From 543e0060151a0e12d3e7f49b476c4fff897df034 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Carn=C3=AB=20Draug?= Date: Tue, 25 Sep 2018 19:24:19 +0100 Subject: [PATCH] t/*: remove "use lib '.'" and t/lib/Error.pm I'm guessing this was here for a reason a long time ago but seems like it's no longer necessary. --- t/Align/AlignStats.t | 1 - t/Align/AlignUtil.t | 1 - t/Align/SimpleAlign.t | 1 - t/Align/TreeBuild.t | 1 - t/Align/Utilities.t | 1 - t/AlignIO/AlignIO.t | 1 - t/AlignIO/arp.t | 1 - t/AlignIO/bl2seq.t | 1 - t/AlignIO/clustalw.t | 1 - t/AlignIO/emboss.t | 1 - t/AlignIO/fasta.t | 1 - t/AlignIO/largemultifasta.t | 1 - t/AlignIO/maf.t | 1 - t/AlignIO/mase.t | 1 - t/AlignIO/mega.t | 1 - t/AlignIO/meme.t | 1 - t/AlignIO/metafasta.t | 1 - t/AlignIO/msf.t | 1 - t/AlignIO/nexus.t | 1 - t/AlignIO/pfam.t | 1 - t/AlignIO/phylip.t | 1 - t/AlignIO/po.t | 1 - t/AlignIO/prodom.t | 1 - t/AlignIO/psi.t | 1 - t/AlignIO/selex.t | 1 - t/AlignIO/xmfa.t | 1 - t/Alphabet.t | 1 - t/Annotation/Annotation.t | 1 - t/Annotation/AnnotationAdaptor.t | 1 - t/LocalDB/Fasta.t | 1 - t/LocalDB/Flat.t | 1 - t/LocalDB/Index/Blast.t | 1 - t/LocalDB/Index/BlastTable.t | 1 - t/LocalDB/Index/Index.t | 1 - t/LocalDB/Qual.t | 1 - t/LocalDB/Registry.t | 1 - t/LocalDB/Taxonomy/greengenes.t | 1 - t/LocalDB/Taxonomy/silva.t | 1 - t/Map/Cyto.t | 1 - t/Map/Linkage.t | 1 - t/Map/Map.t | 1 - t/Map/MapIO.t | 1 - t/Map/MicrosatelliteMarker.t | 1 - t/Map/Physical.t | 1 - t/Matrix/IO/masta.t | 1 - t/Matrix/IO/psm.t | 1 - t/Matrix/InstanceSite.t | 1 - t/Matrix/Matrix.t | 1 - t/Matrix/ProtMatrix.t | 1 - t/Matrix/ProtPsm.t | 1 - t/Matrix/SiteMatrix.t | 1 - t/Ontology/GOterm.t | 1 - t/Ontology/GraphAdaptor.t | 1 - t/Ontology/IO/go.t | 1 - t/Ontology/IO/interpro.t | 1 - t/Ontology/IO/obo.t | 1 - t/Ontology/Ontology.t | 1 - t/Ontology/OntologyEngine.t | 1 - t/Ontology/OntologyStore.t | 1 - t/Ontology/Relationship.t | 1 - t/Ontology/RelationshipType.t | 1 - t/Ontology/Term.t | 1 - t/RemoteDB/BioFetch.t | 1 - t/RemoteDB/EMBL.t | 1 - t/RemoteDB/EntrezGene.t | 1 - t/RemoteDB/GenBank.t | 1 - t/RemoteDB/GenPept.t | 1 - t/RemoteDB/Query/GenBank.t | 1 - t/RemoteDB/RefSeq.t | 1 - t/RemoteDB/SeqRead_fail.t | 1 - t/RemoteDB/SeqVersion.t | 1 - t/RemoteDB/SwissProt.t | 1 - t/RemoteDB/Taxonomy.t | 1 - t/Root/HTTPget.t | 1 - t/Root/IO.t | 1 - t/Root/RootI.t | 1 - t/Root/RootIO.t | 1 - t/Root/Storable.t | 1 - t/Root/Utilities.t | 1 - t/SearchIO/CigarString.t | 1 - t/SearchIO/SearchIO.t | 1 - t/SearchIO/SimilarityPair.t | 1 - t/SearchIO/Tiling.t | 1 - t/SearchIO/Writer/GbrowseGFF.t | 1 - t/SearchIO/Writer/HSPTableWriter.t | 1 - t/SearchIO/Writer/HTMLWriter.t | 1 - t/SearchIO/Writer/HitTableWriter.t | 1 - t/SearchIO/Writer/TextWriter.t | 1 - t/SearchIO/axt.t | 1 - t/SearchIO/blast.t | 1 - t/SearchIO/blast_pull.t | 1 - t/SearchIO/blasttable.t | 1 - t/SearchIO/cross_match.t | 1 - t/SearchIO/erpin.t | 1 - t/SearchIO/exonerate.t | 1 - t/SearchIO/fasta.t | 1 - t/SearchIO/gmap_f9.t | 1 - t/SearchIO/infernal.t | 1 - t/SearchIO/megablast.t | 1 - t/SearchIO/psl.t | 1 - t/SearchIO/rnamotif.t | 1 - t/SearchIO/sim4.t | 1 - t/SearchIO/waba.t | 1 - t/SearchIO/wise.t | 1 - t/Seq/DBLink.t | 1 - t/Seq/EncodedSeq.t | 1 - t/Seq/LargeLocatableSeq.t | 1 - t/Seq/LargePSeq.t | 1 - t/Seq/LocatableSeq.t | 1 - t/Seq/MetaSeq.t | 1 - t/Seq/PrimaryQual.t | 1 - t/Seq/PrimarySeq.t | 1 - t/Seq/PrimedSeq.t | 1 - t/Seq/Quality.t | 1 - t/Seq/Seq.t | 1 - t/Seq/SimulatedRead.t | 1 - t/Seq/WithQuality.t | 1 - t/SeqFeature/Amplicon.t | 1 - t/SeqFeature/Clone.t | 1 - t/SeqFeature/Collection.t | 1 - t/SeqFeature/Computation.t | 1 - t/SeqFeature/FeaturePair.t | 1 - t/SeqFeature/Gene.t | 1 - t/SeqFeature/Generic.t | 1 - t/SeqFeature/Location.t | 1 - t/SeqFeature/LocationFactory.t | 1 - t/SeqFeature/Primer.t | 1 - t/SeqFeature/Range.t | 1 - t/SeqFeature/RangeI.t | 1 - t/SeqFeature/SeqAnalysisParser.t | 1 - t/SeqFeature/SubSeq.t | 1 - t/SeqFeature/Unflattener.t | 1 - t/SeqIO/Handler.t | 1 - t/SeqIO/MultiFile.t | 1 - t/SeqIO/Multiple_fasta.t | 1 - t/SeqIO/SeqBuilder.t | 1 - t/SeqIO/SeqIO.t | 1 - t/SeqIO/Splicedseq.t | 1 - t/SeqIO/ace.t | 1 - t/SeqIO/agave.t | 1 - t/SeqIO/asciitree.t | 1 - t/SeqIO/bsml.t | 1 - t/SeqIO/bsml_sax.t | 1 - t/SeqIO/chadoxml.t | 1 - t/SeqIO/chaos.t | 1 - t/SeqIO/chaosxml.t | 1 - t/SeqIO/embl.t | 1 - t/SeqIO/fasta.t | 1 - t/SeqIO/fastq.t | 1 - t/SeqIO/flybase_chadoxml.t | 1 - t/SeqIO/game.t | 1 - t/SeqIO/gbxml.t | 1 - t/SeqIO/gcg.t | 1 - t/SeqIO/genbank.t | 1 - t/SeqIO/interpro.t | 1 - t/SeqIO/kegg.t | 1 - t/SeqIO/largefasta.t | 1 - t/SeqIO/lasergene.t | 1 - t/SeqIO/locuslink.t | 1 - t/SeqIO/mbsout.t | 1 - t/SeqIO/metafasta.t | 1 - t/SeqIO/msout.t | 1 - t/SeqIO/phd.t | 1 - t/SeqIO/pir.t | 1 - t/SeqIO/qual.t | 1 - t/SeqIO/raw.t | 1 - t/SeqIO/scf.t | 1 - t/SeqIO/strider.t | 1 - t/SeqIO/swiss.t | 1 - t/SeqIO/tab.t | 1 - t/SeqIO/table.t | 1 - t/SeqIO/tigr.t | 1 - t/SeqIO/tigrxml.t | 1 - t/SeqIO/tinyseq.t | 1 - t/SeqTools/CodonTable.t | 1 - t/SeqTools/ECnumber.t | 1 - t/SeqTools/GuessSeqFormat.t | 1 - t/SeqTools/OddCodes.t | 1 - t/SeqTools/SeqPattern.t | 1 - t/SeqTools/SeqStats.t | 1 - t/SeqTools/SeqUtils.t | 1 - t/SeqTools/SeqWords.t | 1 - t/Species.t | 1 - t/Symbol.t | 1 - t/TaxonTree.t | 1 - t/Tools/Alignment/Consed.t | 1 - t/Tools/AmpliconSearch.t | 1 - t/Tools/Analysis/DNA/ESEfinder.t | 1 - t/Tools/Analysis/Protein/Domcut.t | 1 - t/Tools/Analysis/Protein/ELM.t | 1 - t/Tools/Analysis/Protein/GOR4.t | 1 - t/Tools/Analysis/Protein/HNN.t | 1 - t/Tools/Analysis/Protein/NetPhos.t | 1 - t/Tools/Analysis/Protein/Scansite.t | 1 - t/Tools/Analysis/Protein/Sopma.t | 1 - t/Tools/EMBOSS/Palindrome.t | 1 - t/Tools/Est2Genome.t | 1 - t/Tools/FootPrinter.t | 1 - t/Tools/GFF.t | 1 - t/Tools/Geneid.t | 1 - t/Tools/Genewise.t | 1 - t/Tools/Genomewise.t | 1 - t/Tools/Genpred.t | 1 - t/Tools/IUPAC.t | 1 - t/Tools/Lucy.t | 1 - t/Tools/Match.t | 1 - t/Tools/Phylo/Gerp.t | 1 - t/Tools/Phylo/Molphy.t | 1 - t/Tools/Phylo/Phylip/ProtDist.t | 1 - t/Tools/Primer3.t | 1 - t/Tools/Promoterwise.t | 1 - t/Tools/PrositeScan.t | 1 - t/Tools/Pseudowise.t | 1 - t/Tools/QRNA.t | 1 - t/Tools/RandDistFunctions.t | 1 - t/Tools/RepeatMasker.t | 1 - t/Tools/Seg.t | 1 - t/Tools/SiRNA.t | 1 - t/Tools/Sigcleave.t | 1 - t/Tools/Signalp.t | 1 - t/Tools/Signalp/ExtendedSignalp.t | 1 - t/Tools/Sim4.t | 1 - t/Tools/Spidey/Spidey.t | 1 - t/Tools/TandemRepeatsFinder.t | 1 - t/Tools/TargetP.t | 1 - t/Tools/Tmhmm.t | 1 - t/Tools/ePCR.t | 1 - t/Tools/pICalculator.t | 1 - t/Tools/tRNAscanSE.t | 1 - t/Tree/Compatible.t | 1 - t/Tree/Node.t | 1 - t/Tree/RandomTreeFactory.t | 1 - t/Tree/Tree.t | 1 - t/Tree/TreeIO.t | 1 - t/Tree/TreeIO/lintree.t | 1 - t/Tree/TreeIO/newick.t | 1 - t/Tree/TreeIO/nexus.t | 1 - t/Tree/TreeIO/nhx.t | 1 - t/Tree/TreeIO/phyloxml.t | 1 - t/Tree/TreeIO/tabtree.t | 1 - t/Tree/TreeStatistics.t | 1 - t/lib/Error.pm | 741 ------------------------------------ 242 files changed, 982 deletions(-) delete mode 100644 t/lib/Error.pm diff --git a/t/Align/AlignStats.t b/t/Align/AlignStats.t index 019000a2c..fc617be21 100644 --- a/t/Align/AlignStats.t +++ b/t/Align/AlignStats.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 45); diff --git a/t/Align/AlignUtil.t b/t/Align/AlignUtil.t index 9f6263af0..94b17c24f 100644 --- a/t/Align/AlignUtil.t +++ b/t/Align/AlignUtil.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 47 ); diff --git a/t/Align/SimpleAlign.t b/t/Align/SimpleAlign.t index af1dd3529..5386aa6ad 100644 --- a/t/Align/SimpleAlign.t +++ b/t/Align/SimpleAlign.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 206 ); diff --git a/t/Align/TreeBuild.t b/t/Align/TreeBuild.t index f11da43f6..fdcdb2971 100644 --- a/t/Align/TreeBuild.t +++ b/t/Align/TreeBuild.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 13); diff --git a/t/Align/Utilities.t b/t/Align/Utilities.t index b67cb0982..edb7e2ee6 100644 --- a/t/Align/Utilities.t +++ b/t/Align/Utilities.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/AlignIO/AlignIO.t b/t/AlignIO/AlignIO.t index e4d110c2d..925c8d2d8 100644 --- a/t/AlignIO/AlignIO.t +++ b/t/AlignIO/AlignIO.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27, diff --git a/t/AlignIO/arp.t b/t/AlignIO/arp.t index 869da432c..25f527377 100644 --- a/t/AlignIO/arp.t +++ b/t/AlignIO/arp.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 48, diff --git a/t/AlignIO/bl2seq.t b/t/AlignIO/bl2seq.t index d5cbb9753..e1d547c7d 100644 --- a/t/AlignIO/bl2seq.t +++ b/t/AlignIO/bl2seq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 7); diff --git a/t/AlignIO/clustalw.t b/t/AlignIO/clustalw.t index 56f5473aa..f09eadc0d 100644 --- a/t/AlignIO/clustalw.t +++ b/t/AlignIO/clustalw.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 6); diff --git a/t/AlignIO/emboss.t b/t/AlignIO/emboss.t index 643c10b20..9f79e69f2 100644 --- a/t/AlignIO/emboss.t +++ b/t/AlignIO/emboss.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 37); diff --git a/t/AlignIO/fasta.t b/t/AlignIO/fasta.t index af0064411..0b649d0fb 100644 --- a/t/AlignIO/fasta.t +++ b/t/AlignIO/fasta.