Bioperl就像个大柜子，里面存放各种模块。Bio::SeqIO是Bioperl最基本的模块，本文介绍其在CentOS7-64bit下的安装方法。
STEP1：prepare to install
yum update #更新yum源。
yum install expat-devel 包 #Bioperl官网说要用XML功能需要安装expat和expat-devel包，由于expat包CentOS7自带，所以安装expat-devel包，究竟是不是必不可少的还需验证。
yum install ruby #Gudiance说要安装ruby，暂且记下
yum install cpan #安装perl的cpan包
cpan #初次运行cpan需要设置，一路选择默认设置即可。
cpan>install Bundle::CPAN #更新CPAN
cpan>install Module::Build #安装Module::Build 模块并设置
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>install LWP #安装LWP，这步很重要，不然Bio::SeqIO编译不成功。
cpan>install Digest::MD5 #安装或更新Digest::MD5，否则Bio::SeqIO编译不成功。
STEP2: Install Bio::SeqIO
cpan>install Bio::SeqIO #安装Bioperl最基本的模块Bio::SeqIO
#以下是CPAN对此包的依赖性检查，其中必须要的模块cpan会自动安装，推荐模块如在使用中遇到问题请安装此模块。
Reading ‘/root/.cpan/Metadata’
Database was generated on Fri, 26 Feb 2016 12:17:02 GMT
Running install for module ‘Bio::SeqIO’
Fetching with LWP:
http://cpan.develooper.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
Fetching with LWP:
http://cpan.develooper.com/authors/id/C/CJ/CJFIELDS/CHECKSUMS
Checksum for /root/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz ok
Scanning cache /root/.cpan/build for sizes
………………………………………………………………….DONE
Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
Checking prerequisites…
requires:
! Data::Stag is not installed
! IO::String is not installed
build_requires:
! Test::Most is not installed
recommends:
* Algorithm::Munkres is not installed
* Array::Compare is not installed
* Bio::Phylo is not installed
* Clone is not installed
* Convert::Binary::C is not installed
* DB_File is not installed
* GD is not installed
* Graph is not installed
* GraphViz is not installed
* HTML::TableExtract is not installed
* IO::Scalar is not installed
* List::MoreUtils is not installed
* PostScript::TextBlock is not installed
* SOAP::Lite is not installed
* SVG is not installed
* SVG::Graph is not installed
* Set::Scalar is not installed
* Sort::Naturally is not installed
* Spreadsheet::ParseExcel is not installed
* XML::DOM is not installed
* XML::DOM::XPath is not installed
* XML::LibXML is not installed
* XML::Parser::PerlSAX is not installed
* XML::SAX is not installed
* XML::SAX::Writer is not installed
* XML::Simple is not installed
* XML::Twig is not installed
* XML::Writer is not installed
Database was generated on Fri, 26 Feb 2016 12:17:02 GMT
Running install for module ‘Bio::SeqIO’
Fetching with LWP:
http://cpan.develooper.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
Fetching with LWP:
http://cpan.develooper.com/authors/id/C/CJ/CJFIELDS/CHECKSUMS
Checksum for /root/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz ok
Scanning cache /root/.cpan/build for sizes
………………………………………………………………….DONE
Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
Checking prerequisites…
requires:
! Data::Stag is not installed
! IO::String is not installed
build_requires:
! Test::Most is not installed
recommends:
* Algorithm::Munkres is not installed
* Array::Compare is not installed
* Bio::Phylo is not installed
* Clone is not installed
* Convert::Binary::C is not installed
* DB_File is not installed
* GD is not installed
* Graph is not installed
* GraphViz is not installed
* HTML::TableExtract is not installed
* IO::Scalar is not installed
* List::MoreUtils is not installed
* PostScript::TextBlock is not installed
* SOAP::Lite is not installed
* SVG is not installed
* SVG::Graph is not installed
* Set::Scalar is not installed
* Sort::Naturally is not installed
* Spreadsheet::ParseExcel is not installed
* XML::DOM is not installed
* XML::DOM::XPath is not installed
* XML::LibXML is not installed
* XML::Parser::PerlSAX is not installed
* XML::SAX is not installed
* XML::SAX::Writer is not installed
* XML::Simple is not installed
* XML::Twig is not installed
* XML::Writer is not installed
Checking optional features…
Bio::DB::GFF Tests….disabled
requires:
! DBI is not installed
DB_File Tests………disabled
requires:
! DB_File is not installed
EntrezGene…………disabled
requires:
! Bio::ASN1::EntrezGene is not installed
MySQL Tests………..disabled
requires:
! DBD::mysql is not installed
! DBI is not installed
Pg Tests…………..disabled
requires:
! DBD::Pg is not installed
! DBI is not installed
SQLite Tests……….disabled
requires:
! DBD::SQLite is not installed
! DBI is not installed
Bio::DB::GFF Tests….disabled
requires:
! DBI is not installed
DB_File Tests………disabled
requires:
! DB_File is not installed
EntrezGene…………disabled
requires:
! Bio::ASN1::EntrezGene is not installed
MySQL Tests………..disabled
requires:
! DBD::mysql is not installed
! DBI is not installed
Pg Tests…………..disabled
requires:
! DBD::Pg is not installed
! DBI is not installed
SQLite Tests……….disabled
requires:
! DBD::SQLite is not installed
! DBI is not installed
