 build 809
and everything is okay; however, you must remember that any ppm packages
for 5.6 will not be binary-compatible for 5.8 and vice versa.
Okay, I may have found the issue. One problem is ActiveState has listed
IO-String as failing when building (see
http://ppm.activestate.com/BuildStatus/5.6-I.html). You can still download
the zipped archive for IO-String (and others if needed) and install them
locally using PPM (the zipped archives are at
http://ppm.activestate.com/PPMPackages/zips/6xx-builds-only/). This is
done by one of two methods
(1) adding a local repository (such as 'rep add local_rep
"C:\Perl\local"'), decompressing the zip archives directly into the local
repository directory, then searching the local repository within PPM3 and
installing it, or ...
(2) using 'ppm install package-name.ppd' in the directory where the .ppd
file for the module package is located (normally the directory in which the
archive is decompressed).
>What I had to do in that case was download the IO-String module from CPAN
>in a temp directory and run nmake etc on it. Not sure if this is the
>proper way of doing things??
You can do it this way, but installing the ppm package is recommended by
ActiveState b/c it is easier to remove and upgrade modules plus keep track
of documentation (you can generate nice HTML docs with PPM3). You can also
install Bioperl using nmake, but you'll get normally get errors under
BTW, this method works for purely perl modules, but it's a good idea to
always run 'nmake test' to make sure everything works okay. When some C
code is thrown in (GD, for instance), nmake will almost always crash and
burn (being Microsoft software, what would you expect?).
> > From: Chris Fields <cjfields at uiuc.edu>
> > Date: 2004/04/07 Wed PM 05:22:55 EDT
> > To: <omid at rogers.com>, <bioperl-l at bioperl.org>
> > Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3
> > Everything works when using ActiveState Perl 5.8.3 Build 809, which comes
> > with PPM3 as the default package manager. It may be due to the earlier
> > version. I checked the ActiveState web site documentation for ActivePerl
> > 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is a
> > fix listed for PPM3.
> > The following link describes a problem very like yours and is from the PPM
> > bug database (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go)
> > and is likely the bug that is fixed in 5.6.1 build 635, so you might want
> > to upgrade to that version or to the newest 5.8.3 release for the fix.
> > Chris
> > At 02:08 PM 4/7/2004, omid at rogers.com wrote:
> > >Hello all,
> > >
> > >I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine
> > >running windows 2000 and I do the following:
> > >
> > >I type "ppm3" at the command prompt
> > >then type "search bioperl" (the repository is set to
> > >http://www.bioperl.org/DIST/).
> > >
> > >a listing is displayed with numbers and when I attemp to issue the
> > >"describe 20" or describe "package name" I get an error saying:
> > >
> > >Can't call method "name" without a package or object reference at
> > >E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9.
> > >
> > >I don't know what it means. I searched the bioperl site and looked at
> > >various installation documents but nothing seems to address this type of
> > >problem.
> > >
> > >Any help you are able to provide is greatly appreciated.
> > >Thanks
> > >Omid
> > >
> > >
> > >
> > >
> > >1
> > >
> > >_______________________________________________
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> > >Bioperl-l at portal.open-bio.org
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> > __________________________________
> > Chris Fields - Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Address:
> > University of Illinois at Urbana-Champaign
> > Dept. of Biochemistry - 323 RAL
> > 600 S. Mathews Ave.
> > Urbana, IL 61801
> > Phone : (217) 333-7098
> > Fax : (217) 244-5858
Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer
University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801
Phone : (217) 333-7098
Fax : (217) 244-5858
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