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 12); diff --git a/t/AlignIO/largemultifasta.t b/t/AlignIO/largemultifasta.t index 45c3f1437..ebf28c9d5 100644 --- a/t/AlignIO/largemultifasta.t +++ b/t/AlignIO/largemultifasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 7); diff --git a/t/AlignIO/maf.t b/t/AlignIO/maf.t index ac73f0fd2..6096b38c8 100644 --- a/t/AlignIO/maf.t +++ b/t/AlignIO/maf.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 11); diff --git a/t/AlignIO/mase.t b/t/AlignIO/mase.t index e4f39af13..e1dff55ea 100644 --- a/t/AlignIO/mase.t +++ b/t/AlignIO/mase.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 3); diff --git a/t/AlignIO/mega.t b/t/AlignIO/mega.t index af9959322..5e3f3ab60 100644 --- a/t/AlignIO/mega.t +++ b/t/AlignIO/mega.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 6); diff --git a/t/AlignIO/meme.t b/t/AlignIO/meme.t index 5759f8450..cebd13e53 100644 --- a/t/AlignIO/meme.t +++ b/t/AlignIO/meme.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 20); diff --git a/t/AlignIO/metafasta.t b/t/AlignIO/metafasta.t index a7067ea24..531366f03 100644 --- a/t/AlignIO/metafasta.t +++ b/t/AlignIO/metafasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 4); diff --git a/t/AlignIO/msf.t b/t/AlignIO/msf.t index 456133623..3a6df7588 100644 --- a/t/AlignIO/msf.t +++ b/t/AlignIO/msf.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 4); diff --git a/t/AlignIO/nexus.t b/t/AlignIO/nexus.t index 8f53cb5bc..6773c9c99 100644 --- a/t/AlignIO/nexus.t +++ b/t/AlignIO/nexus.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 43); diff --git a/t/AlignIO/pfam.t b/t/AlignIO/pfam.t index 15fc303a5..dd1865838 100644 --- a/t/AlignIO/pfam.t +++ b/t/AlignIO/pfam.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5); diff --git a/t/AlignIO/phylip.t b/t/AlignIO/phylip.t index 0d20ee82e..875190fec 100644 --- a/t/AlignIO/phylip.t +++ b/t/AlignIO/phylip.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 20); diff --git a/t/AlignIO/po.t b/t/AlignIO/po.t index ae763828d..c75e3027f 100644 --- a/t/AlignIO/po.t +++ b/t/AlignIO/po.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 11); diff --git a/t/AlignIO/prodom.t b/t/AlignIO/prodom.t index 5721aed3e..62bc0d58c 100644 --- a/t/AlignIO/prodom.t +++ b/t/AlignIO/prodom.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 3); diff --git a/t/AlignIO/psi.t b/t/AlignIO/psi.t index 91402401c..2f46515ab 100644 --- a/t/AlignIO/psi.t +++ b/t/AlignIO/psi.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5); diff --git a/t/AlignIO/selex.t b/t/AlignIO/selex.t index ae89eb1a6..b5cb0d4a0 100644 --- a/t/AlignIO/selex.t +++ b/t/AlignIO/selex.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 4); diff --git a/t/AlignIO/xmfa.t b/t/AlignIO/xmfa.t index bada12bb6..bbb4af707 100644 --- a/t/AlignIO/xmfa.t +++ b/t/AlignIO/xmfa.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 30); diff --git a/t/Alphabet.t b/t/Alphabet.t index 0be221683..38033362e 100644 --- a/t/Alphabet.t +++ b/t/Alphabet.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 100); diff --git a/t/Annotation/Annotation.t b/t/Annotation/Annotation.t index 25748a8fd..a84db9055 100644 --- a/t/Annotation/Annotation.t +++ b/t/Annotation/Annotation.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 148, diff --git a/t/Annotation/AnnotationAdaptor.t b/t/Annotation/AnnotationAdaptor.t index 8825cde99..6e54202a9 100644 --- a/t/Annotation/AnnotationAdaptor.t +++ b/t/Annotation/AnnotationAdaptor.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 23); diff --git a/t/LocalDB/Fasta.t b/t/LocalDB/Fasta.t index 212f82e39..478a08b6a 100644 --- a/t/LocalDB/Fasta.t +++ b/t/LocalDB/Fasta.t @@ -1,5 +1,4 @@ BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 109, diff --git a/t/LocalDB/Flat.t b/t/LocalDB/Flat.t index 7d8a67382..0df394535 100644 --- a/t/LocalDB/Flat.t +++ b/t/LocalDB/Flat.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27, diff --git a/t/LocalDB/Index/Blast.t b/t/LocalDB/Index/Blast.t index 66ce0b319..686f7e4d3 100644 --- a/t/LocalDB/Index/Blast.t +++ b/t/LocalDB/Index/Blast.t @@ -6,7 +6,6 @@ use File::Spec; use File::Temp; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5, diff --git a/t/LocalDB/Index/BlastTable.t b/t/LocalDB/Index/BlastTable.t index 54aaf95e6..86a08b103 100644 --- a/t/LocalDB/Index/BlastTable.t +++ b/t/LocalDB/Index/BlastTable.t @@ -7,7 +7,6 @@ use File::Temp; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27, diff --git a/t/LocalDB/Index/Index.t b/t/LocalDB/Index/Index.t index d457a57b4..07be79f6b 100644 --- a/t/LocalDB/Index/Index.t +++ b/t/LocalDB/Index/Index.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 65, diff --git a/t/LocalDB/Qual.t b/t/LocalDB/Qual.t index e22876d4d..e9ff4a03e 100644 --- a/t/LocalDB/Qual.t +++ b/t/LocalDB/Qual.t @@ -1,5 +1,4 @@ BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 56, diff --git a/t/LocalDB/Registry.t b/t/LocalDB/Registry.t index b11b5aca1..8c6d1bbe6 100644 --- a/t/LocalDB/Registry.t +++ b/t/LocalDB/Registry.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/LocalDB/Taxonomy/greengenes.t b/t/LocalDB/Taxonomy/greengenes.t index f355d66b1..9f1fbd5bb 100644 --- a/t/LocalDB/Taxonomy/greengenes.t +++ b/t/LocalDB/Taxonomy/greengenes.t @@ -1,7 +1,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 38 ); use_ok('Bio::DB::Taxonomy'); diff --git a/t/LocalDB/Taxonomy/silva.t b/t/LocalDB/Taxonomy/silva.t index c4c2a3850..afc90923a 100644 --- a/t/LocalDB/Taxonomy/silva.t +++ b/t/LocalDB/Taxonomy/silva.t @@ -1,7 +1,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 42 ); use_ok('Bio::DB::Taxonomy'); diff --git a/t/Map/Cyto.t b/t/Map/Cyto.t index 57bb79ef8..1cceae054 100644 --- a/t/Map/Cyto.t +++ b/t/Map/Cyto.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 110); diff --git a/t/Map/Linkage.t b/t/Map/Linkage.t index af43aa04c..bc614a537 100644 --- a/t/Map/Linkage.t +++ b/t/Map/Linkage.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 18); diff --git a/t/Map/Map.t b/t/Map/Map.t index e44bb1946..84ecbe1e8 100644 --- a/t/Map/Map.t +++ b/t/Map/Map.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 267); diff --git a/t/Map/MapIO.t b/t/Map/MapIO.t index 505a26832..2360368be 100644 --- a/t/Map/MapIO.t +++ b/t/Map/MapIO.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 51); diff --git a/t/Map/MicrosatelliteMarker.t b/t/Map/MicrosatelliteMarker.t index d4a9d2d1a..562f66576 100644 --- a/t/Map/MicrosatelliteMarker.t +++ b/t/Map/MicrosatelliteMarker.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/Map/Physical.t b/t/Map/Physical.t index 649028bee..1d2ecabc8 100644 --- a/t/Map/Physical.t +++ b/t/Map/Physical.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 40); diff --git a/t/Matrix/IO/masta.t b/t/Matrix/IO/masta.t index d819a205b..14843903d 100644 --- a/t/Matrix/IO/masta.t +++ b/t/Matrix/IO/masta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16); diff --git a/t/Matrix/IO/psm.t b/t/Matrix/IO/psm.t index 53152b5e9..3382f3d74 100644 --- a/t/Matrix/IO/psm.t +++ b/t/Matrix/IO/psm.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 63); diff --git a/t/Matrix/InstanceSite.t b/t/Matrix/InstanceSite.t index fd2530241..c59f1a20b 100644 --- a/t/Matrix/InstanceSite.t +++ b/t/Matrix/InstanceSite.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 6); diff --git a/t/Matrix/Matrix.t b/t/Matrix/Matrix.t index adb4e61d9..2cffe051a 100644 --- a/t/Matrix/Matrix.t +++ b/t/Matrix/Matrix.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 77); diff --git a/t/Matrix/ProtMatrix.t b/t/Matrix/ProtMatrix.t index 6644e53e7..48de7cf45 100644 --- a/t/Matrix/ProtMatrix.t +++ b/t/Matrix/ProtMatrix.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/Matrix/ProtPsm.t b/t/Matrix/ProtPsm.t index a8b5a9cbd..5fd5facb6 100644 --- a/t/Matrix/ProtPsm.t +++ b/t/Matrix/ProtPsm.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/Matrix/SiteMatrix.t b/t/Matrix/SiteMatrix.t index 3e8bd99ab..9d8702826 100644 --- a/t/Matrix/SiteMatrix.t +++ b/t/Matrix/SiteMatrix.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/Ontology/GOterm.t b/t/Ontology/GOterm.t index d80b5bc66..13de385c9 100644 --- a/t/Ontology/GOterm.t +++ b/t/Ontology/GOterm.t @@ -5,7 +5,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 62, diff --git a/t/Ontology/GraphAdaptor.t b/t/Ontology/GraphAdaptor.t index eda8a246a..8bac08350 100644 --- a/t/Ontology/GraphAdaptor.t +++ b/t/Ontology/GraphAdaptor.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 28, diff --git a/t/Ontology/IO/go.t b/t/Ontology/IO/go.t index 086dfffd2..1817d38a7 100644 --- a/t/Ontology/IO/go.t +++ b/t/Ontology/IO/go.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 102, diff --git a/t/Ontology/IO/interpro.t b/t/Ontology/IO/interpro.t index e36eb587b..c86ff7b48 100644 --- a/t/Ontology/IO/interpro.t +++ b/t/Ontology/IO/interpro.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 69, diff --git a/t/Ontology/IO/obo.t b/t/Ontology/IO/obo.t index 66ff14283..dfea2ba79 100644 --- a/t/Ontology/IO/obo.t +++ b/t/Ontology/IO/obo.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 92, diff --git a/t/Ontology/Ontology.t b/t/Ontology/Ontology.t index c73b9a50c..b74d9e074 100644 --- a/t/Ontology/Ontology.t +++ b/t/Ontology/Ontology.