[Bioperl-l] Budle::BioPerl dependency issues

Chris Dagdigian dag at sonsorol.org
Sat Nov 18 17:47:07 UTC 2006 

Hi folks,

On November 17th, Victor de Jager filed a bug report with CPAN  
(thanks Victor!) covering the following issues with the 2.1.6 bundle:

> Bundle summary: The following items in bundle Bundle::BioPerl had
> installation problems:
> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel
>
> This should be Spreadsheet::ParseExcel of course.
> Data::Stag::writer does not exist in CPAN, should be  
> Data::Stag::Writer
>
> Hope it helps, meanwhile I got around using the CVS version.
> Best regards

I immediately fixed the errors and uploaded version 2.1.7 on the same  
day, by now it has probably propagated through the CPAN mirror system  
but you can find it directly here:

http://search.cpan.org/~craffi/

Please let me know directly (email: dag at sonsorol.org) if there are  
*other* things that need to be added or updated.

Sorry for the problems with 2.1.6 -- the contents of that Bundle were  
given to me by someone else on Oct 17th :) and I think I was sitting  
on a plane at the time and did not have time to do a local CPAN test  
with it. My apologies.

Regards,
Chris





On Nov 18, 2006, at 9:35 AM, Chris Fields wrote:

> 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
>>>>>
>>>>>
>>>>
>>>>
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>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>>
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>

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