[Bioperl-l] Budle::BioPerl dependency issues

Sat Nov 18 14:35:38 UTC 2006

It probably doesn't need to be pulled, just updated to fix errors,  
spelling, etc.  The problems reported with GD are common and normally  
are due to libgd issues or C code compilation problems during the  
test run (the DEPENDENCIES doc and wiki page indicate this).  DBI/ 
DBD::mysql is another one that sometimes requires finessing (I  
remember it giving problems on CygWin and Mac OS X).  Chris D.  
probably just needs a list of issues that need fixing.  You also have  
to realize we're heading into Thanksgiving so some people may be  
incommunicado for the time being.

Spelling is the main problem.  Beyond that there really isn't  
anything we can do about those requirements beside not requiring them  
(i.e. removing them then explaining that particular components won't  
work), but then it wouldn't be a proper Bundle package.  It's a  
catch-22.  If there isn't a place in the install docs yet some of  
these issues could use a bit more detail or explanation, or at least  
redirect to some proper installation instructions based on the platform.

I think, now that this is on CPAN, you'll likely see many more  
questions popping up.

Chris (F.)

On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote:

> Hi Chris,
>
> Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it  
> contains some errors. I think Sendu *may* have some further  
> instructions regarding
> this package a bit closer to the 1.5.2 release.
>
> Cheers
> Nathan
>
>
>
> Quoting gang wu <gwu at molbio.mgh.harvard.edu>:
>
>> Hi Nathan,
>>
>> Thanks for your message. I saw the
>> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you
>> use 'install Bundle::BioPerl', which will definitely frustrate a  
>> bunch
>> of users. Can this release be held for a while before most of the  
>> bugs
>> are cleared?
>>
>> Thanks again.
>> Gang
>>
>>
>> Gang
>>
>> Nathan Haigh wrote:
>>> Hi Gang,
>>>
>>> At the moment we are having a few teathing problems with CPAN  
>>> packages. I notice that you are trying to install the 1.5.2  
>>> release candidate 3 -
>> we are
>>> in the final stages of getting out the official 1.5.2 developer  
>>> release (hopefully in the next couple of weeks). There are indeed  
>>> a few things
>> wrong
>>> with the latest Bundle::BioPerl package but we thought we'd hold  
>>> off updating it until the 1.5.2 release (or shortly before).
>>>
>>> I think that the problem with CPAN installing dependencies is  
>>> that it has no way to correctly ordering the installation of  
>>> dependencies, such
>> that it
>>> may be neccessary to run the install several time in order to get  
>>> everything installed. For example, if prerequisite 2 depends on  
>>> prerequisite 1
>> and
>>> CPAN installs prerequisite 2 first, then it's test suite will  
>>> probably fail and thus the installation of the package siting  
>>> both these as
>>> dependencies will fail to install.
>>>
>>> I believe you are correct in the way you are installing bioperl,  
>>> but we still have a few issues to sort out with regards to the  
>>> CPAN packages -
>> these
>>> will definately be sorted out by the time of the 1.5.2 release in  
>>> a matter of weeks.
>>>
>>> If anyone is aware of a way to force CPAN to install modules in a  
>>> specific order, please let Sendu know - we may be able to make  
>>> the install
>> process
>>> much easier to the users.
>>>
>>> Thanks
>>> Nathan
>>>
>>>
>>> Quoting gang wu <gwu at molbio.mgh.harvard.edu>:
>>>
>>>
>>>> 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. 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.
>>>>
>>>> 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.
>>>>
>>>> So my question is : Is this the right way to install BioPerl? It  
>>>> took me
>>>> two days to figure it out but still not 100% sure all packages are
>>>> installed properly.
>>>>
>>>> Any feedback is appreciated.
>>>>
>>>> Gang
>>>>
>>>> =================================================
>>>> cpan> install Bundle::BioPerl
>>>> Ace is up to date.
>>>> Bio::ASN1::EntrezGene is up to date.
>>>> Class::AutoClass is up to date.
>>>> Clone is up to date.
>>>> Convert::Binary::C is up to date.
>>>> Running install for module Data::Stag::writer
>>>>
>>>>   The module Data::Stag::writer isn't available on CPAN.
>>>>
>>>>   Either the module has not yet been uploaded to CPAN, or it is
>>>>   temporary unavailable. Please contact the author to find out
>>>>   more about the status. Try 'i Data::Stag::writer'.
>>>> DBD::mysql is up to date.
>>>> GD::SVG is up to date.
>>>> GD is up to date.
>>>> Graph::Directed is up to date.
>>>> HTML::Parser is up to date.
>>>> Running install for module HTTP::Request::Common-
>>>>
>>>>   The module HTTP::Request::Common- isn't available on CPAN.
>>>>
>>>>   Either the module has not yet been uploaded to CPAN, or it is
>>>>   temporary unavailable. Please contact the author to find out
>>>>   more about the status. Try 'i HTTP::Request::Common-'.
>>>> LWP::UserAgent is up to date.
>>>> Set::Scalar is up to date.
>>>> SOAP::Lite is up to date.
>>>> Running install for module Spreadhseet::ParseExcel
>>>>
>>>>   The module Spreadhseet::ParseExcel isn't available on CPAN.
>>>>
>>>>   Either the module has not yet been uploaded to CPAN, or it is
>>>>   temporary unavailable. Please contact the author to find out
>>>>   more about the status. Try 'i Spreadhseet::ParseExcel'.
>>>> Storable is up to date.
>>>> SVG is up to date.
>>>> SVG::Graph is up to date.
>>>> Text::Shellwords is up to date.
>>>> XML::DOM::XPath is up to date.
>>>> XML::Parser::PerlSAX is up to date.
>>>> XML::SAX is up to date.
>>>> XML::SAX::Base is up to date.
>>>> XML::SAX::Writer is up to date.
>>>> XML::Simple is up to date.
>>>> XML::Twig is up to date.
>>>> XML::Writer is up to date.
>>>> Bundle summary: The following items in bundle Bundle::BioPerl had
>>>> installation problems:
>>>>   Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel
>>>> ====================================================
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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