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
of the modules indicated above before proceeding with this installation
of the modules indicated above before proceeding with this installation
附件中有我第一次安装Bio::SeqIO时完成的test文档，哪个包需要哪些依赖包请参考。
#从这里开始正式要装Bio::Perl了
CJFIELDS/BioPerl-1.6.924.tar.gz
Has already been unwrapped into directory /root/.cpan/build/BioPerl-1.6.924-4qo47i
CJFIELDS/BioPerl-1.6.924.tar.gz
Has already been prepared
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
Building BioPerl
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build — OK
Running Build test
t/Align/AlignStats.t ………………. ok
t/Align/AlignUtil.t ……………….. ok
t/Align/Graphics.t ………………… skipped: The optional module GD (or dependencies thereof) was not installed
t/Align/SimpleAlign.t ……………… ok
t/Align/TreeBuild.t ……………….. ok
t/Align/Utilities.t ……………….. ok
t/AlignIO/AlignIO.t ……………….. ok
t/AlignIO/arp.t …………………… ok
t/AlignIO/bl2seq.t ………………… ok
t/AlignIO/clustalw.t ………………. ok
t/AlignIO/emboss.t ………………… ok
t/AlignIO/fasta.t …………………. ok
t/AlignIO/largemultifasta.t ………… ok
t/AlignIO/maf.t …………………… ok
t/AlignIO/mase.t ………………….. ok
t/AlignIO/mega.t ………………….. ok
t/AlignIO/meme.t ………………….. ok
t/AlignIO/metafasta.t ……………… ok
t/AlignIO/msf.t …………………… ok
t/AlignIO/nexml.t …………………. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/nexus.t …………………. ok
t/AlignIO/pfam.t ………………….. ok
t/AlignIO/phylip.t ………………… ok
t/AlignIO/po.t ……………………. ok
t/AlignIO/prodom.t ………………… ok
t/AlignIO/psi.t …………………… ok
t/AlignIO/selex.t …………………. ok
t/AlignIO/stockholm.t ……………… ok
t/AlignIO/xmfa.t ………………….. ok
t/Alphabet.t ……………………… ok
t/Annotation/Annotation.t ………….. ok
t/Annotation/AnnotationAdaptor.t ……. ok
t/Assembly/ContigSpectrum.t ………… skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/bowtie.t …………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/sam.t ……………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/core.t …………………. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Cluster/UniGene.t ……………….. ok
t/ClusterIO/ClusterIO.t ……………. ok
t/ClusterIO/SequenceFamily.t ……….. ok
t/ClusterIO/unigene.t ……………… ok
t/Coordinate/CoordinateBoundaryTest.t .. ok
t/Coordinate/CoordinateGraph.t ……… ok
t/Coordinate/CoordinateMapper.t …….. ok
t/Coordinate/GeneCoordinateMapper.t …. ok
t/Draw/Pictogram.t ………………… skipped: The optional module SVG (or dependencies thereof) was not installed
t/LiveSeq/Chain.t …………………. ok
t/LiveSeq/LiveSeq.t ……………….. ok
t/LiveSeq/Mutation.t ………………. ok
t/LiveSeq/Mutator.t ……………….. ok
t/LocalDB/BioDBGFF.t ………………. 7/275
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
CJFIELDS/BioPerl-1.6.924.tar.gz
Has already been unwrapped into directory /root/.cpan/build/BioPerl-1.6.924-4qo47i
CJFIELDS/BioPerl-1.6.924.tar.gz
Has already been prepared
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
Building BioPerl
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build — OK
Running Build test
t/Align/AlignStats.t ………………. ok
t/Align/AlignUtil.t ……………….. ok
t/Align/Graphics.t ………………… skipped: The optional module GD (or dependencies thereof) was not installed
t/Align/SimpleAlign.t ……………… ok
t/Align/TreeBuild.t ……………….. ok
t/Align/Utilities.t ……………….. ok
t/AlignIO/AlignIO.t ……………….. ok
t/AlignIO/arp.t …………………… ok
t/AlignIO/bl2seq.t ………………… ok
t/AlignIO/clustalw.t ………………. ok
t/AlignIO/emboss.t ………………… ok
t/AlignIO/fasta.t …………………. ok
t/AlignIO/largemultifasta.t ………… ok
t/AlignIO/maf.t …………………… ok
t/AlignIO/mase.t ………………….. ok
t/AlignIO/mega.t ………………….. ok
t/AlignIO/meme.t ………………….. ok
t/AlignIO/metafasta.t ……………… ok
t/AlignIO/msf.t …………………… ok
t/AlignIO/nexml.t …………………. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/nexus.t …………………. ok
t/AlignIO/pfam.t ………………….. ok
t/AlignIO/phylip.t ………………… ok
t/AlignIO/po.t ……………………. ok
t/AlignIO/prodom.t ………………… ok
t/AlignIO/psi.t …………………… ok
t/AlignIO/selex.t …………………. ok
t/AlignIO/stockholm.t ……………… ok
t/AlignIO/xmfa.t ………………….. ok
t/Alphabet.t ……………………… ok
t/Annotation/Annotation.t ………….. ok
t/Annotation/AnnotationAdaptor.t ……. ok
t/Assembly/ContigSpectrum.t ………… skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/bowtie.t …………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/sam.t ……………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/core.t …………………. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Cluster/UniGene.t ……………….. ok
t/ClusterIO/ClusterIO.t ……………. ok
t/ClusterIO/SequenceFamily.t ……….. ok
t/ClusterIO/unigene.t ……………… ok
t/Coordinate/CoordinateBoundaryTest.t .. ok
t/Coordinate/CoordinateGraph.t ……… ok
t/Coordinate/CoordinateMapper.t …….. ok
t/Coordinate/GeneCoordinateMapper.t …. ok
t/Draw/Pictogram.t ………………… skipped: The optional module SVG (or dependencies thereof) was not installed
t/LiveSeq/Chain.t …………………. ok
t/LiveSeq/LiveSeq.t ……………….. ok
