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

[Dan Bolser]

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.


> 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.
>>
>