Commit b22bf0eb authored by Andreas Tille's avatar Andreas Tille

For some reason Ensembl.t test is executed in autopkgtest run even if it...

For some reason Ensembl.t test is executed in autopkgtest run even if it should be skipped due to missing preconditions
parent 45506cab
......@@ -3,3 +3,9 @@ are disabled by default as network connectivity is not guaranteed in the Debian
build daemons. But it is very recommended to run them locally before uploading
this package. To do this, set the DEB_MAINTAINER_MODE environment variable
(see debian/rules).
Further tests need packaging of:
Bio/DB/EUtilities.pm (http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm)
Bio/FeatureIO.pm (http://search.cpan.org/~cjfields/Bio-FeatureIO-1.6.905/lib/Bio/FeatureIO.pm)
Bio/SeqFeature/Annotated.pm (http://search.cpan.org/~cjfields/Bio-FeatureIO-1.6.905/lib/Bio/SeqFeature/Annotated.pm)
bioperl-run (1.7.1-4) UNRELEASED; urgency=medium
* For some reason Ensembl.t test is executed in autopkgtest run even
if it should be skipped due to missing preconditions
(http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm)
The test will now be fully removed to make sure it is skipped.
-- Andreas Tille <tille@debian.org> Sat, 14 Jan 2017 19:13:53 +0100
bioperl-run (1.7.1-3) unstable; urgency=medium
* s/Conflicts/Breaks/
......
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 14 Jan 2017 19:13:53 +0100
Description: For some reason Ensembl.t test is executed in autopkgtest run even
if it should be skipped due to missing preconditions
(http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm)
The test will now be fully removed to make sure it is skipped.
--- a/t/Ensembl.t
+++ /dev/null
@@ -1,71 +0,0 @@
-# -*-Perl-*-
-## Bioperl Test Harness Script for Modules
-
-use strict;
-
-BEGIN {
- use Bio::Root::Test;
- test_begin(-tests => 7,
- -requires_networking => 1);
- use_ok('Bio::Tools::Run::Ensembl');
-}
-
-my $setup_ok = Bio::Tools::Run::Ensembl->registry_setup();
-
-# test database access
-SKIP: {
- test_skip(-tests => 6, -requires_module => 'Bio::EnsEMBL::Registry');
- skip("There was some problem contacting the EnsEMBL database?", 6) unless $setup_ok;
-
- # get an adaptor
- ok my $adaptor = Bio::Tools::Run::Ensembl->get_adaptor('human', 'Exon');
- isa_ok $adaptor, 'Bio::EnsEMBL::DBSQL::ExonAdaptor';
- if ($adaptor->can('species_id')) {
- is $adaptor->species_id, 1;
- }
- else {
- ok 1;
- }
-
- # get an 'easy' gene - one that is in Ensembl
- ok my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- -name => 'BRCA2');
- isa_ok $gene, 'Bio::EnsEMBL::Gene';
- is $gene->external_name, 'BRCA2';
-
-
- #*** don't know suitable gene names to test the following, to be completed...
-
- # get one that isn't in human, but is in an orthologue
- my $orth_only = '??';
- #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- # -name => $orth_only);
- #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- # -use_orthologues => 'Mus musculus',
- # -name => $orth_only);
- #is $gene->external_name, $orth_only;
-
- # get one that isn't in Ensembl but is in Swissprot
- my $swiss_only = '??';
- #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- # -use_orthologues => 'Mus musculus',
- # -name => $swiss_only);
- #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- # -use_orthologues => 'Mus musculus',
- # -use_swiss_lookup => 1,
- # -name => $swiss_only);
- #is $gene->external_name, $swiss_only;
-
- # get one that isn't in Swissprot either, but is in NCBI
- my $ncbi_only = '??';
- #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- # -use_orthologues => 'Mus musculus',
- # -use_swiss_lookup => 1,
- # -name => $ncbi_only);
- #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
- # -use_orthologues => 'Mus musculus',
- # -use_swiss_lookup => 1,
- # -use_entrez_lookup => 1,
- # -name => $ncbi_only);
- #is $gene->external_name, $ncbi_only;
-}
......@@ -8,3 +8,4 @@ skip_tests_for_muscle.patch
skip_tests_for_ncbi-blast+.patch
skip_tests_for_maq.patch
hyphy.patch
remove_tests_for_ensembl.patch
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