Bug #89439 for Bio-Homology-InterologWalk: bug report

>>> Sun Oct 13 17:15:46 2013: Request 89439 was acted upon. >>> Transaction: Ticket created by karaltn@gmail.com >>> Queue: Bio-Homology-InterologWalk >>> Subject: bug report >>> Broken in: (no value) >>> Severity: (no value) >>> Owner: Nobody >>> Requestors: karaltn@gmail.com >>> Status: new >>> Ticket <URL: https://rt.cpan.org/Ticket/Display.html?id=89439 > >>> >>> >>> Hi, >>> >>> I recently installed "Bio-Homology-InterologWalk-0.6b" and when I run >>> "doInterologWalk.pl" I am getting following two error. First error not >>> stopping the script but after second error its killing the process. I >>> copied and pasted errors from terminal and I also copied and pasted

>>> lines with error from my script (InterologWalk.pm). I am using ensemble >>> version 73. >>> >>> I hope this information will be enough for you to help me solve this >>> problem. If you need anything else please inform me about it. >>> ......... >>> ......... >>> ........ >>> >>> Querying Ensembl Compara (multi) for orthologues---- >>> *First error:* Use of uninitialized value in hash element at >>> /usr/local/lib/perl5/site_perl/5.18.1/Bio/Homology/InterologWalk.pm line >>> 945. >>> >>> "line945 : foreach my $genome (@{$all_genome_dbs}){ >>> $genome_taxon_ids{$genome->taxon_id} = 1; >>> $genome_names{$genome->name} = 1; >>> }" >>> >>> 64 genomes found in database: multi. >>> >>> ENSMUSG00000000326 Comt ..69 orthologue(s). >>> ENSMUSG00000001323 Srr ..64 orthologue(s). >>> ENSMUSG00000001632 Brpf1 ..61 orthologue(s). >>> ...... >>> ...... >>> ...... >>> Total number of interactions: 101. >>> Total Number of Unique NCBI taxa IDs: 7. >>> >>> ----Querying Ensembl Compara (multi) for orthologues back in Mus >>> musculus---- >>> *Second error:*Use of uninitialized value in hash element at >>> /usr/local/lib/perl5/site_perl/5.18.1/Bio/Homology/InterologWalk.pm line >>> 1436. >>> get_backward_orthologies: impossible to get a protein tree adaptor for

>>> multi >>> No orthologues found back in Mus musculus. Exiting.. >>> There were errors. Stopping.. >>> >>> >>> line 1436 : "foreach my $genome (@{$all_genome_dbs}){ >>> $genome_taxon_ids{$genome->taxon_id} = 1; >>> $genome_names{$genome->name} = 1; >>> }" >>> >>> I am looking forward to hear from you. >>> >>> Best regards >>> Altan >>>