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( diff --git a/t/Ontology/OntologyEngine.t b/t/Ontology/OntologyEngine.t index 426982ccd..82415eeb4 100644 --- a/t/Ontology/OntologyEngine.t +++ b/t/Ontology/OntologyEngine.t @@ -6,7 +6,6 @@ use strict; my $ERROR_CLASS; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( diff --git a/t/Ontology/OntologyStore.t b/t/Ontology/OntologyStore.t index d7c9d19ec..b7e6fac85 100644 --- a/t/Ontology/OntologyStore.t +++ b/t/Ontology/OntologyStore.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 6, diff --git a/t/Ontology/Relationship.t b/t/Ontology/Relationship.t index e8df0deec..533e7daa7 100644 --- a/t/Ontology/Relationship.t +++ b/t/Ontology/Relationship.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 12, diff --git a/t/Ontology/RelationshipType.t b/t/Ontology/RelationshipType.t index 0c85065a9..bc32d81c1 100644 --- a/t/Ontology/RelationshipType.t +++ b/t/Ontology/RelationshipType.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 23, diff --git a/t/Ontology/Term.t b/t/Ontology/Term.t index 0892f113e..b69373da9 100644 --- a/t/Ontology/Term.t +++ b/t/Ontology/Term.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 54, diff --git a/t/RemoteDB/BioFetch.t b/t/RemoteDB/BioFetch.t index 9ba007c51..d0706dc05 100644 --- a/t/RemoteDB/BioFetch.t +++ b/t/RemoteDB/BioFetch.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 36, diff --git a/t/RemoteDB/EMBL.t b/t/RemoteDB/EMBL.t index 7f196f2c2..778662325 100644 --- a/t/RemoteDB/EMBL.t +++ b/t/RemoteDB/EMBL.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16, diff --git a/t/RemoteDB/EntrezGene.t b/t/RemoteDB/EntrezGene.t index eaffa0476..4e7afcac0 100644 --- a/t/RemoteDB/EntrezGene.t +++ b/t/RemoteDB/EntrezGene.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/RemoteDB/GenBank.t b/t/RemoteDB/GenBank.t index f8e4fa059..1a025438c 100644 --- a/t/RemoteDB/GenBank.t +++ b/t/RemoteDB/GenBank.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 44, diff --git a/t/RemoteDB/GenPept.t b/t/RemoteDB/GenPept.t index ffc223890..73c49c9ab 100644 --- a/t/RemoteDB/GenPept.t +++ b/t/RemoteDB/GenPept.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 21, diff --git a/t/RemoteDB/Query/GenBank.t b/t/RemoteDB/Query/GenBank.t index 35bf2da35..bfa3bef2c 100644 --- a/t/RemoteDB/Query/GenBank.t +++ b/t/RemoteDB/Query/GenBank.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 18, diff --git a/t/RemoteDB/RefSeq.t b/t/RemoteDB/RefSeq.t index 369172356..86271b533 100644 --- a/t/RemoteDB/RefSeq.t +++ b/t/RemoteDB/RefSeq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16, diff --git a/t/RemoteDB/SeqRead_fail.t b/t/RemoteDB/SeqRead_fail.t index bf10434e7..6b82aa472 100644 --- a/t/RemoteDB/SeqRead_fail.t +++ b/t/RemoteDB/SeqRead_fail.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 18, diff --git a/t/RemoteDB/SeqVersion.t b/t/RemoteDB/SeqVersion.t index a43b21b48..720448b3e 100644 --- a/t/RemoteDB/SeqVersion.t +++ b/t/RemoteDB/SeqVersion.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( #-tests => 10, diff --git a/t/RemoteDB/SwissProt.t b/t/RemoteDB/SwissProt.t index 3c538b295..29eab2ca2 100644 --- a/t/RemoteDB/SwissProt.t +++ b/t/RemoteDB/SwissProt.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 23, diff --git a/t/RemoteDB/Taxonomy.t b/t/RemoteDB/Taxonomy.t index 306c99d12..7c2c6c382 100644 --- a/t/RemoteDB/Taxonomy.t +++ b/t/RemoteDB/Taxonomy.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( diff --git a/t/Root/HTTPget.t b/t/Root/HTTPget.t index 934cdba6f..1096bda23 100644 --- a/t/Root/HTTPget.t +++ b/t/Root/HTTPget.t @@ -4,7 +4,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 29, diff --git a/t/Root/IO.t b/t/Root/IO.t index 4e95caabf..e4b80a411 100644 --- a/t/Root/IO.t +++ b/t/Root/IO.t @@ -4,7 +4,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 154); use_ok 'Bio::Root::IO'; diff --git a/t/Root/RootI.t b/t/Root/RootI.t index d95703fd9..277555db7 100644 --- a/t/Root/RootI.t +++ b/t/Root/RootI.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 61); diff --git a/t/Root/RootIO.t b/t/Root/RootIO.t index 97e3738e3..d179da828 100644 --- a/t/Root/RootIO.t +++ b/t/Root/RootIO.t @@ -6,7 +6,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 3, -requires_networking => 1); diff --git a/t/Root/Storable.t b/t/Root/Storable.t index 14461a9bb..8b768c853 100644 --- a/t/Root/Storable.t +++ b/t/Root/Storable.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 35); diff --git a/t/Root/Utilities.t b/t/Root/Utilities.t index d59733b94..0406dc5ee 100644 --- a/t/Root/Utilities.t +++ b/t/Root/Utilities.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 56); diff --git a/t/SearchIO/CigarString.t b/t/SearchIO/CigarString.t index 24d9f1315..7d426a107 100644 --- a/t/SearchIO/CigarString.t +++ b/t/SearchIO/CigarString.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 4); diff --git a/t/SearchIO/SearchIO.t b/t/SearchIO/SearchIO.t index fff438f20..7fa1aefa8 100644 --- a/t/SearchIO/SearchIO.t +++ b/t/SearchIO/SearchIO.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 19); diff --git a/t/SearchIO/SimilarityPair.t b/t/SearchIO/SimilarityPair.t index 476182cb9..388d27dbb 100644 --- a/t/SearchIO/SimilarityPair.t +++ b/t/SearchIO/SimilarityPair.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 12); diff --git a/t/SearchIO/Tiling.t b/t/SearchIO/Tiling.t index c13572d5a..f571ffa17 100644 --- a/t/SearchIO/Tiling.t +++ b/t/SearchIO/Tiling.t @@ -4,7 +4,6 @@ use strict; use warnings; use vars qw($EXHAUSTIVE $VERBOSE); BEGIN { - use lib '.'; use lib '../..'; use Bio::Root::Test; diff --git a/t/SearchIO/Writer/GbrowseGFF.t b/t/SearchIO/Writer/GbrowseGFF.t index 289f5c347..c76a66af9 100644 --- a/t/SearchIO/Writer/GbrowseGFF.t +++ b/t/SearchIO/Writer/GbrowseGFF.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 4); diff --git a/t/SearchIO/Writer/HSPTableWriter.t b/t/SearchIO/Writer/HSPTableWriter.t index ed5122e27..6f73ac843 100644 --- a/t/SearchIO/Writer/HSPTableWriter.t +++ b/t/SearchIO/Writer/HSPTableWriter.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/SearchIO/Writer/HTMLWriter.t b/t/SearchIO/Writer/HTMLWriter.t index 20ac6370e..a120f9a93 100644 --- a/t/SearchIO/Writer/HTMLWriter.t +++ b/t/SearchIO/Writer/HTMLWriter.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/SearchIO/Writer/HitTableWriter.t b/t/SearchIO/Writer/HitTableWriter.t index c64b4fdc5..27882e16d 100644 --- a/t/SearchIO/Writer/HitTableWriter.t +++ b/t/SearchIO/Writer/HitTableWriter.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/SearchIO/Writer/TextWriter.t b/t/SearchIO/Writer/TextWriter.t index 2d35eb496..03c84f909 100644 --- a/t/SearchIO/Writer/TextWriter.t +++ b/t/SearchIO/Writer/TextWriter.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/SearchIO/axt.t b/t/SearchIO/axt.t index 2b1c40576..5ddf75882 100644 --- a/t/SearchIO/axt.t +++ b/t/SearchIO/axt.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 19); diff --git a/t/SearchIO/blast.t b/t/SearchIO/blast.t index 65c3d1eae..4fbfb9c67 100644 --- a/t/SearchIO/blast.t +++ b/t/SearchIO/blast.t @@ -5,7 +5,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 1389); diff --git a/t/SearchIO/blast_pull.t b/t/SearchIO/blast_pull.t index f853b7bad..2af3f3bbd 100644 --- a/t/SearchIO/blast_pull.t +++ b/t/SearchIO/blast_pull.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 289); diff --git a/t/SearchIO/blasttable.t b/t/SearchIO/blasttable.t index 1a7f507ee..99920c817 100644 --- a/t/SearchIO/blasttable.t +++ b/t/SearchIO/blasttable.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 166); diff --git a/t/SearchIO/cross_match.t b/t/SearchIO/cross_match.t index 24b4656b4..10ebf0f93 100644 --- a/t/SearchIO/cross_match.t +++ b/t/SearchIO/cross_match.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 15); diff --git a/t/SearchIO/erpin.t b/t/SearchIO/erpin.t index 111a77909..205b690d7 100644 --- a/t/SearchIO/erpin.t +++ b/t/SearchIO/erpin.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 91); diff --git a/t/SearchIO/exonerate.t b/t/SearchIO/exonerate.t index 6dfcef560..5c9405ef5 100644 --- a/t/SearchIO/exonerate.t +++ b/t/SearchIO/exonerate.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 52 ); diff --git a/t/SearchIO/fasta.t b/t/SearchIO/fasta.t index 9135b0c2a..c72fa7c55 100644 --- a/t/SearchIO/fasta.t +++ b/t/SearchIO/fasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 301); diff --git a/t/SearchIO/gmap_f9.t b/t/SearchIO/gmap_f9.t index 4fb20745b..58157a6f3 100644 --- a/t/SearchIO/gmap_f9.t +++ b/t/SearchIO/gmap_f9.t @@ -4,7 +4,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 54); diff --git a/t/SearchIO/infernal.t b/t/SearchIO/infernal.t index 9137f7fbc..bdc1ffe24 100644 --- a/t/SearchIO/infernal.t +++ b/t/SearchIO/infernal.t @@ -5,7 +5,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 496); diff --git a/t/SearchIO/megablast.t b/t/SearchIO/megablast.t index ebd9c7b4b..563434a46 100644 --- a/t/SearchIO/megablast.t +++ b/t/SearchIO/megablast.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 31); diff --git a/t/SearchIO/psl.t b/t/SearchIO/psl.t index fbd56c688..2fad8ff50 100644 --- a/t/SearchIO/psl.t +++ b/t/SearchIO/psl.