t/LiveSeq/Mutation.t ………………. ok
t/LiveSeq/Mutator.t ……………….. ok
t/LocalDB/BioDBGFF.t ………………. 7/275
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
t/LocalDB/BioDBGFF.t ………………. ok
t/LocalDB/Fasta.t …………………. 1/107 Can’t locate Digest/MD5.pm in @INC (@INC contains: . /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/lib /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/arch /root/.cpan/build/BioPerl-1.6.924-4qo47i /root/perl5/lib/perl5/5.16.3/x86_64-linux-thread-multi /root/perl5/lib/perl5/5.16.3 /root/perl5/lib/perl5/x86_64-linux-thread-multi /root/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at Bio/DB/IndexedBase.pm line 503.
# Looks like you planned 107 tests but ran 95.
# Looks like your test exited with 2 just after 95.
t/LocalDB/Fasta.t …………………. Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/107 subtests
(less 1 skipped subtest: 94 okay)
t/LocalDB/Flat.t ………………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Index/Blast.t ……………. ok
t/LocalDB/Index/BlastTable.t ……….. ok
t/LocalDB/Index/Index.t ……………. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Qual.t ………………….. ok
t/LocalDB/Registry.t ………………. ok
t/LocalDB/SeqFeature.t …………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Taxonomy/greengenes.t …….. ok
t/LocalDB/Taxonomy/silva.t …………. ok
t/LocalDB/transfac_pro.t …………… skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Map/Cyto.t ……………………… ok
t/Map/Linkage.t …………………… ok
t/Map/Map.t ………………………. ok
t/Map/MapIO.t …………………….. ok
t/Map/MicrosatelliteMarker.t ……….. ok
t/Map/Physical.t ………………….. ok
t/Matrix/IO/masta.t ……………….. ok
t/Matrix/IO/psm.t …………………. ok
t/Matrix/InstanceSite.t ……………. ok
t/Matrix/Matrix.t …………………. ok
t/Matrix/ProtMatrix.t ……………… ok
t/Matrix/ProtPsm.t ………………… ok
t/Matrix/SiteMatrix.t ……………… ok
t/Ontology/GOterm.t ……………….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t ………….. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.t ………………… skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.t …………… skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/Ontology/IO/obo.t ……………….. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Ontology.t ……………… skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine.t ………… skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.t …………. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Relationship.t ………….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType.t ………. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term.t …………………. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Perl.t …………………………. ok
t/Phenotype/Correlate.t ……………. ok
t/Phenotype/MeSH.t ………………… ok
t/Phenotype/Measure.t ……………… ok
t/Phenotype/MiniMIMentry.t …………. ok
t/Phenotype/OMIMentry.t ……………. ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMparser.t …………… ok
t/Phenotype/Phenotype.t ……………. ok
t/PodSyntax.t …………………….. skipped: Test::Pod 1.00 required for testing POD
t/PopGen/Coalescent.t ……………… ok
t/PopGen/HtSNP.t ………………….. ok
t/PopGen/MK.t …………………….. ok
t/PopGen/PopGen.t …………………. ok
t/PopGen/PopGenSims.t ……………… ok
t/PopGen/TagHaplotype.t ……………. ok
t/RemoteDB/BioFetch.t ……………… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/CUTG.t …………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EMBL.t …………………. skipped: The optional module HTTP::Request::Common (or dependencies thereof) was not installed
t/RemoteDB/EntrezGene.t ……………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenPept.t ………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIV.t ………………. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVAnnotProcessor.t ….. ok
t/RemoteDB/HIV/HIVQuery.t ………….. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVQueryHelper.t …….. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/MeSH.t …………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Query/GenBank.t …………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/RefSeq.t ……………….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqHound.t ……………… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqRead_fail.t ………….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqVersion.t ……………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t …………….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Taxonomy.t ……………… skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Restriction/Analysis-refac.t ……… ok
t/Restriction/Analysis.t …………… ok
t/Restriction/Gel.t ……………….. ok
t/Restriction/IO.t ………………… ok
t/Root/Exception.t ………………… ok
t/Root/HTTPget.t ………………….. skipped: Network tests have not been requested
t/Root/IO.t ………………………. ok
t/Root/RootI.t ……………………. ok
t/Root/Storable.t …………………. ok
t/Root/Utilities.t ………………… 1/56
——————— WARNING ———————
MSG: Not owner of file t/data/test.txt. Compressing to temp file /tmp/DN1geA3UTk.tmp.bioperl.gz.
