[Bioperl-l] [bioperl-network] Not indexed by CPAN (#1)

Fields, Christopher J cjfields at illinois.edu
Mon Oct 17 15:40:26 EDT 2011


I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded.  It may take a little time to propagate, but try it out in a couple of hours, it should be fixed.

chris

On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote:

> Yes, I planned on that  but wanted to make sure everything was working from your end.   Will upload that in a bit. 
> 
> chris
> 
> On Oct 17, 2011, at 3:08 AM, Chad Davis wrote:
> 
>> The index looks good now, I'm able to get the bioperl-network distro
>> by depending on a module within it.
>> Would it be possible to do the same for a bioperl-run 1.6.901 release?
>> 
>> Cheers,
>> Chad
>> 
>> 
>> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J
>> <cjfields at illinois.edu> wrote:
>>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer).  We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo.
>>> 
>>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index?
>>> 
>>> chris
>>> 
>>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote:
>>> 
>>>> It's very likely related; bioperl-db suffers the same thing.  I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was.  We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works).
>>>> 
>>>> chris
>>>> 
>>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote:
>>>> 
>>>>> Because it may be related, I wanted to mention that I am having the
>>>>> same problem with Bioperl-Run. In this case, however, I can find the
>>>>> distribution via:
>>>>> 
>>>>> i /bioperl-run/
>>>>> 
>>>>> But searching for a containing module does not return the distribution:
>>>>> 
>>>>> i /clustalw/
>>>>> 
>>>>> Chad
>>>>> 
>>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>>>> Chris,
>>>>>> 
>>>>>> OK, tell me what they say when you hear from them.
>>>>>> 
>>>>>> BIO
>>>>>> 
>>>>>> 
>>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote:
>>>>>> 
>>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section.  I've emailed modules at perl to see if they can diagnose it.  It's likely due to the version in that section.
>>>>>>> 
>>>>>>> chris
>>>>>>> 
>>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote:
>>>>>>> 
>>>>>>>> Yes, BOSBORNE.
>>>>>>>> 
>>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote:
>>>>>>>> 
>>>>>>>>> Brian,
>>>>>>>>> 
>>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer).  Is yours BOSBORNE?
>>>>>>>>> 
>>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org.  I did notice that cpanm attempted to install an older version (1.6.0).  I'll try a new upload (1.6.901), see if that helps.
>>>>>>>>> 
>>>>>>>>> chris
>>>>>>>>> 
>>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote:
>>>>>>>>> 
>>>>>>>>>> bioperl-l,
>>>>>>>>>> 
>>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this.
>>>>>>>>>> 
>>>>>>>>>> Brian O.
>>>>>>>>>> 
>>>>>>>>>> Begin forwarded message:
>>>>>>>>>> 
>>>>>>>>>>> From: "Chad A. Davis" <reply+i-1899390-b955d156f163b5a53fbf88e3f2e177363804adfa at reply.github.com>
>>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT
>>>>>>>>>>> To: bosborne <bosborne11 at verizon.net>
>>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1)
>>>>>>>>>>> 
>>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step.
>>>>>>>>>>> 
>>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi
>>>>>>>>>>> 
>>>>>>>>>>> CPAN 1.9800
>>>>>>>>>>> 
>>>>>>>>>>> --
>>>>>>>>>>> Reply to this email directly or view it on GitHub:
>>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1
>>>>>>>>>> 
>>>>>>>>>> 
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>>>>>>> 
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