>>> <URL: https://rt.cpan.org/Ticket/Display.html?id=89439 > >>> >>> Hello Altan >>> >>> I am testing Bio::Homology::InterologWalk v 0.6b with Ensembl v64 and it >>> seems to work on my platform. >>> >>> In order to make it easier for me to debug the errors you're seeing, >>> could you please test it once more, following these steps (I'm assuming >>> you're on a linux machine): >>> >>> 1-Please delete any instances of the ensembl API you might have >>> previously installed. In your home directory, create a src directory and >>> cd into it. >>> >>> #------------ >>> cd ~ >>> mkdir src >>> cd src >>> #------------ >>> >>> 2-Install Bioperl 1.2.3 as described here >>> >>> http://www.ensembl.org/info/docs/api/api_cvs.html >>> >>> 3-Install the full Ensembl-64 api typing the following commands: >>> >>> #------------------------------------- >>> cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl login >>> Logging in to :pserver:cvsuser@cvs.sanger.ac.uk:2401/cvsroot/ensembl >>> CVS password: CVSUSER >>> >>> cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r >>> branch-ensembl-64 ensembl-api >>> #------------------------------------- >>> The second command is particularly important - you will need ALL the >>> APIs for the module to work correctly. >>> >>> 4-At this stage, if all has gone smoothly, you should have the following >>> four directories under /home/YOURNAME/src: >>> >>> bioperl-live >>> ensembl >>> ensembl-compara >>> ensembl-external >>> ensembl-functgenomics >>> ensembl-tools >>> ensembl-variation >>> >>> 5-Set up your environment as described here >>> http://www.ensembl.org/info/docs/api/api_installation.html >>> >>> For example, for a fedora/RH linux machine, you'd open your .bashrc file >>> and type in the paths to those directories in point (4), as follows (I'm >>> assuming the vim editor is installed on your system, otherwise maybe try >>> gedit): >>> >>> #------------- >>> vim ~/.bashrc >>> #------------- >>> and type the following at the bottom of the file: >>> #-------------- >>> PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-1.2.3 >>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules >>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules >>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules >>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules >>> export PERL5LIB >>> #----------------- >>> #(no need to export paths to ensembl-tools and ensembl-external) >>> >>> Now save the file, and exit. Log off the session and log in again (This >>> is very important for the changes you've made to .bashrc to have effect) >>> >>> 6-At this time your Ensembl/Bioperl configuration should be complete. >>> You may now attempt the installation of Bio::Homology::InterologWalk. >>> Download it from here: >>> >>> #---------- >>> wget >>> >>> http://search.cpan.org/CPAN/authors/id/G/GG/GGALLONE/Bio-Homology-InterologWalk-0.6b.tar.gz >>> #---------- >>> >>> then >>> >>> #---------- >>> tar xzvf Bio-Homology-InterologWalk-0.6b.tar.gz >>> #---------- >>> >>> and >>> >>> #---------- >>> cd Bio-Homology-InterologWalk-0.6b >>> #---------- >>> >>> now you can follow the included README for installation. Basically you'll >>> do >>> >>> #---------- >>> perl Makefile.PL >>> #---------- >>> >>> the output should be the following (provided you have all the >>> prerequisite modules installed) >>> >>> #---------- >>> Checking for recommended module Algorithm::Combinatorics >= 0.25 ... ok. >>> Checking for required module Bio::EnsEMBL::Registry ... ok. >>> Checking for required module Bio::Perl ... ok. >>> Checking for required module Carp ... ok. >>> Checking for required module DBD::CSV ... ok. >>> Checking for recommended module Data::PowerSet >= 0.05 ... ok. >>> Checking for required module File::Glob ... ok. >>> Checking for required module GO::Parser ... ok. >>> Checking for recommended module Getopt::Long >= 2.38 ... ok. >>> Checking for recommended module Graph >= 0.94 ... ok. >>> Checking for required module List::Util ... ok. >>> Checking for required module REST::Client ... ok. >>> Checking for required module String::Approx ... ok. >>> Checking for recommended module URI::Escape >= 1.53 ... ok. >>> >>> Checking if your kit is complete... >>> Looks good >>> Writing Makefile for Bio::Homology::InterologWalk >>> #----------- >>> >>> Then you should do >>> >>> #---------- >>> make >>> #---------- >>> >>> which should give you the following output >>> >>> #------------------ >>> cp lib/Bio/Homology/InterologWalk.pm >>> blib/lib/Bio/Homology/InterologWalk.pm >>> Manifying blib/man3/Bio::Homology::InterologWalk.3pm >>> #------------------ >>> >>> next do a >>> >>> #------------ >>> make test >>> #------------ >>> This will take a while, and it will need a internet connection. It will >>> fail if the Ensembl/Intact services are down. A typical successful run >>> would look like this: >>> >>> #---------------------------- >>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >>> t/Bio-Homology-InterologWalk.t .. 1/19 # >>> # >>> # #######PLEASE NOTE###### >>> # ######################## >>> # In order for some of the following tests to succeed, >>> # remote services provided by Ensembl and Intact MUST BE ACTIVE. >>> # in case of multiple test failure, >>> # please check status of Ensembl services on announce@ensembl.org >>> # and status of EBI Intact PSICQUIC service on >>> # >>> www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS >>> # ######################## >>> # ######################## >>> # >>> # Testing interfaces to remote services..Please be patient.. >>> # >>> t/Bio-Homology-InterologWalk.t .. 13/19 add method for created_by at >>> /usr/local/share/perl5/GO/Handlers/obj.pm line 289, <GEN103> line 7644. >>> add method for creation_date at >>> /usr/local/share/perl5/GO/Handlers/obj.pm line 289, <GEN103> line 7644. >>> t/Bio-Homology-InterologWalk.t .. ok >>> All tests successful. >>> Files=1, Tests=19, 111 wallclock secs ( 0.05 usr 0.00 sys + 6.36 cusr >>> 0.26 csys = 6.67 CPU) >>> Result: PASS >>> #---------------------------------- >>> >>> After this you'd just do a >>> >>> make install >>> >>> Let me know how it goes. I'm in the process of simplifying the >>> documentation for a new release - apologies for the complexity. >>> >>> Cheers, G >>> >>> >>> >>> On 10/14/13 19:40, Altan Kara via RT wrote: >>> line 7. >>> line 7. >>> which >>> >>>