—————————————————
t/Root/Utilities.t ………………… ok
t/SearchDist.t ……………………. skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.t …………… ok
t/SearchIO/SearchIO.t ……………… ok
t/SearchIO/SimilarityPair.t ………… ok
t/SearchIO/Tiling.t ……………….. ok
t/SearchIO/Writer/GbrowseGFF.t ……… ok
t/SearchIO/Writer/HSPTableWriter.t ….. ok
t/SearchIO/Writer/HTMLWriter.t ……… ok
t/SearchIO/Writer/HitTableWriter.t ….. ok
t/SearchIO/Writer/TextWriter.t ……… ok
t/SearchIO/axt.t ………………….. ok
t/SearchIO/blast.t ………………… ok
t/SearchIO/blast_pull.t ……………. ok
t/SearchIO/blasttable.t ……………. ok
t/SearchIO/blastxml.t ……………… skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SearchIO/cross_match.t …………… ok
t/SearchIO/erpin.t ………………… ok
t/SearchIO/exonerate.t …………….. ok
t/SearchIO/fasta.t ………………… ok
t/SearchIO/gmap_f9.t ………………. ok
t/SearchIO/hmmer.t ………………… ok
t/SearchIO/hmmer_pull.t ……………. ok
t/SearchIO/infernal.t ……………… ok
t/SearchIO/megablast.t …………….. ok
t/SearchIO/psl.t ………………….. ok
t/SearchIO/rnamotif.t ……………… ok
t/SearchIO/sim4.t …………………. ok
t/SearchIO/waba.t …………………. ok
t/SearchIO/wise.t …………………. ok
t/Seq/DBLink.t ……………………. ok
t/Seq/EncodedSeq.t ………………… ok
t/Seq/LargeLocatableSeq.t ………….. ok
t/Seq/LargePSeq.t …………………. ok
t/Seq/LocatableSeq.t ………………. ok
t/Seq/MetaSeq.t …………………… ok
t/Seq/PrimaryQual.t ……………….. ok
t/Seq/PrimarySeq.t ………………… ok
t/Seq/PrimedSeq.t …………………. ok
t/Seq/Quality.t …………………… ok
t/Seq/Seq.t ………………………. ok
t/Seq/SimulatedRead.t ……………… ok
t/Seq/WithQuality.t ……………….. ok
t/SeqEvolution.t ………………….. ok
t/SeqFeature/Amplicon.t ……………. ok
t/SeqFeature/Clone.t ………………. ok
t/SeqFeature/Collection.t ………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/SeqFeature/Computation.t …………. ok
t/SeqFeature/FeaturePair.t …………. ok
t/SeqFeature/Gene.t ……………….. ok
t/SeqFeature/Generic.t …………….. ok
t/SeqFeature/Location.t ……………. ok
t/SeqFeature/LocationFactory.t ……… ok
t/SeqFeature/Primer.t ……………… ok
t/SeqFeature/Range.t ………………. ok
t/SeqFeature/RangeI.t ……………… ok
t/SeqFeature/SeqAnalysisParser.t ……. ok
t/SeqFeature/SubSeq.t ……………… ok
t/SeqFeature/Unflattener.t …………. ok
t/SeqIO/Handler.t …………………. ok
t/SeqIO/MultiFile.t ……………….. ok
t/SeqIO/Multiple_fasta.t …………… ok
t/SeqIO/SeqBuilder.t ………………. ok
t/SeqIO/SeqIO.t …………………… ok
t/SeqIO/Splicedseq.t ………………. 1/19 Can’t locate LWP/UserAgent.pm in @INC (@INC contains: . /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/lib /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/arch /root/.cpan/build/BioPerl-1.6.924-4qo47i /root/perl5/lib/perl5/5.16.3/x86_64-linux-thread-multi /root/perl5/lib/perl5/5.16.3 /root/perl5/lib/perl5/x86_64-linux-thread-multi /root/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at Bio/DB/Query/WebQuery.pm line 85.
BEGIN failed–compilation aborted at Bio/DB/Query/WebQuery.pm line 85.
Compilation failed in require at (eval 59) line 2.
…propagated at /usr/share/perl5/base.pm line 84.
BEGIN failed–compilation aborted at Bio/DB/Query/GenBank.pm line 115.
Compilation failed in require at Bio/DB/NCBIHelper.pm line 90.
BEGIN failed–compilation aborted at Bio/DB/NCBIHelper.pm line 90.
Compilation failed in require at (eval 58) line 2.
…propagated at /usr/share/perl5/base.pm line 84.
BEGIN failed–compilation aborted at Bio/DB/GenBank.pm line 171.