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 53); diff --git a/t/SearchIO/rnamotif.t b/t/SearchIO/rnamotif.t index a1ae0b077..e1ccf14de 100644 --- a/t/SearchIO/rnamotif.t +++ b/t/SearchIO/rnamotif.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 60); diff --git a/t/SearchIO/sim4.t b/t/SearchIO/sim4.t index 3fec76dc1..221aff6a8 100644 --- a/t/SearchIO/sim4.t +++ b/t/SearchIO/sim4.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 102); diff --git a/t/SearchIO/waba.t b/t/SearchIO/waba.t index 72f02ef68..3a088ad32 100644 --- a/t/SearchIO/waba.t +++ b/t/SearchIO/waba.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 64); diff --git a/t/SearchIO/wise.t b/t/SearchIO/wise.t index d7e0c0b5b..8943344c0 100644 --- a/t/SearchIO/wise.t +++ b/t/SearchIO/wise.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 20); diff --git a/t/Seq/DBLink.t b/t/Seq/DBLink.t index da3c6ba06..6b78b30e2 100644 --- a/t/Seq/DBLink.t +++ b/t/Seq/DBLink.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 131); diff --git a/t/Seq/EncodedSeq.t b/t/Seq/EncodedSeq.t index 0c4caa5ae..49a88ac42 100644 --- a/t/Seq/EncodedSeq.t +++ b/t/Seq/EncodedSeq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 37); diff --git a/t/Seq/LargeLocatableSeq.t b/t/Seq/LargeLocatableSeq.t index 071145811..1cb8451c6 100644 --- a/t/Seq/LargeLocatableSeq.t +++ b/t/Seq/LargeLocatableSeq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/Seq/LargePSeq.t b/t/Seq/LargePSeq.t index 5b96d84fb..7f26cd32b 100644 --- a/t/Seq/LargePSeq.t +++ b/t/Seq/LargePSeq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 30); diff --git a/t/Seq/LocatableSeq.t b/t/Seq/LocatableSeq.t index 82da3fdd2..bde029e40 100644 --- a/t/Seq/LocatableSeq.t +++ b/t/Seq/LocatableSeq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 119); diff --git a/t/Seq/MetaSeq.t b/t/Seq/MetaSeq.t index 967c3e5dd..0ffbc03a7 100644 --- a/t/Seq/MetaSeq.t +++ b/t/Seq/MetaSeq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 132); diff --git a/t/Seq/PrimaryQual.t b/t/Seq/PrimaryQual.t index 4cb68bdd1..43f161169 100644 --- a/t/Seq/PrimaryQual.t +++ b/t/Seq/PrimaryQual.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 70); diff --git a/t/Seq/PrimarySeq.t b/t/Seq/PrimarySeq.t index 22fed4a02..e5292d37b 100644 --- a/t/Seq/PrimarySeq.t +++ b/t/Seq/PrimarySeq.t @@ -5,7 +5,6 @@ use strict; use Data::Dumper; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 312 ); diff --git a/t/Seq/PrimedSeq.t b/t/Seq/PrimedSeq.t index 99aee8859..f40e99552 100644 --- a/t/Seq/PrimedSeq.t +++ b/t/Seq/PrimedSeq.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 65); diff --git a/t/Seq/Quality.t b/t/Seq/Quality.t index 40069d551..30fb127e7 100644 --- a/t/Seq/Quality.t +++ b/t/Seq/Quality.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 85); diff --git a/t/Seq/Seq.t b/t/Seq/Seq.t index 0ae1b4283..caa3fa196 100644 --- a/t/Seq/Seq.t +++ b/t/Seq/Seq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 76); diff --git a/t/Seq/SimulatedRead.t b/t/Seq/SimulatedRead.t index 2228c0140..c5c557c5f 100644 --- a/t/Seq/SimulatedRead.t +++ b/t/Seq/SimulatedRead.t @@ -5,7 +5,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 194); diff --git a/t/Seq/WithQuality.t b/t/Seq/WithQuality.t index 309ed1363..2513d78ee 100644 --- a/t/Seq/WithQuality.t +++ b/t/Seq/WithQuality.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 22); diff --git a/t/SeqFeature/Amplicon.t b/t/SeqFeature/Amplicon.t index 26d9f4ce6..c48a981ec 100644 --- a/t/SeqFeature/Amplicon.t +++ b/t/SeqFeature/Amplicon.t @@ -1,7 +1,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 21); diff --git a/t/SeqFeature/Clone.t b/t/SeqFeature/Clone.t index 9016b7e3a..1bcc0a05d 100644 --- a/t/SeqFeature/Clone.t +++ b/t/SeqFeature/Clone.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; use Bio::SeqFeature::Generic; use Bio::Location::Split; diff --git a/t/SeqFeature/Collection.t b/t/SeqFeature/Collection.t index 887b74e76..c36d1c808 100644 --- a/t/SeqFeature/Collection.t +++ b/t/SeqFeature/Collection.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( diff --git a/t/SeqFeature/Computation.t b/t/SeqFeature/Computation.t index c6fc9921f..130c3a052 100644 --- a/t/SeqFeature/Computation.t +++ b/t/SeqFeature/Computation.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 12); diff --git a/t/SeqFeature/FeaturePair.t b/t/SeqFeature/FeaturePair.t index 9982e2730..4fce26f37 100644 --- a/t/SeqFeature/FeaturePair.t +++ b/t/SeqFeature/FeaturePair.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 19); diff --git a/t/SeqFeature/Gene.t b/t/SeqFeature/Gene.t index b4044309c..1cb7ad7d9 100644 --- a/t/SeqFeature/Gene.t +++ b/t/SeqFeature/Gene.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 28); diff --git a/t/SeqFeature/Generic.t b/t/SeqFeature/Generic.t index c380917ad..4e996fdae 100644 --- a/t/SeqFeature/Generic.t +++ b/t/SeqFeature/Generic.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 364); diff --git a/t/SeqFeature/Location.t b/t/SeqFeature/Location.t index d737739f4..faf7e862c 100644 --- a/t/SeqFeature/Location.t +++ b/t/SeqFeature/Location.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 109); diff --git a/t/SeqFeature/LocationFactory.t b/t/SeqFeature/LocationFactory.t index ef9a0d61f..1beb95253 100644 --- a/t/SeqFeature/LocationFactory.t +++ b/t/SeqFeature/LocationFactory.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 325); diff --git a/t/SeqFeature/Primer.t b/t/SeqFeature/Primer.t index c5e3bc732..0f10b3eea 100644 --- a/t/SeqFeature/Primer.t +++ b/t/SeqFeature/Primer.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 47); use_ok('Bio::SeqFeature::Primer'); diff --git a/t/SeqFeature/Range.t b/t/SeqFeature/Range.t index 0dbbc1269..08bed17c1 100644 --- a/t/SeqFeature/Range.t +++ b/t/SeqFeature/Range.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 49); diff --git a/t/SeqFeature/RangeI.t b/t/SeqFeature/RangeI.t index 45f108e72..5bff03d1f 100644 --- a/t/SeqFeature/RangeI.t +++ b/t/SeqFeature/RangeI.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 45); diff --git a/t/SeqFeature/SeqAnalysisParser.t b/t/SeqFeature/SeqAnalysisParser.t index 30e3f108c..486afac94 100644 --- a/t/SeqFeature/SeqAnalysisParser.t +++ b/t/SeqFeature/SeqAnalysisParser.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/SeqFeature/SubSeq.t b/t/SeqFeature/SubSeq.t index cb1f52b18..df169d245 100644 --- a/t/SeqFeature/SubSeq.t +++ b/t/SeqFeature/SubSeq.t @@ -1,7 +1,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 37); diff --git a/t/SeqFeature/Unflattener.t b/t/SeqFeature/Unflattener.t index cbfe72c1f..2bccda50b 100644 --- a/t/SeqFeature/Unflattener.t +++ b/t/SeqFeature/Unflattener.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 21); diff --git a/t/SeqIO/Handler.t b/t/SeqIO/Handler.t index 69d4aed90..311610a32 100644 --- a/t/SeqIO/Handler.t +++ b/t/SeqIO/Handler.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 561, diff --git a/t/SeqIO/MultiFile.t b/t/SeqIO/MultiFile.t index 1c8f4cb7b..40f2a21f7 100644 --- a/t/SeqIO/MultiFile.t +++ b/t/SeqIO/MultiFile.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5); diff --git a/t/SeqIO/Multiple_fasta.t b/t/SeqIO/Multiple_fasta.t index b5b2c08b7..583b1346b 100644 --- a/t/SeqIO/Multiple_fasta.t +++ b/t/SeqIO/Multiple_fasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 9); diff --git a/t/SeqIO/SeqBuilder.t b/t/SeqIO/SeqBuilder.t index 3be6e4d6b..dc918213a 100644 --- a/t/SeqIO/SeqBuilder.t +++ b/t/SeqIO/SeqBuilder.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 137); use_ok('Bio::SeqIO'); diff --git a/t/SeqIO/SeqIO.t b/t/SeqIO/SeqIO.t index 290fac6f0..b41d60b02 100644 --- a/t/SeqIO/SeqIO.t +++ b/t/SeqIO/SeqIO.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 58); diff --git a/t/SeqIO/Splicedseq.t b/t/SeqIO/Splicedseq.t index a42ed0d66..9aeb02b91 100644 --- a/t/SeqIO/Splicedseq.t +++ b/t/SeqIO/Splicedseq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27); diff --git a/t/SeqIO/ace.t b/t/SeqIO/ace.t index 727002e12..1daa2a10e 100644 --- a/t/SeqIO/ace.t +++ b/t/SeqIO/ace.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 7); diff --git a/t/SeqIO/agave.t b/t/SeqIO/agave.t index 916b7961b..137957c69 100644 --- a/t/SeqIO/agave.t +++ b/t/SeqIO/agave.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/SeqIO/asciitree.t b/t/SeqIO/asciitree.t index a042b89da..ab9e54a8e 100644 --- a/t/SeqIO/asciitree.t +++ b/t/SeqIO/asciitree.t @@ -6,7 +6,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 2); diff --git a/t/SeqIO/bsml.t b/t/SeqIO/bsml.t index c655c896e..0e3535f02 100644 --- a/t/SeqIO/bsml.t +++ b/t/SeqIO/bsml.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16, diff --git a/t/SeqIO/bsml_sax.t b/t/SeqIO/bsml_sax.t index 2b4d800af..f22d5bf1b 100644 --- a/t/SeqIO/bsml_sax.t +++ b/t/SeqIO/bsml_sax.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 15, diff --git a/t/SeqIO/chadoxml.t b/t/SeqIO/chadoxml.t index c65129563..caed6c154 100644 --- a/t/SeqIO/chadoxml.t +++ b/t/SeqIO/chadoxml.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/SeqIO/chaos.t b/t/SeqIO/chaos.t index ccc4e5c28..ca98e610e 100644 --- a/t/SeqIO/chaos.t +++ b/t/SeqIO/chaos.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/SeqIO/chaosxml.t b/t/SeqIO/chaosxml.t index 1272e5f13..e14e14c61 100644 --- a/t/SeqIO/chaosxml.t +++ b/t/SeqIO/chaosxml.