[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?

Or should I simply not be using GBrowse from SVN?


> 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?
>
>
> 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.
>>
>