Compilation failed in require at t/SeqIO/Splicedseq.t line 74.
BEGIN failed–compilation aborted at t/SeqIO/Splicedseq.t line 74.
# Looks like you planned 19 tests but ran 1.
# Looks like your test exited with 2 just after 1.
t/SeqIO/Splicedseq.t ………………. Dubious, test returned 2 (wstat 512, 0x200)
Failed 18/19 subtests
t/SeqIO/abi.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace.t …………………….. ok
t/SeqIO/agave.t …………………… skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/alf.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/asciitree.t ……………….. ok
t/SeqIO/bsml.t ……………………. skipped: The optional module XML::DOM (or dependencies thereof) was not installed
t/SeqIO/bsml_sax.t ………………… skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/chadoxml.t ………………… skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/chaos.t …………………… ok
t/SeqIO/chaosxml.t ………………… ok
t/SeqIO/ctf.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.t ……………………. ok
t/SeqIO/entrezgene.t ………………. skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel.t …………………… skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
t/SeqIO/exp.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t …………………… ok
t/SeqIO/fastq.t …………………… ok
t/SeqIO/flybase_chadoxml.t …………. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/game.t ……………………. skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/gbxml.t …………………… skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/gcg.t …………………….. ok
t/SeqIO/genbank.t …………………. ok
t/SeqIO/interpro.t ………………… skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.t ……………………. ok
t/SeqIO/largefasta.t ………………. ok
t/SeqIO/lasergene.t ……………….. ok
t/SeqIO/locuslink.t ……………….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/mbsout.t ………………….. ok
t/SeqIO/metafasta.t ……………….. ok
t/SeqIO/msout.t …………………… ok
t/SeqIO/nexml.t …………………… skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/SeqIO/phd.t …………………….. ok
t/SeqIO/pir.t …………………….. ok
t/SeqIO/pln.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ……………………. ok
t/SeqIO/raw.t …………………….. ok
t/SeqIO/scf.t …………………….. ok
t/SeqIO/seqxml.t ………………….. skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/SeqIO/strider.t …………………. skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss.t …………………… ok
t/SeqIO/tab.t …………………….. ok
t/SeqIO/table.t …………………… skipped: The optional module IO::Scalar (or dependencies thereof) was not installed
t/SeqIO/tigr.t ……………………. ok
t/SeqIO/tigrxml.t …………………. skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/tinyseq.t …………………. skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/ztr.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t …………. skipped: The optional module List::MoreUtils (or dependencies thereof) was not installed
t/SeqTools/CodonTable.t ……………. ok
t/SeqTools/ECnumber.t ……………… ok
t/SeqTools/GuessSeqFormat.t ………… ok
t/SeqTools/OddCodes.t ……………… ok
t/SeqTools/SeqPattern.t ……………. ok
t/SeqTools/SeqStats.t ……………… ok
t/SeqTools/SeqUtils.t ……………… ok
t/SeqTools/SeqWords.t ……………… ok
t/Species.t ………………………. ok
t/Structure/IO.t ………………….. ok
t/Structure/Structure.t ……………. ok
t/Symbol.t ……………………….. ok
t/TaxonTree.t …………………….. skipped: These modules are now probably deprecated
t/Tools/Alignment/Consed.t …………. ok
t/Tools/AmpliconSearch.t …………… ok
t/Tools/Analysis/DNA/ESEfinder.t ……. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Domcut.t …… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/ELM.t ……… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/GOR4.t …….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/HNN.t ……… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Mitoprot.t …. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/NetPhos.t ….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Scansite.t …. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Sopma.t ……. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/EMBOSS/Palindrome.t ………… ok
t/Tools/Est2Genome.t ………………. ok
t/Tools/FootPrinter.t ……………… ok
t/Tools/GFF.t …………………….. ok
t/Tools/Geneid.t ………………….. ok
t/Tools/Genewise.t ………………… ok
t/Tools/Genomewise.t ………………. ok
t/Tools/Genpred.t …………………. ok
t/Tools/Hmmer.t …………………… ok
t/Tools/IUPAC.t …………………… ok
t/Tools/Lucy.t ……………………. ok
t/Tools/Match.t …………………… ok
t/Tools/Phylo/Gerp.t ………………. ok
t/Tools/Phylo/Molphy.t …………….. ok
t/Tools/Phylo/PAML.t ………………. ok
t/Tools/Phylo/Phylip/ProtDist.t …….. ok
t/Tools/Primer3.t …………………. ok
t/Tools/Promoterwise.t …………….. ok
t/Tools/Pseudowise.t ………………. ok
t/Tools/QRNA.t ……………………. ok
t/Tools/RandDistFunctions.t ………… ok
t/Tools/RepeatMasker.t …………….. ok
t/Tools/Run/RemoteBlast.t ………….. skipped: The optional module LWP (or dependencies thereof) was not installed
t/Tools/Run/RemoteBlast_rpsblast.t ….. skipped: The optional module LWP (or dependencies thereof) was not installed
t/Tools/Run/StandAloneBlast.t ………. ok
t/Tools/Run/WBCommandExts.t ………… skipped: The optional module Bio::Tools::Run::WrapperBase::CommandExts (or dependencies thereof) was not installed
t/Tools/Run/WrapperBase.t ………….. ok
t/Tools/Seg.t …………………….. ok
t/Tools/SiRNA.t …………………… ok
t/Tools/Sigcleave.t ……………….. ok
t/Tools/Signalp.t …………………. ok
t/Tools/Signalp/ExtendedSignalp.t …… ok
t/Tools/Sim4.t ……………………. ok
t/Tools/Spidey/Spidey.t ……………. ok
t/Tools/TandemRepeatsFinder.t ………. ok
t/Tools/TargetP.t …………………. ok
t/Tools/Tmhmm.t …………………… ok
t/Tools/ePCR.t ……………………. ok
t/Tools/pICalculator.t …………….. ok
t/Tools/rnamotif.t ………………… skipped: These modules are now probably deprecated
t/Tools/tRNAscanSE.t ………………. ok
t/Tree/Compatible.t ……………….. skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
t/Tree/Node.t …………………….. ok
t/Tree/PhyloNetwork/Factory.t ………. skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.t ……… skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ……… ok