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 2, diff --git a/t/SeqIO/embl.t b/t/SeqIO/embl.t index 6f7b7ea4e..68886f7d4 100644 --- a/t/SeqIO/embl.t +++ b/t/SeqIO/embl.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use lib '../..'; use Bio::Root::Test; diff --git a/t/SeqIO/fasta.t b/t/SeqIO/fasta.t index 3e03ac8ed..5e7823266 100644 --- a/t/SeqIO/fasta.t +++ b/t/SeqIO/fasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 22, diff --git a/t/SeqIO/fastq.t b/t/SeqIO/fastq.t index 6e2372f39..db4e40d09 100644 --- a/t/SeqIO/fastq.t +++ b/t/SeqIO/fastq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 149 ); diff --git a/t/SeqIO/flybase_chadoxml.t b/t/SeqIO/flybase_chadoxml.t index 613076a65..1dc68bfa9 100644 --- a/t/SeqIO/flybase_chadoxml.t +++ b/t/SeqIO/flybase_chadoxml.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/SeqIO/game.t b/t/SeqIO/game.t index 255c8b4bc..b43e16c16 100644 --- a/t/SeqIO/game.t +++ b/t/SeqIO/game.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 24, diff --git a/t/SeqIO/gbxml.t b/t/SeqIO/gbxml.t index 3ad9205c3..212f81462 100644 --- a/t/SeqIO/gbxml.t +++ b/t/SeqIO/gbxml.t @@ -1,7 +1,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14, diff --git a/t/SeqIO/gcg.t b/t/SeqIO/gcg.t index d67200539..c10576c61 100644 --- a/t/SeqIO/gcg.t +++ b/t/SeqIO/gcg.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 17, diff --git a/t/SeqIO/genbank.t b/t/SeqIO/genbank.t index db6443254..5ec3b4932 100644 --- a/t/SeqIO/genbank.t +++ b/t/SeqIO/genbank.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 301); use_ok('Bio::SeqIO::genbank'); diff --git a/t/SeqIO/interpro.t b/t/SeqIO/interpro.t index d4ba5dbe2..101f06386 100644 --- a/t/SeqIO/interpro.t +++ b/t/SeqIO/interpro.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 20, diff --git a/t/SeqIO/kegg.t b/t/SeqIO/kegg.t index 23169fb83..e1970c6f6 100644 --- a/t/SeqIO/kegg.t +++ b/t/SeqIO/kegg.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16); diff --git a/t/SeqIO/largefasta.t b/t/SeqIO/largefasta.t index e9aa50c8f..8ea77f510 100644 --- a/t/SeqIO/largefasta.t +++ b/t/SeqIO/largefasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16); diff --git a/t/SeqIO/lasergene.t b/t/SeqIO/lasergene.t index dd8cc889a..4e6362a89 100644 --- a/t/SeqIO/lasergene.t +++ b/t/SeqIO/lasergene.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 13); diff --git a/t/SeqIO/locuslink.t b/t/SeqIO/locuslink.t index 97f7438f8..d154d50b9 100644 --- a/t/SeqIO/locuslink.t +++ b/t/SeqIO/locuslink.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 26, diff --git a/t/SeqIO/mbsout.t b/t/SeqIO/mbsout.t index 33a4500e9..7d1e71252 100644 --- a/t/SeqIO/mbsout.t +++ b/t/SeqIO/mbsout.t @@ -7,7 +7,6 @@ use File::Path qw(mkpath rmtree); use Carp; BEGIN { - use lib '.'; # for core package test scripts only use Bio::Root::Test; test_begin( diff --git a/t/SeqIO/metafasta.t b/t/SeqIO/metafasta.t index f4a40b96b..cc454ab9a 100644 --- a/t/SeqIO/metafasta.t +++ b/t/SeqIO/metafasta.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 6); diff --git a/t/SeqIO/msout.t b/t/SeqIO/msout.t index 7b7e8ae66..536462d9e 100644 --- a/t/SeqIO/msout.t +++ b/t/SeqIO/msout.t @@ -5,7 +5,6 @@ use strict; use File::Path qw(mkpath rmtree); BEGIN { - use lib '.'; # for core package test scripts only use Bio::Root::Test; test_begin( diff --git a/t/SeqIO/phd.t b/t/SeqIO/phd.t index 8c3e54a00..2f1eade1a 100644 --- a/t/SeqIO/phd.t +++ b/t/SeqIO/phd.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 21); diff --git a/t/SeqIO/pir.t b/t/SeqIO/pir.t index 1b08769eb..fbd40d382 100644 --- a/t/SeqIO/pir.t +++ b/t/SeqIO/pir.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin( -tests => 12 ); diff --git a/t/SeqIO/qual.t b/t/SeqIO/qual.t index 43abdce72..4cd7b0bb5 100644 --- a/t/SeqIO/qual.t +++ b/t/SeqIO/qual.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 18); diff --git a/t/SeqIO/raw.t b/t/SeqIO/raw.t index e1e6f1ee0..49fbfa891 100644 --- a/t/SeqIO/raw.t +++ b/t/SeqIO/raw.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 25, diff --git a/t/SeqIO/scf.t b/t/SeqIO/scf.t index d2fb5383b..b8d586922 100644 --- a/t/SeqIO/scf.t +++ b/t/SeqIO/scf.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 80); diff --git a/t/SeqIO/strider.t b/t/SeqIO/strider.t index adfcd0cba..3c49f5e24 100644 --- a/t/SeqIO/strider.t +++ b/t/SeqIO/strider.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/SeqIO/swiss.t b/t/SeqIO/swiss.t index 6049f0d3d..cb4ce4cf6 100644 --- a/t/SeqIO/swiss.t +++ b/t/SeqIO/swiss.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 247, diff --git a/t/SeqIO/tab.t b/t/SeqIO/tab.t index 526487b6e..e2eee57ba 100644 --- a/t/SeqIO/tab.t +++ b/t/SeqIO/tab.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8); diff --git a/t/SeqIO/table.t b/t/SeqIO/table.t index d84e50159..c2e6745aa 100644 --- a/t/SeqIO/table.t +++ b/t/SeqIO/table.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 351, diff --git a/t/SeqIO/tigr.t b/t/SeqIO/tigr.t index 408620de9..73edc1d4c 100644 --- a/t/SeqIO/tigr.t +++ b/t/SeqIO/tigr.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 8, diff --git a/t/SeqIO/tigrxml.t b/t/SeqIO/tigrxml.t index 81d729301..f26e7a4ab 100644 --- a/t/SeqIO/tigrxml.t +++ b/t/SeqIO/tigrxml.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 49, diff --git a/t/SeqIO/tinyseq.t b/t/SeqIO/tinyseq.t index bb8ff1be2..2f6552d45 100644 --- a/t/SeqIO/tinyseq.t +++ b/t/SeqIO/tinyseq.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16, diff --git a/t/SeqTools/CodonTable.t b/t/SeqTools/CodonTable.t index d7eebb75b..f8cba9c4e 100644 --- a/t/SeqTools/CodonTable.t +++ b/t/SeqTools/CodonTable.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 84); diff --git a/t/SeqTools/ECnumber.t b/t/SeqTools/ECnumber.t index 15d67ca65..e72ee175b 100644 --- a/t/SeqTools/ECnumber.t +++ b/t/SeqTools/ECnumber.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27); diff --git a/t/SeqTools/GuessSeqFormat.t b/t/SeqTools/GuessSeqFormat.t index c63080d94..efe277a7f 100644 --- a/t/SeqTools/GuessSeqFormat.t +++ b/t/SeqTools/GuessSeqFormat.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 105); diff --git a/t/SeqTools/OddCodes.t b/t/SeqTools/OddCodes.t index 3e19598e2..e2ec8b001 100644 --- a/t/SeqTools/OddCodes.t +++ b/t/SeqTools/OddCodes.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 11); diff --git a/t/SeqTools/SeqPattern.t b/t/SeqTools/SeqPattern.t index 7f0964b1a..e5f6351d9 100644 --- a/t/SeqTools/SeqPattern.t +++ b/t/SeqTools/SeqPattern.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 28); diff --git a/t/SeqTools/SeqStats.t b/t/SeqTools/SeqStats.t index 2bca15434..91aef7a2b 100644 --- a/t/SeqTools/SeqStats.t +++ b/t/SeqTools/SeqStats.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 47); diff --git a/t/SeqTools/SeqUtils.t b/t/SeqTools/SeqUtils.t index a540d4c27..dec7ee16e 100644 --- a/t/SeqTools/SeqUtils.t +++ b/t/SeqTools/SeqUtils.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; # use List::MoreUtils qw(uniq); use Bio::Root::Test; diff --git a/t/SeqTools/SeqWords.t b/t/SeqTools/SeqWords.t index eb2e627dd..9916b7ed7 100644 --- a/t/SeqTools/SeqWords.t +++ b/t/SeqTools/SeqWords.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 22); diff --git a/t/Species.t b/t/Species.t index f5f8e64a5..87258d138 100644 --- a/t/Species.t +++ b/t/Species.t @@ -5,7 +5,6 @@ my $CYCLE; my $WEAKEN; BEGIN { - use lib '.'; use Bio::Root::Test; eval { require Test::Memory::Cycle; 1; }; $CYCLE = $@ ? 0 : 1; diff --git a/t/Symbol.t b/t/Symbol.t index 49a1ec984..795e2aaca 100644 --- a/t/Symbol.t +++ b/t/Symbol.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 9); diff --git a/t/TaxonTree.t b/t/TaxonTree.t index 6ba6d9852..c200f8d18 100644 --- a/t/TaxonTree.t +++ b/t/TaxonTree.t @@ -10,7 +10,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 0); diff --git a/t/Tools/Alignment/Consed.t b/t/Tools/Alignment/Consed.t index b218a258f..ab2157171 100644 --- a/t/Tools/Alignment/Consed.t +++ b/t/Tools/Alignment/Consed.t @@ -11,7 +11,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 15); diff --git a/t/Tools/AmpliconSearch.t b/t/Tools/AmpliconSearch.t index 15f8e1aeb..90d93fc93 100644 --- a/t/Tools/AmpliconSearch.t +++ b/t/Tools/AmpliconSearch.t @@ -1,5 +1,4 @@ BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 185); diff --git a/t/Tools/Analysis/DNA/ESEfinder.t b/t/Tools/Analysis/DNA/ESEfinder.t index 513d03974..25f56e620 100644 --- a/t/Tools/Analysis/DNA/ESEfinder.t +++ b/t/Tools/Analysis/DNA/ESEfinder.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 13, diff --git a/t/Tools/Analysis/Protein/Domcut.t b/t/Tools/Analysis/Protein/Domcut.t index 0f981e0f4..ebf4b6ff8 100644 --- a/t/Tools/Analysis/Protein/Domcut.t +++ b/t/Tools/Analysis/Protein/Domcut.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 26, diff --git a/t/Tools/Analysis/Protein/ELM.t b/t/Tools/Analysis/Protein/ELM.t index 554f03ed5..de839a88b 100644 --- a/t/Tools/Analysis/Protein/ELM.t +++ b/t/Tools/Analysis/Protein/ELM.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 16, diff --git a/t/Tools/Analysis/Protein/GOR4.t b/t/Tools/Analysis/Protein/GOR4.t index 2fa1e5b03..f0ae63031 100644 --- a/t/Tools/Analysis/Protein/GOR4.t +++ b/t/Tools/Analysis/Protein/GOR4.