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

[Dan Bolser]

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?


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.
>