[Bioperl-l] Budle::BioPerl dependency issues

Lincoln Stein lincoln.stein at gmail.com
Sat Nov 18 12:13:10 EST 2006


What version of libgd do you have installed? With recent versions of libgd
(more recent than two years old) you will not be given the chance to select
whether to compile JPEG, GIF and XPM support, since these options are
selected automatically by running libgd-config.

Lincoln

On 11/18/06, gang wu <gwu at molbio.mgh.harvard.edu> wrote:
>
>
> Sendu Bala wrote:
> > gang wu wrote:
> >> Hi everyone,
> >>
> >> I saw some problems when installing BioPerl
> >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN
> could
> >> not solve all the dependency issues with one shot of 'install
> >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be
> >> installed.
> >
> > What problems did you run into specifically with GD?
> If I enable JPEG, GIFS and  XPM,  none of the test could pass. Since I
> usually use only PNG for output, I can live without them. I am not sure
> if it's system related problem. All of them work fine with my 32 bit
> Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer
> libgd runnig Redhat AS4 AMD/EM64T does not work.
> >
> >> And it turned out that CPAN refused to install BioPerl with
> >> some test return value 255. Then I went to /root/.cpan/build to
> >> configure, test, rebuild those problematic packages. After several more
> >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl
> >> successfully.
> >
> > Do you remember what the other problematic packages were, and what you
> > had to do to get them working?
> >
> XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I
> guess it should be XML::DOM::XPath.pm. I could not recall what other
> packages had issues, but basically it's special package configuration
> issue.
> >> Below attached is the output of CPAN, which stills complains three
> >> packages have issues: Data::Stag::writer HTTP::Request::Common-
> >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in
> >> the Bundle::BioPerl. And the third module is not on the server and
> could
> >> be found on the CPAN site.
> >
> > All three are typos. We'll get those fixed.
> >
> >
> >> So my question is : Is this the right way to install BioPerl?
> >
> > At the present moment, yes. For 1.5.2 I'll probably be recommending
> > not using Bundle::BioPerl once I fix some other things.
> >
> See my another message for other issues.
> >
> >> It took me two days to figure it out but still not 100% sure all
> >> packages are
> >> installed properly.
> >
> > I'm sorry for the troubles you ran into. We'll try and do better for
> > the final release of 1.5.2.
> Actually your hard work is benifiting the whole community and we all owe
> you a Thank You.
>
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>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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