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 0, diff --git a/t/Tools/Analysis/Protein/HNN.t b/t/Tools/Analysis/Protein/HNN.t index 03c4ed428..f5c8147a9 100644 --- a/t/Tools/Analysis/Protein/HNN.t +++ b/t/Tools/Analysis/Protein/HNN.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 0, diff --git a/t/Tools/Analysis/Protein/NetPhos.t b/t/Tools/Analysis/Protein/NetPhos.t index 1371bf3b8..b2890ed45 100644 --- a/t/Tools/Analysis/Protein/NetPhos.t +++ b/t/Tools/Analysis/Protein/NetPhos.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14, diff --git a/t/Tools/Analysis/Protein/Scansite.t b/t/Tools/Analysis/Protein/Scansite.t index 34b62b1ac..9f840095c 100644 --- a/t/Tools/Analysis/Protein/Scansite.t +++ b/t/Tools/Analysis/Protein/Scansite.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14, diff --git a/t/Tools/Analysis/Protein/Sopma.t b/t/Tools/Analysis/Protein/Sopma.t index 54c8c7a72..b2e367353 100644 --- a/t/Tools/Analysis/Protein/Sopma.t +++ b/t/Tools/Analysis/Protein/Sopma.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 0, diff --git a/t/Tools/EMBOSS/Palindrome.t b/t/Tools/EMBOSS/Palindrome.t index e49e80aa3..b3004d452 100644 --- a/t/Tools/EMBOSS/Palindrome.t +++ b/t/Tools/EMBOSS/Palindrome.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 13); diff --git a/t/Tools/Est2Genome.t b/t/Tools/Est2Genome.t index 2ff188d29..958bbfa4e 100644 --- a/t/Tools/Est2Genome.t +++ b/t/Tools/Est2Genome.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 61); diff --git a/t/Tools/FootPrinter.t b/t/Tools/FootPrinter.t index 745768ce6..d9983659a 100644 --- a/t/Tools/FootPrinter.t +++ b/t/Tools/FootPrinter.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27); diff --git a/t/Tools/GFF.t b/t/Tools/GFF.t index 2e523bea4..c76c59c62 100644 --- a/t/Tools/GFF.t +++ b/t/Tools/GFF.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 34); diff --git a/t/Tools/Geneid.t b/t/Tools/Geneid.t index e2b59ae95..05b422733 100644 --- a/t/Tools/Geneid.t +++ b/t/Tools/Geneid.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 26); diff --git a/t/Tools/Genewise.t b/t/Tools/Genewise.t index 4e5fc2623..d42082b01 100644 --- a/t/Tools/Genewise.t +++ b/t/Tools/Genewise.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 33); diff --git a/t/Tools/Genomewise.t b/t/Tools/Genomewise.t index b92019791..92e2eddd5 100644 --- a/t/Tools/Genomewise.t +++ b/t/Tools/Genomewise.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 21); diff --git a/t/Tools/Genpred.t b/t/Tools/Genpred.t index e011a2e41..c338b24c3 100644 --- a/t/Tools/Genpred.t +++ b/t/Tools/Genpred.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 185); diff --git a/t/Tools/IUPAC.t b/t/Tools/IUPAC.t index 4bacc317e..ac0183f54 100644 --- a/t/Tools/IUPAC.t +++ b/t/Tools/IUPAC.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 46); diff --git a/t/Tools/Lucy.t b/t/Tools/Lucy.t index 30e4d1c8c..ea60ea59f 100644 --- a/t/Tools/Lucy.t +++ b/t/Tools/Lucy.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 22); diff --git a/t/Tools/Match.t b/t/Tools/Match.t index 8535e9b49..30d960af0 100644 --- a/t/Tools/Match.t +++ b/t/Tools/Match.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 38, diff --git a/t/Tools/Phylo/Gerp.t b/t/Tools/Phylo/Gerp.t index e20921b33..5dd993d65 100644 --- a/t/Tools/Phylo/Gerp.t +++ b/t/Tools/Phylo/Gerp.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 33, diff --git a/t/Tools/Phylo/Molphy.t b/t/Tools/Phylo/Molphy.t index 2a1ab622b..3f9a42eaa 100644 --- a/t/Tools/Phylo/Molphy.t +++ b/t/Tools/Phylo/Molphy.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 18, diff --git a/t/Tools/Phylo/Phylip/ProtDist.t b/t/Tools/Phylo/Phylip/ProtDist.t index 2b6ca4d91..ccad4af9f 100644 --- a/t/Tools/Phylo/Phylip/ProtDist.t +++ b/t/Tools/Phylo/Phylip/ProtDist.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 47); diff --git a/t/Tools/Primer3.t b/t/Tools/Primer3.t index 7936a7b39..35f87b957 100644 --- a/t/Tools/Primer3.t +++ b/t/Tools/Primer3.t @@ -5,7 +5,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/Tools/Promoterwise.t b/t/Tools/Promoterwise.t index 6fe3f9c19..819bc86ce 100644 --- a/t/Tools/Promoterwise.t +++ b/t/Tools/Promoterwise.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 7); diff --git a/t/Tools/PrositeScan.t b/t/Tools/PrositeScan.t index bd983c598..3ac291afe 100644 --- a/t/Tools/PrositeScan.t +++ b/t/Tools/PrositeScan.t @@ -1,7 +1,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 3); diff --git a/t/Tools/Pseudowise.t b/t/Tools/Pseudowise.t index f302e025e..105f3c363 100644 --- a/t/Tools/Pseudowise.t +++ b/t/Tools/Pseudowise.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 21); diff --git a/t/Tools/QRNA.t b/t/Tools/QRNA.t index 6a981344b..38b8edebc 100644 --- a/t/Tools/QRNA.t +++ b/t/Tools/QRNA.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 30); diff --git a/t/Tools/RandDistFunctions.t b/t/Tools/RandDistFunctions.t index 86372206e..7681ffbf2 100644 --- a/t/Tools/RandDistFunctions.t +++ b/t/Tools/RandDistFunctions.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5); diff --git a/t/Tools/RepeatMasker.t b/t/Tools/RepeatMasker.t index 78e43e472..1d5b5a7bc 100644 --- a/t/Tools/RepeatMasker.t +++ b/t/Tools/RepeatMasker.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 28); diff --git a/t/Tools/Seg.t b/t/Tools/Seg.t index 84d6a923a..744da14ff 100644 --- a/t/Tools/Seg.t +++ b/t/Tools/Seg.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 15); diff --git a/t/Tools/SiRNA.t b/t/Tools/SiRNA.t index 9d250673b..b8b66057c 100644 --- a/t/Tools/SiRNA.t +++ b/t/Tools/SiRNA.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 11); diff --git a/t/Tools/Sigcleave.t b/t/Tools/Sigcleave.t index fe04e0890..99520bb97 100644 --- a/t/Tools/Sigcleave.t +++ b/t/Tools/Sigcleave.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 18); diff --git a/t/Tools/Signalp.t b/t/Tools/Signalp.t index 9e8390837..e25d435d7 100644 --- a/t/Tools/Signalp.t +++ b/t/Tools/Signalp.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 11); diff --git a/t/Tools/Signalp/ExtendedSignalp.t b/t/Tools/Signalp/ExtendedSignalp.t index 96a6870b0..b66f38d18 100644 --- a/t/Tools/Signalp/ExtendedSignalp.t +++ b/t/Tools/Signalp/ExtendedSignalp.t @@ -4,7 +4,6 @@ use strict; use Data::Dumper; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 185); diff --git a/t/Tools/Sim4.t b/t/Tools/Sim4.t index ae36b02d3..c07142875 100644 --- a/t/Tools/Sim4.t +++ b/t/Tools/Sim4.t @@ -3,7 +3,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27); diff --git a/t/Tools/Spidey/Spidey.t b/t/Tools/Spidey/Spidey.t index e7d8a7069..fbd51c1f9 100644 --- a/t/Tools/Spidey/Spidey.t +++ b/t/Tools/Spidey/Spidey.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 26); diff --git a/t/Tools/TandemRepeatsFinder.t b/t/Tools/TandemRepeatsFinder.t index ae0fe5bdf..7f939a459 100644 --- a/t/Tools/TandemRepeatsFinder.t +++ b/t/Tools/TandemRepeatsFinder.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 66); diff --git a/t/Tools/TargetP.t b/t/Tools/TargetP.t index 27d74aedd..bc40a39e6 100644 --- a/t/Tools/TargetP.t +++ b/t/Tools/TargetP.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 124); diff --git a/t/Tools/Tmhmm.t b/t/Tools/Tmhmm.t index 6e3939cab..e52d10c73 100644 --- a/t/Tools/Tmhmm.t +++ b/t/Tools/Tmhmm.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 12); diff --git a/t/Tools/ePCR.t b/t/Tools/ePCR.t index 2cbc9d619..784a30456 100644 --- a/t/Tools/ePCR.t +++ b/t/Tools/ePCR.t @@ -3,7 +3,6 @@ BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 27); diff --git a/t/Tools/pICalculator.t b/t/Tools/pICalculator.t index 64e9b98c6..5c4987252 100644 --- a/t/Tools/pICalculator.t +++ b/t/Tools/pICalculator.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 38); diff --git a/t/Tools/tRNAscanSE.t b/t/Tools/tRNAscanSE.t index c76410fec..9f8d61b6a 100644 --- a/t/Tools/tRNAscanSE.t +++ b/t/Tools/tRNAscanSE.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 14); diff --git a/t/Tree/Compatible.t b/t/Tree/Compatible.t index 236c11a1f..983d14023 100644 --- a/t/Tree/Compatible.t +++ b/t/Tree/Compatible.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5, diff --git a/t/Tree/Node.t b/t/Tree/Node.t index e8d29f58b..49833ee61 100644 --- a/t/Tree/Node.t +++ b/t/Tree/Node.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; use File::Temp qw(tempfile); test_begin( -tests => 33 ); diff --git a/t/Tree/RandomTreeFactory.t b/t/Tree/RandomTreeFactory.t index 81e76234e..f52914e2e 100644 --- a/t/Tree/RandomTreeFactory.t +++ b/t/Tree/RandomTreeFactory.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 5); diff --git a/t/Tree/Tree.t b/t/Tree/Tree.t index 167204576..b955131ed 100644 --- a/t/Tree/Tree.t +++ b/t/Tree/Tree.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 66); use_ok('Bio::TreeIO'); diff --git a/t/Tree/TreeIO.t b/t/Tree/TreeIO.t index e84ebb365..4c992c6e1 100644 --- a/t/Tree/TreeIO.t +++ b/t/Tree/TreeIO.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 76); diff --git a/t/Tree/TreeIO/lintree.t b/t/Tree/TreeIO/lintree.t index ba1045bab..a0660be10 100644 --- a/t/Tree/TreeIO/lintree.t +++ b/t/Tree/TreeIO/lintree.