[Bioperl-l] problem with installation of Bioperl1.4 on Windows XPPC using ActivePerl PPM

Chris Fields cjfields at uiuc.edu
Fri Sep 22 16:23:44 UTC 2006

> Did you get round to trying this? Did you find anything?

Yes I have.  PPM4 is interesting, but I find the lack of a full command-line
version a bit frustrating (though I can see why they are moving in this
direction).  It doesn't require the use of a package.lst in the ppm
directory, but it looks for it first.  If it isn't present it looks for the
ppd files.  This would be nice for Bioperl except we want to continue
support for Perl 5.6.1, so we must include package.lst in the repository.

I can definitely replicate the error reported before when adding the
repository using ppm4:

ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version
3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and
File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2
to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from
version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2

I think this comes from the various versioning requirements for those
modules, which probably arise from the v 1.4 Makefile.PL.  The new version
doesn't have those requirements but a few others are present.  When a new
PPM is made we probably need to take that into consideration.

I noticed that the GMOD repository (http://www.gmod.org/ggb/ppm/) carries a
newer bioperl version (1.512) which is needed for GBrowse.  This is a
minimal installation w/o any requirements added and is accessible from PPM4;
it installs w/o a hitch.
> I'm still working on getting Bioperl 1.5.2 installed on ActivePerl 5.6.1
> and as many dependencies as I can in order to run the test suit -
> however, I'm have a lot of headaches! I'm about to work through it a bit
> more systematically, and note the problems I'm having. One that comes to
> mind straight away is:
> To run the tests, I need nmake. However, nmake fails if commands break
> the command line length limit - which is shorter on Windows than other
> OS's. This was solved by the authors of ExtUtils::MakeMaker when I
> informed them, some time ago. So, to run the tests, I need
> ExtUtils::MakeMaker >=6.06 installed. However, I'm having problems with
> installing this! I've informed the authors, but they resorted to
> manually copying over the files and suggested using ActivePerl 5.8.8!
> This is not good as far as making testing easy - although I hope that
> once i've installed the latest version of ExtUtils::MakeMaker and the
> Bioperl dependencies, I'll be able to run the tests.

If you download the free MS Visual C++ Express Edition, it comes with a much
newer version of nmake:

G:\Program Files\Microsoft Visual Studio 8\VC>nmake -help

Microsoft (R) Program Maintenance Utility Version 8.00.50727.42

It's available here:


That may resolve the issue.

> Another thing is the lack of the correct implementation of some ppd
> modules, but that hopefully, should be reasonable straight forward.
> Nathan

Which ones were you thinking of?  GD::SVG and Text::Shellwords are both
available on the bioperl site; we could add others as needed if they aren't
available through ActiveState or the other repositories.

The critical issue is that of binary compatibility between 5.6.1 and the
various 5.8.x versions of perl.  However, there are no binary components for
Bioperl.  One could probably modify the ppd file to deal with both versions
(similar to the older ppd files in bioperl.org/DIST.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign


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