[Bioperl-l] Undefined subroutine &Bio::DB::SeqFeature::Store::uncompress called

[Dan Bolser]

On 27 January 2011 10:37, Dan Bolser <dan.bolser at gmail.com> wrote:
> On 27 January 2011 10:13, Dan Bolser <dan.bolser at gmail.com> wrote:
>> On 26 January 2011 16:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>>> Hi,
>>>
>>> I just updated BioPerl from git / GBrowse from svn (to check if a
>>
>> So is it true that 'latest' GBrowse has a maximum BioPerl version requirement?
>>
>> v1.6.1 ?
>>
>> The only only 'release' branch I could find was "origin/release-1-6-2"...
>>
>> After ./Build install I still see the same error. Can someone create a
>> v1.6.1 branch? Or should I use a tag?
>
> OK, I used the bioperl-release-1-6-1 tag.
>
> perl Build.PL gave the following error (for reference):
>
> Can't find dist packages without a MANIFEST file - run 'manifest'
> action first at Bio/Root/Build.pm line 605, <STDIN> line 4.
>
> WARNING: Possible missing or corrupt 'MANIFEST' file.
> Nothing to enter for 'provides' field in META.yml
> Creating new 'Build' script for 'BioPerl' version '1.006001'
>
>
> Tested and installed fine, but didn't fix the GBrowse issue. I guess
> this requires a GB roll back rather than a BP roll back.

So... I'm rolling back GB release by release using "svn switch" here:
https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/


I'm back to 2.17 and I finally see this problem clear up. As
mentioned, this is with BioPerl 'tag' 1.6.1.

Interestingly, I still don't see any features (I don't see the error,
and I do see the overview and details panels showing correctly). Now
I'm seeing an error in the error_log like this:

[Thu Jan 27 12:10:32 2011] [error] [client x.x.x.x] Use of
uninitialized value in string comparison (cmp) at
/homes/www-potato/perl5/lib/perl5/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm
line 1909., referer:
https://x/potato/cgi-bin/gbrowse2/gbrowse/pot_qa/?name=PGSC0003DMB000000115%3A1..600%2C001


However, updating back to the latest bioperl-live fixes this issue
(i.e. the bioperl version was a red-herring).


Cheers,
Dan.

>> Cheers,
>> Dan.
>>
>> P.S. I have largely revised* and then followed the the guide here:
>>
>> http://www.bioperl.org/wiki/Using_Git
>> http://www.bioperl.org/wiki/Using_Git#Release_branches
>>
>>
>> After perl Build.PL I see the following error (just for reference):
>>
>> Use of uninitialized value in split at Bio/Root/Build.pm line 769,
>> <STDIN> line 3.
>>
>>
>> After ./Build test:
>>
>> Test Summary Report
>> -------------------
>> t/SeqIO/embl.t                             (Wstat: 512 Tests: 85 Failed: 0)
>>  Non-zero exit status: 2
>>  Parse errors: Bad plan.  You planned 95 tests but ran 85.
>> Files=350, Tests=24189, 280 wallclock secs ( 8.85 usr  2.37 sys +
>> 210.23 cusr 28.67 csys = 250.12 CPU)
>> Result: FAIL
>> Failed 1/350 test programs. 0/24189 subtests failed.
>>
>>
>> * I moved the bulk of the content here (as it is only relevant for a
>> small group of developers):
>> http://www.bioperl.org/wiki/Using_Git/Advanced
>>
>> I figure splitting out the page gives each part a clearer focus,
>> allowing them to be improved more easily.
>>
>>> particular bug was fixed), and I'm seeing the following message in
>>> large friendly red letters across the top of my GBrowse instance:
>>>
>>> Undefined subroutine &Bio::DB::SeqFeature::Store::uncompress called.
>>>
>>>
>>> Unfortunately, none of the usual sequence features are displayed (no
>>> overview or details panels).
>>>
>>> Here is a snippet of the Apache error log:
>>>
>>> [Wed Jan 26 16:55:15 2011] [error] [client x.x.x.x] Math::BigInt:
>>> couldn't load specified math lib(s), fallback to Math::BigInt::Calc at
>>> /homes/www-potato/perl5/lib/perl5/Crypt/DH.pm line 6, referer:
>>> https://x/potato/cgi-bin/gbrowse2/gbrowse/pot_qa/?name=PGSC0003DMB000000115%3A1..600%2C001
>>> [Wed Jan 26 16:55:15 2011] [error] [client x.x.x.x] Math::BigInt:
>>> couldn't load specified math lib(s), fallback to Math::BigInt::Calc at
>>> /homes/www-potato/perl5/lib/perl5/Crypt/DH.pm line 6, referer:
>>> https://x/potato/cgi-bin/gbrowse2/gbrowse/pot_qa/?name=PGSC0003DMB000000115%3A1..600%2C001
>>> [Wed Jan 26 16:55:15 2011] [error] [client x.x.x.x] Undefined
>>> subroutine &Bio::DB::SeqFeature::Store::uncompress called at
>>> /homes/www-potato/perl5/lib/perl5/Bio/DB/SeqFeature/Store.pm line
>>> 2531., referer:
>>> https://x/potato/cgi-bin/gbrowse2/gbrowse/pot_qa/?name=PGSC0003DMB000000115%3A1..600%2C001
>>>
>>>
>>>
>>> Thanks for guidance,
>>> Dan.
>>>
>>
>