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 24); diff --git a/t/Tree/TreeIO/newick.t b/t/Tree/TreeIO/newick.t index 0d3dcd961..8a01025a4 100644 --- a/t/Tree/TreeIO/newick.t +++ b/t/Tree/TreeIO/newick.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 51); diff --git a/t/Tree/TreeIO/nexus.t b/t/Tree/TreeIO/nexus.t index 957e0ca7b..209d4e3e9 100644 --- a/t/Tree/TreeIO/nexus.t +++ b/t/Tree/TreeIO/nexus.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 24); diff --git a/t/Tree/TreeIO/nhx.t b/t/Tree/TreeIO/nhx.t index 73ed689d6..cee8fb578 100644 --- a/t/Tree/TreeIO/nhx.t +++ b/t/Tree/TreeIO/nhx.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; use File::Temp qw(tempfile); diff --git a/t/Tree/TreeIO/phyloxml.t b/t/Tree/TreeIO/phyloxml.t index 5aaaa9b68..89e7e5153 100644 --- a/t/Tree/TreeIO/phyloxml.t +++ b/t/Tree/TreeIO/phyloxml.t @@ -4,7 +4,6 @@ use strict; use warnings; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 98, diff --git a/t/Tree/TreeIO/tabtree.t b/t/Tree/TreeIO/tabtree.t index 2b429fabd..29c2b93df 100644 --- a/t/Tree/TreeIO/tabtree.t +++ b/t/Tree/TreeIO/tabtree.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 24); diff --git a/t/Tree/TreeStatistics.t b/t/Tree/TreeStatistics.t index 2544933e2..e0ac8308e 100644 --- a/t/Tree/TreeStatistics.t +++ b/t/Tree/TreeStatistics.t @@ -4,7 +4,6 @@ use strict; BEGIN { - use lib '.'; use Bio::Root::Test; test_begin(-tests => 42); diff --git a/t/lib/Error.pm b/t/lib/Error.pm deleted file mode 100644 index 1930320c1..000000000 --- a/t/lib/Error.pm +++ /dev/null @@ -1,741 +0,0 @@ -# Error.pm -# -# Copyright (c) 1997-8 Graham Barr . All rights reserved. -# This program is free software; you can redistribute it and/or -# modify it under the same terms as Perl itself. -# -# Based on my original Error.pm, and Exceptions.pm by Peter Seibel -# and adapted by Jesse Glick . -# -# but modified ***significantly*** - -package Error; - -use strict; -use 5.004; - -use overload ( - '""' => 'stringify', - '0+' => 'value', - 'bool' => sub { return 1; }, - 'fallback' => 1 -); - -$Error::Depth = 0; # Depth to pass to caller() -$Error::Debug = 0; # Generate verbose stack traces -@Error::STACK = (); # Clause stack for try -$Error::THROWN = undef; # last error thrown, a workaround until die $ref works - -my $LAST; # Last error created -my %ERROR; # Last error associated with package - -# Exported subs are defined in Error::subs - -sub import { - shift; - local $Exporter::ExportLevel = $Exporter::ExportLevel + 1; - Error::subs->import(@_); -} - -# I really want to use last for the name of this method, but it is a keyword -# which prevent the syntax last Error - -sub prior { - shift; # ignore - - return $LAST unless @_; - - my $pkg = shift; - return exists $ERROR{$pkg} ? $ERROR{$pkg} : undef - unless ref($pkg); - - my $obj = $pkg; - my $err = undef; - if($obj->isa('HASH')) { - $err = $obj->{'__Error__'} - if exists $obj->{'__Error__'}; - } - elsif($obj->isa('GLOB')) { - $err = ${*$obj}{'__Error__'} - if exists ${*$obj}{'__Error__'}; - } - - $err; -} - -# Return as much information as possible about where the error -# happened. The -stacktrace element only exists if $Error::DEBUG -# was set when the error was created - -sub stacktrace { - my $self = shift; - - return $self->{'-stacktrace'} - if exists $self->{'-stacktrace'}; - - my $text = exists $self->{'-text'} ? $self->{'-text'} : "Died"; - - $text .= sprintf(" at %s line %d.\n", $self->file, $self->line) - unless($text =~ /\n$/s); - - $text; -} - -# Allow error propagation, ie -# -# $ber->encode(...) or -# return Error->prior($ber)->associate($ldap); - -sub associate { - my $err = shift; - my $obj = shift; - - return unless ref($obj); - - if($obj->isa('HASH')) { - $obj->{'__Error__'} = $err; - } - elsif($obj->isa('GLOB')) { - ${*$obj}{'__Error__'} = $err; - } - $obj = ref($obj); - $ERROR{ ref($obj) } = $err; - - return; -} - -sub new { - my $self = shift; - my($pkg,$file,$line) = caller($Error::Depth); - - my $err = bless { - '-package' => $pkg, - '-file' => $file, - '-line' => $line, - @_ - }, $self; - - $err->associate($err->{'-object'}) - if(exists $err->{'-object'}); - - # To always create a stacktrace would be very inefficient, so - # we only do it if $Error::Debug is set - - if($Error::Debug) { - require Carp; - local $Carp::CarpLevel = $Error::Depth; - my $text = defined($err->{'-text'}) ? $err->{'-text'} : "Error"; - my $trace = Carp::longmess($text); - # Remove try calls from the trace - $trace =~ s/(\n\s+\S+__ANON__[^\n]+)?\n\s+eval[^\n]+\n\s+Error::subs::try[^\n]+(?=\n)//sog; - $trace =~ s/(\n\s+\S+__ANON__[^\n]+)?\n\s+eval[^\n]+\n\s+Error::subs::run_clauses[^\n]+\n\s+Error::subs::try[^\n]+(?=\n)//sog; - $err->{'-stacktrace'} = $trace - } - - $@ = $LAST = $ERROR{$pkg} = $err; -} - -# Throw an error. this contains some very gory code. - -sub throw { - my $self = shift; - local $Error::Depth = $Error::Depth + 1; - - # if we are not rethrow-ing then create the object to throw - $self = $self->new(@_) unless ref($self); - - die $Error::THROWN = $self; -} - -# syntactic sugar for -# -# die with Error( ... ); - -sub with { - my $self = shift; - local $Error::Depth = $Error::Depth + 1; - - $self->new(@_); -} - -# syntactic sugar for -# -# record Error( ... ) and return; - -sub record { - my $self = shift; - local $Error::Depth = $Error::Depth + 1; - - $self->new(@_); -} - -# catch clause for -# -# try { ... } catch CLASS with { ... } - -sub catch { - my $pkg = shift; - my $code = shift; - my $clauses = shift || {}; - my $catch = $clauses->{'catch'} ||= []; - - unshift @$catch, $pkg, $code; - - $clauses; -} - -# Object query methods - -sub object { - my $self = shift; - exists $self->{'-object'} ? $self->{'-object'} : undef; -} - -sub file { - my $self = shift; - exists $self->{'-file'} ? $self->{'-file'} : undef; -} - -sub line { - my $self = shift; - exists $self->{'-line'} ? $self->{'-line'} : undef; -} - -sub text { - my $self = shift; - exists $self->{'-text'} ? $self->{'-text'} : undef; -} - -# overload methods - -sub stringify { - my $self = shift; - defined $self->{'-text'} ? $self->{'-text'} : "Died"; -} - -sub value { - my $self = shift; - exists $self->{'-value'} ? $self->{'-value'} : undef; -} - -package Error::Simple; - -@Error::Simple::ISA = qw(Error); - -sub new { - my $self = shift; - my $text = "" . shift; - my $value = shift; - my(@args) = (); - - local $Error::Depth = $Error::Depth + 1; - - @args = ( -file => $1, -line => $2) - if($text =~ s/ at (\S+) line (\d+)(\.\n)?$//s); - - push(@args, '-value', 0 + $value) - if defined($value); - - $self->SUPER::new(-text => $text, @args); -} - -sub stringify { - my $self = shift; - my $text = $self->SUPER::stringify; - $text .= sprintf(" at %s line %d.\n", $self->file, $self->line) - unless($text =~ /\n$/s); - $text; -} - -########################################################################## -########################################################################## - -# Inspired by code from Jesse Glick and -# Peter Seibel - -package Error::subs; - -use Exporter (); -use vars qw(@EXPORT_OK @ISA %EXPORT_TAGS); - -@EXPORT_OK = qw(try with finally except otherwise); -%EXPORT_TAGS = (try => \@EXPORT_OK); - -@ISA = qw(Exporter); - -sub run_clauses ($$$\@) { - my($clauses,$err,$wantarray,$result) = @_; - my $code = undef; - - $err = new Error::Simple($err) unless ref($err); - - CATCH: { - - # catch - my $catch; - if(defined($catch = $clauses->{'catch'})) { - my $i = 0; - - CATCHLOOP: - for( ; $i < @$catch ; $i += 2) { - my $pkg = $catch->[$i]; - unless(defined $pkg) { - #except - splice(@$catch,$i,2,$catch->[$i+1]->()); - $i -= 2; - next CATCHLOOP; - } - elsif($err->isa($pkg)) { - $code = $catch->[$i+1]; - while(1) { - my $more = 0; - local($Error::THROWN); - my $ok = eval { - if($wantarray) { - @{$result} = $code->($err,\$more); - } - elsif(defined($wantarray)) { - @{$result} = (); - $result->[0] = $code->($err,\$more); - } - else { - $code->($err,\$more); - } - 1; - }; - if( $ok ) { - next CATCHLOOP if $more; - undef $err; - } - else { - $err = defined($Error::THROWN) - ? $Error::THROWN : $@; - $err = new Error::Simple($err) - unless ref($err); - } - last CATCH; - }; - } - } - } - - # otherwise - my $owise; - if(defined($owise = $clauses->{'otherwise'})) { - my $code = $clauses->{'otherwise'}; - my $more = 0; - my $ok = eval { - if($wantarray) { - @{$result} = $code->($err,\$more); - } - elsif(defined($wantarray)) { - @{$result} = (); - $result->[0] = $code->($err,\$more); - } - else { - $code->($err,\$more); - } - 1; - }; - if( $ok ) { - undef $err; - } - else { - $err = defined($Error::THROWN) - ? $Error::THROWN : $@; - $err = new Error::Simple($err) - unless ref($err); - } - } - } - $err; -} - -sub try (&;$) { - my $try = shift; - my $clauses = @_ ? shift : {}; - my $ok = 0; - my $err = undef; - my @result = (); - - unshift @Error::STACK, $clauses; - - my $wantarray = wantarray(); - - do { - local $Error::THROWN = undef; - - $ok = eval { - if($wantarray) { - @result = $try->(); - } - elsif(defined $wantarray) { - $result[0] = $try->(); - } - else { - $try->(); - } - 