[ensembl-dev] updating ensembl 79->80 issue

[mag]

Hi Nathalie,

The script seems to be complaining about a missing PrimarySeqI.pm module
This module is part of bioperl and that dependency has been in Ensembl 
since 2004.

Can you please check if it is in your local bioperl installation?
Also, I notice that you checked out bioperl version 1.6.1, which is now 
the officially used version, but your PERL5LIB points to a bioperl-1.2.3 
directory.
PrimarySeqI.pm is included in both versions of bioperl, so that should 
not matter here, but it might be worth checking both directories are 
complete.


Regards,
Magali

On 17/06/2015 13:49, Nathalie Conte wrote:
> hi
> I am updating ensembl from 79 to 80 using git
> $ mkdir src
> $ cd src
> $ git clone https://github.com/bioperl/bioperl-live.git
> $ cd bioperl-live
> $ git checkout bioperl-release-1-6-1
> $ cd -
> $ git clone https://github.com/Ensembl/ensembl-git-tools.git
> $ export PATH=$PWD/ensembl-git-tools/bin:$PATH
> $ git clone https://github.com/Ensembl/ensembl.git
> $ git clone https://github.com/Ensembl/ensembl-variation.git
> $ git clone https://github.com/Ensembl/ensembl-funcgen.git
> $ git clone https://github.com/Ensembl/ensembl-compara.git
>
> I check that everything is installed fine.
>
>
> I get this error message using a script to get LD scores from slice objects. the script works well on 79
>
> -------------------- WARNING ----------------------
> MSG: 'Bio::EnsEMBL::DBSQL::SliceAdaptor' cannot be found.
> Exception Can't locate Bio/PrimarySeqI.pm in @INC (@INC contains: /homes/perl5lib/lib/perl5/x86_64-linux-thread-multi /homes/perl5lib/lib/perl5 home/src home/src/bioperl-1.2.3 home/src/ensembl/modules home/src/ensembl-compara/modules home/src/ensembl-variation/modules home/src/ensembl-functgenomics/modules home/src/ensembl-functgenomics/modules /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib/x86_64-linux-thread-multi /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib64 /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib64/perl5/site_perl /nfs/ma/home/svn-database/PhenoBridge/Scripts/BioSD-master/lib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at home/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 74.
> BEGIN failed--compilation aborted at home/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 74.
> Compilation failed in require at home/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 108.
> BEGIN failed--compilation aborted at home/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 108.
> Compilation failed in require at (eval 194) line 3.
>
>
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1040
> CALLED BY: ./testLD.pl  LINE: 19
> Date (localtime)    = Wed Jun 17 12:11:20 2015
> Ensembl API version = 80
> ---------------------------------------------------
> Can't call method "fetch_by_region" on an undefined value at ./testLD.pl line 21.
>
> any idea on what is wrong?
> thanks
> Nathalie
>
>
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