t/Tree/PhyloNetwork/PhyloNetwork.t ….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory.t …. skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t …… skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.t …………. ok
t/Tree/Tree.t …………………….. ok
t/Tree/TreeIO.t …………………… ok
t/Tree/TreeIO/lintree.t ……………. ok
t/Tree/TreeIO/newick.t …………….. ok
t/Tree/TreeIO/nexml.t ……………… skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nexus.t ……………… ok
t/Tree/TreeIO/nhx.t ……………….. ok
t/Tree/TreeIO/phyloxml.t …………… skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/Tree/TreeIO/svggraph.t …………… ok
t/Tree/TreeIO/tabtree.t ……………. ok
t/Tree/TreeStatistics.t ……………. ok
t/Variation/AAChange.t …………….. ok
t/Variation/AAReverseMutate.t ………. ok
t/Variation/Allele.t ………………. ok
t/Variation/DNAMutation.t ………….. ok
t/Variation/RNAChange.t ……………. ok
t/Variation/SNP.t …………………. ok
t/Variation/SeqDiff.t ……………… ok
t/Variation/Variation_IO.t …………. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/nexml.t ………………………… skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/LocalDB/Fasta.t …………………. 1/107 Can’t locate Digest/MD5.pm in @INC (@INC contains: . /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/lib /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/arch /root/.cpan/build/BioPerl-1.6.924-4qo47i /root/perl5/lib/perl5/5.16.3/x86_64-linux-thread-multi /root/perl5/lib/perl5/5.16.3 /root/perl5/lib/perl5/x86_64-linux-thread-multi /root/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at Bio/DB/IndexedBase.pm line 503.
# Looks like you planned 107 tests but ran 95.
# Looks like your test exited with 2 just after 95.
t/LocalDB/Fasta.t …………………. Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/107 subtests
(less 1 skipped subtest: 94 okay)
t/LocalDB/Flat.t ………………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Index/Blast.t ……………. ok
t/LocalDB/Index/BlastTable.t ……….. ok
t/LocalDB/Index/Index.t ……………. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Qual.t ………………….. ok
t/LocalDB/Registry.t ………………. ok
t/LocalDB/SeqFeature.t …………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Taxonomy/greengenes.t …….. ok
t/LocalDB/Taxonomy/silva.t …………. ok
t/LocalDB/transfac_pro.t …………… skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Map/Cyto.t ……………………… ok
t/Map/Linkage.t …………………… ok
t/Map/Map.t ………………………. ok
t/Map/MapIO.t …………………….. ok
t/Map/MicrosatelliteMarker.t ……….. ok
t/Map/Physical.t ………………….. ok
t/Matrix/IO/masta.t ……………….. ok
t/Matrix/IO/psm.t …………………. ok
t/Matrix/InstanceSite.t ……………. ok
t/Matrix/Matrix.t …………………. ok
t/Matrix/ProtMatrix.t ……………… ok
t/Matrix/ProtPsm.t ………………… ok
t/Matrix/SiteMatrix.t ……………… ok
t/Ontology/GOterm.t ……………….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t ………….. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.t ………………… skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.t …………… skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/Ontology/IO/obo.t ……………….. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Ontology.t ……………… skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine.t ………… skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.t …………. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Relationship.t ………….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType.t ………. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term.t …………………. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Perl.t …………………………. ok
t/Phenotype/Correlate.t ……………. ok
t/Phenotype/MeSH.t ………………… ok
t/Phenotype/Measure.t ……………… ok
t/Phenotype/MiniMIMentry.t …………. ok
t/Phenotype/OMIMentry.t ……………. ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMparser.t …………… ok
t/Phenotype/Phenotype.t ……………. ok
t/PodSyntax.t …………………….. skipped: Test::Pod 1.00 required for testing POD
t/PopGen/Coalescent.t ……………… ok
t/PopGen/HtSNP.t ………………….. ok
t/PopGen/MK.t …………………….. ok
t/PopGen/PopGen.t …………………. ok
t/PopGen/PopGenSims.t ……………… ok
t/PopGen/TagHaplotype.t ……………. ok
t/RemoteDB/BioFetch.t ……………… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/CUTG.t …………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EMBL.t …………………. skipped: The optional module HTTP::Request::Common (or dependencies thereof) was not installed
t/RemoteDB/EntrezGene.t ……………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenPept.t ………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIV.t ………………. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVAnnotProcessor.t ….. ok
t/RemoteDB/HIV/HIVQuery.t ………….. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVQueryHelper.t …….. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/MeSH.t …………………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Query/GenBank.t …………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/RefSeq.t ……………….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqHound.t ……………… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqRead_fail.t ………….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqVersion.t ……………. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t …………….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Taxonomy.t ……………… skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Restriction/Analysis-refac.t ……… ok
t/Restriction/Analysis.t …………… ok
t/Restriction/Gel.t ……………….. ok
t/Restriction/IO.t ………………… ok
t/Root/Exception.t ………………… ok
t/Root/HTTPget.t ………………….. skipped: Network tests have not been requested
t/Root/IO.t ………………………. ok
t/Root/RootI.t ……………………. ok
t/Root/Storable.t …………………. ok
t/Root/Utilities.t ………………… 1/56
——————— WARNING ———————
MSG: Not owner of file t/data/test.txt. Compressing to temp file /tmp/DN1geA3UTk.tmp.bioperl.gz.