1; - }; - - $err = defined($Error::THROWN) ? $Error::THROWN : $@ - unless $ok; - }; - - shift @Error::STACK; - - $err = run_clauses($clauses,$err,wantarray,@result) - unless($ok); - - $clauses->{'finally'}->() - if(defined($clauses->{'finally'})); - - throw $err if defined($err); - - wantarray ? @result : $result[0]; -} - -# Each clause adds a sub to the list of clauses. The finally clause is -# always the last, and the otherwise clause is always added just before -# the finally clause. -# -# All clauses, except the finally clause, add a sub which takes one argument -# this argument will be the error being thrown. The sub will return a code ref -# if that clause can handle that error, otherwise undef is returned. -# -# The otherwise clause adds a sub which unconditionally returns the users -# code reference, this is why it is forced to be last. -# -# The catch clause is defined in Error.pm, as the syntax causes it to -# be called as a method - -sub with (&;$) { - @_ -} - -sub finally (&) { - my $code = shift; - my $clauses = { 'finally' => $code }; - $clauses; -} - -# The except clause is a block which returns a hashref or a list of -# key-value pairs, where the keys are the classes and the values are subs. - -sub except (&;$) { - my $code = shift; - my $clauses = shift || {}; - my $catch = $clauses->{'catch'} ||= []; - - my $sub = sub { - my $ref; - my(@array) = $code->($_[0]); - if(@array == 1 && ref($array[0])) { - $ref = $array[0]; - $ref = [ %$ref ] - if(UNIVERSAL::isa($ref,'HASH')); - } - else { - $ref = \@array; - } - @$ref - }; - - unshift @{$catch}, undef, $sub; - - $clauses; -} - -sub otherwise (&;$) { - my $code = shift; - my $clauses = shift || {}; - - if(exists $clauses->{'otherwise'}) { - require Carp; - Carp::croak("Multiple otherwise clauses"); - } - - $clauses->{'otherwise'} = $code; - - $clauses; -} - -1; -__END__ - -=head1 NAME - -Error - Error/exception handling in an OO-ish way - -=head1 SYNOPSIS - - use Error qw(:try); - - throw Error::Simple( "A simple error"); - - sub xyz { - ... - record Error::Simple("A simple error") - and return; - } - - unlink($file) or throw Error::Simple("$file: $!",$!); - - try { - do_some_stuff(); - die "error!" if $condition; - throw Error::Simple -text => "Oops!" if $other_condition; - } - catch Error::IO with { - my $E = shift; - print STDERR "File ", $E->{'-file'}, " had a problem\n"; - } - except { - my $E = shift; - my $general_handler=sub {send_message $E->{-description}}; - return { - UserException1 => $general_handler, - UserException2 => $general_handler - }; - } - otherwise { - print STDERR "Well I don't know what to say\n"; - } - finally { - close_the_garage_door_already(); # Should be reliable - }; # Don't forget the trailing ; or you might be surprised - -=head1 DESCRIPTION - -The C package provides two interfaces. Firstly C provides -a procedural interface to exception handling. Secondly C is a -base class for errors/exceptions that can either be thrown, for -subsequent catch, or can simply be recorded. - -Errors in the class C should not be thrown directly, but the -user should throw errors from a sub-class of C. - -=head1 PROCEDURAL INTERFACE - -C exports subroutines to perform exception handling. These will -be exported if the C<:try> tag is used in the C line. - -=over 4 - -=item try BLOCK CLAUSES - -C is the main subroutine called by the user. All other subroutines -exported are clauses to the try subroutine. - -The BLOCK will be evaluated and, if no error is throw, try will return -the result of the block. - -C are the subroutines below, which describe what to do in the -event of an error being thrown within BLOCK. - -=item catch CLASS with BLOCK - -This clauses will cause all errors that satisfy C<$err-Eisa(CLASS)> -to be caught and handled by evaluating C. - -C will be passed two arguments. The first will be the error -being thrown. The second is a reference to a scalar variable. If this -variable is set by the catch block then, on return from the catch -block, try will continue processing as if the catch block was never -found. - -To propagate the error the catch block may call C<$err-Ethrow> - -If the scalar reference by the second argument is not set, and the -error is not thrown. Then the current try block will return with the -result from the catch block. - -=item except BLOCK - -When C is looking for a handler, if an except clause is found -C is evaluated. The return value from this block should be a -HASHREF or a list of key-value pairs, where the keys are class names -and the values are CODE references for the handler of errors of that -type. - -=item otherwise BLOCK - -Catch any error by executing the code in C - -When evaluated C will be passed one argument, which will be the -error being processed. - -Only one otherwise block may be specified per try block - -=item finally BLOCK - -Execute the code in C either after the code in the try block has -successfully completed, or if the try block throws an error then -C will be executed after the handler has completed. - -If the handler throws an error then the error will be caught, the -finally block will be executed and the error will be re-thrown. - -Only one finally block may be specified per try block - -=back - -=head1 CLASS INTERFACE - -=head2 CONSTRUCTORS - -The C object is implemented as a HASH. This HASH is initialized -with the arguments that are passed to it's constructor. The elements -that are used by, or are retrievable by the C class are listed -below, other classes may add to these. - - -file - -line - -text - -value - -object - -If C<-file> or C<-line> are not specified in the constructor arguments -then these will be initialized with the file name and line number where -the constructor was called from. - -If the error is associated with an object then the object should be -passed as the C<-object> argument. This will allow the C package -to associate the error with the object. - -The C package remembers the last error created, and also the -last error associated with a package. This could either be the last -error created by a sub in that package, or the last error which passed -an object blessed into that package as the C<-object> argument. - -=over 4 - -=item throw ( [ ARGS ] ) - -Create a new C object and throw an error, which will be caught -by a surrounding C block, if there is one. Otherwise it will cause -the program to exit. - -C may also be called on an existing error to re-throw it. - -=item with ( [ ARGS ] ) - -Create a new C object and returns it. This is defined for -syntactic sugar, eg - - die with Some::Error ( ... ); - -=item record ( [ ARGS ] ) - -Create a new C object and returns it. This is defined for -syntactic sugar, eg - - record Some::Error ( ... ) - and return; - -=back - -=head2 STATIC METHODS - -=over 4 - -=item prior ( [ PACKAGE ] ) - -Return the last error created, or the last error associated with -C - -=back - -=head2 OBJECT METHODS - -=over 4 - -=item stacktrace - -If the variable C<$Error::Debug> was non-zero when the error was -created, then C returns a string created by calling -C. If the variable was zero the C returns -the text of the error appended with the filename and line number of -where the error was created, providing the text does not end with a -newline. - -=item object - -The object this error was associated with - -=item file - -The file where the constructor of this error was called from - -=item line - -The line where the constructor of this error was called from - -=item text - -The text of the error - -=back - -=head2 OVERLOAD METHODS - -=over 4 - -=item stringify - -A method that converts the object into a string. This method may simply -return the same as the C method, or it may append more -information. For example the file name and line number. - -By default this method returns the C<-text> argument that was passed to -the constructor, or the string C<"Died"> if none was given. - -=item value - -A method that will return a value that can be associated with the -error. For example if an error was created due to the failure of a -system call, then this may return the numeric value of C<$!> at the -time. - -By default this method returns the C<-value> argument that was passed -to the constructor. - -=back - -=head1 PRE-DEFINED ERROR CLASSES - -=over 4 - -=item Error::Simple - -This class can be used to hold simple error strings and values. It's -constructor takes two arguments. The first is a text value, the second -is a numeric value. These values are what will be returned by the -overload methods. - -If the text value ends with C as $@ strings do, then -this infomation will be used to set the C<-file> and C<-line> arguments -of the error object. - -This class is used internally if an eval'd block die's with an error -that is a plain string. - -=back - -=head1 KNOWN BUGS - -None, but that does not mean there are not any. - -=head1 AUTHORS - -Graham Barr, gbarr@pobox.com - -The code that inspired me to write this was originally written by -Peter Seibel Epeter@weblogic.comE and adapted by Jesse Glick -Ejglick@sig.bsh.comE. - -=head1 MAINTAINER - -Arun Kumar U, u_arunkumar@yahoo.com - -=cut -- 2.11.4.GIT