[Bioperl-l] Problems with installing bioperl using PPM3
brian_osborne at cognia.com
Wed Apr 14 22:26:47 EDT 2004
>Another question I had was can we use the CPAN module to download and
>under a windows environment or are we restricted to using PPM from
Yes, you can. Lincoln has made this point a couple of times when people
expressed their frustrations with the ActiveState approach. In the Command
Prompt, for example, you should be able to do:
>perl -e shell -MCPAN
And then things like:
It's been some time since I last used ActiveState, I use Cygwin instead, so
someone should correct me if this is no longer the case.
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of omid at rogers.com
Sent: Wednesday, April 14, 2004 10:00 AM
To: Chris Fields
Cc: Bioperl-l at bioperl.org
Subject: Re: Re: [Bioperl-l] Problems with installing bioperl using PPM3
Thanks for the Reply Chris...
I managed to get things working for the time being.
I am reading the the PPM instructions provided by the Activestate and
getting a feel for how things work.
I tried the first method you mentioned ie setting up a local repository:
Here is what I did.
1) I run PPM3 at command prompt.
2) rep add my_local "E:/Perl/Local_rep/"
I got this error message:
"Can't locate object method "host" via package "URI::_foreign" (perhaps you
forgot to load "URI::_foreign"?) at E:/Perl/site/lib/PPM/Repository/Local.pm
line 18, <FIN> line 3."
I check to see if "URI" is installed (ie query *) and it was. I checked to
see if there are any upgraded to URI and there was not one available.
I don't know if you if have come across this type of errors in the past.
Another question I had was can we use the CPAN module to download and
install packages under a windows environment or are we restricted to using
PPM from activestate?
> From: Chris Fields <cjfields at uiuc.edu>
> Date: 2004/04/09 Fri PM 09:53:08 EDT
> To: <omid at rogers.com>
> CC: <Bioperl-l at bioperl.org>
> Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3
> Not quite sure if this made the Bioperl-l list, so I'll repost the
> general answer here.
> On Apr 8, 2004, at 7:58 AM, <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.
> This may be due to the perl build failing during ActiveState's
> automated packaging procedures. If you check the build status of the
> IO-String module at ActiveState's PPM repository site (specifically,
> http://ppm.activestate.com/BuildStatus/5.6-I.html), it lists it as
> failing. However, the zipped PPM package is available from the same
> You can install this one of two ways:
> 1) Create a local repository from a directory ('rep add local_rep
> "C:\Perl\local"' or something similar). Decompress the zipped archive
> directly into the directory path listed (i.e. the file with the ppd
> extension should not be in a subdirectory under the repository
> directory; other files may be). Search the local directory and install
> from there.
> 2) Decompress the archive into a temp directory. Run PPM3 ('ppm
> IO-String') from a command prompt within the directory.
> I use the first method myself (only have to set up the directory once).
> > 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??
> That works as well, but always make sure to run 'nmake test' to make
> sure the module will work. Some modules (usually older, less
> maintained ones) tend to fail for various reasons, mainly due to
> included C source code that won't compile in the Windows environment.
> Also, nmake has a tendency to sometimes crash even when it works, so it
> may be hard to tell if you get success!
> The main reason to use PPM3 is b/c PPM3 makes it much easier to install
> and upgrade modules (somewhat like a mini version of rpm in Linux, if
> you're familiar with it). The program keeps track of installed modules
> and is capable of producing nicely formatted HTML from POD; if you add
> modules with nmake, PPM3 will not find them (although you might be able
> to rebuild the PPM3 database).
> > Thanks
> > Omid
> >> 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 PPM
> >> 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 bug
> >> 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
> >>> command
> >>> "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
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at portal.open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >> __________________________________
> >> 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
> > 1
> Chris Fields
> Postdoctoral Reseacher - Dept. of Biochemistry
> Laboratory of Dr. Robert Switzer
> University of Illinois at Urbana-Champaign
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