—————————————————
t/Root/Utilities.t ………………… ok
t/SearchDist.t ……………………. skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.t …………… ok
t/SearchIO/SearchIO.t ……………… ok
t/SearchIO/SimilarityPair.t ………… ok
t/SearchIO/Tiling.t ……………….. ok
t/SearchIO/Writer/GbrowseGFF.t ……… ok
t/SearchIO/Writer/HSPTableWriter.t ….. ok
t/SearchIO/Writer/HTMLWriter.t ……… ok
t/SearchIO/Writer/HitTableWriter.t ….. ok
t/SearchIO/Writer/TextWriter.t ……… ok
t/SearchIO/axt.t ………………….. ok
t/SearchIO/blast.t ………………… ok
t/SearchIO/blast_pull.t ……………. ok
t/SearchIO/blasttable.t ……………. ok
t/SearchIO/blastxml.t ……………… skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SearchIO/cross_match.t …………… ok
t/SearchIO/erpin.t ………………… ok
t/SearchIO/exonerate.t …………….. ok
t/SearchIO/fasta.t ………………… ok
t/SearchIO/gmap_f9.t ………………. ok
t/SearchIO/hmmer.t ………………… ok
t/SearchIO/hmmer_pull.t ……………. ok
t/SearchIO/infernal.t ……………… ok
t/SearchIO/megablast.t …………….. ok
t/SearchIO/psl.t ………………….. ok
t/SearchIO/rnamotif.t ……………… ok
t/SearchIO/sim4.t …………………. ok
t/SearchIO/waba.t …………………. ok
t/SearchIO/wise.t …………………. ok
t/Seq/DBLink.t ……………………. ok
t/Seq/EncodedSeq.t ………………… ok
t/Seq/LargeLocatableSeq.t ………….. ok
t/Seq/LargePSeq.t …………………. ok
t/Seq/LocatableSeq.t ………………. ok
t/Seq/MetaSeq.t …………………… ok
t/Seq/PrimaryQual.t ……………….. ok
t/Seq/PrimarySeq.t ………………… ok
t/Seq/PrimedSeq.t …………………. ok
t/Seq/Quality.t …………………… ok
t/Seq/Seq.t ………………………. ok
t/Seq/SimulatedRead.t ……………… ok
t/Seq/WithQuality.t ……………….. ok
t/SeqEvolution.t ………………….. ok
t/SeqFeature/Amplicon.t ……………. ok
t/SeqFeature/Clone.t ………………. ok
t/SeqFeature/Collection.t ………….. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/SeqFeature/Computation.t …………. ok
t/SeqFeature/FeaturePair.t …………. ok
t/SeqFeature/Gene.t ……………….. ok
t/SeqFeature/Generic.t …………….. ok
t/SeqFeature/Location.t ……………. ok
t/SeqFeature/LocationFactory.t ……… ok
t/SeqFeature/Primer.t ……………… ok
t/SeqFeature/Range.t ………………. ok
t/SeqFeature/RangeI.t ……………… ok
t/SeqFeature/SeqAnalysisParser.t ……. ok
t/SeqFeature/SubSeq.t ……………… ok
t/SeqFeature/Unflattener.t …………. ok
t/SeqIO/Handler.t …………………. ok
t/SeqIO/MultiFile.t ……………….. ok
t/SeqIO/Multiple_fasta.t …………… ok
t/SeqIO/SeqBuilder.t ………………. ok
t/SeqIO/SeqIO.t …………………… ok
t/SeqIO/Splicedseq.t ………………. 1/19 Can’t locate LWP/UserAgent.pm in @INC (@INC contains: . /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/lib /root/.cpan/build/BioPerl-1.6.924-4qo47i/blib/arch /root/.cpan/build/BioPerl-1.6.924-4qo47i /root/perl5/lib/perl5/5.16.3/x86_64-linux-thread-multi /root/perl5/lib/perl5/5.16.3 /root/perl5/lib/perl5/x86_64-linux-thread-multi /root/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at Bio/DB/Query/WebQuery.pm line 85.
