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

[Nathalie Conte]

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