BEGIN failed–compilation aborted at Bio/DB/Query/WebQuery.pm line 85.
Compilation failed in require at (eval 59) line 2.
…propagated at /usr/share/perl5/base.pm line 84.
BEGIN failed–compilation aborted at Bio/DB/Query/GenBank.pm line 115.
Compilation failed in require at Bio/DB/NCBIHelper.pm line 90.
BEGIN failed–compilation aborted at Bio/DB/NCBIHelper.pm line 90.
Compilation failed in require at (eval 58) line 2.
…propagated at /usr/share/perl5/base.pm line 84.
BEGIN failed–compilation aborted at Bio/DB/GenBank.pm line 171.
Compilation failed in require at t/SeqIO/Splicedseq.t line 74.
BEGIN failed–compilation aborted at t/SeqIO/Splicedseq.t line 74.
# Looks like you planned 19 tests but ran 1.
# Looks like your test exited with 2 just after 1.
t/SeqIO/Splicedseq.t ………………. Dubious, test returned 2 (wstat 512, 0x200)
Failed 18/19 subtests
t/SeqIO/abi.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace.t …………………….. ok
t/SeqIO/agave.t …………………… skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/alf.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/asciitree.t ……………….. ok
t/SeqIO/bsml.t ……………………. skipped: The optional module XML::DOM (or dependencies thereof) was not installed
t/SeqIO/bsml_sax.t ………………… skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/chadoxml.t ………………… skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/chaos.t …………………… ok
t/SeqIO/chaosxml.t ………………… ok
t/SeqIO/ctf.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.t ……………………. ok
t/SeqIO/entrezgene.t ………………. skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel.t …………………… skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
t/SeqIO/exp.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t …………………… ok
t/SeqIO/fastq.t …………………… ok
t/SeqIO/flybase_chadoxml.t …………. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/game.t ……………………. skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/gbxml.t …………………… skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/gcg.t …………………….. ok
t/SeqIO/genbank.t …………………. ok
t/SeqIO/interpro.t ………………… skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.t ……………………. ok
t/SeqIO/largefasta.t ………………. ok
t/SeqIO/lasergene.t ……………….. ok
t/SeqIO/locuslink.t ……………….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/mbsout.t ………………….. ok
t/SeqIO/metafasta.t ……………….. ok
t/SeqIO/msout.t …………………… ok
t/SeqIO/nexml.t …………………… skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/SeqIO/phd.t …………………….. ok
t/SeqIO/pir.t …………………….. ok
t/SeqIO/pln.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ……………………. ok
t/SeqIO/raw.t …………………….. ok
t/SeqIO/scf.t …………………….. ok
t/SeqIO/seqxml.t ………………….. skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/SeqIO/strider.t …………………. skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss.t …………………… ok
t/SeqIO/tab.t …………………….. ok
t/SeqIO/table.t …………………… skipped: The optional module IO::Scalar (or dependencies thereof) was not installed
t/SeqIO/tigr.t ……………………. ok
t/SeqIO/tigrxml.t …………………. skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/tinyseq.t …………………. skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/ztr.t …………………….. skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t …………. skipped: The optional module List::MoreUtils (or dependencies thereof) was not installed
t/SeqTools/CodonTable.t ……………. ok
t/SeqTools/ECnumber.t ……………… ok
t/SeqTools/GuessSeqFormat.t ………… ok
t/SeqTools/OddCodes.t ……………… ok
t/SeqTools/SeqPattern.t ……………. ok
t/SeqTools/SeqStats.t ……………… ok
t/SeqTools/SeqUtils.t ……………… ok
t/SeqTools/SeqWords.t ……………… ok
t/Species.t ………………………. ok
t/Structure/IO.t ………………….. ok
t/Structure/Structure.t ……………. ok
t/Symbol.t ……………………….. ok
t/TaxonTree.t …………………….. skipped: These modules are now probably deprecated
t/Tools/Alignment/Consed.t …………. ok
t/Tools/AmpliconSearch.t …………… ok
t/Tools/Analysis/DNA/ESEfinder.t ……. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Domcut.t …… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/ELM.t ……… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/GOR4.t …….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/HNN.t ……… skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Mitoprot.t …. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/NetPhos.t ….. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Scansite.t …. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Sopma.t ……. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/EMBOSS/Palindrome.t ………… ok
t/Tools/Est2Genome.t ………………. ok
t/Tools/FootPrinter.t ……………… ok
t/Tools/GFF.t …………………….. ok
t/Tools/Geneid.t ………………….. ok
t/Tools/Genewise.t ………………… ok
t/Tools/Genomewise.t ………………. ok
t/Tools/Genpred.t …………………. ok
t/Tools/Hmmer.t …………………… ok
t/Tools/IUPAC.t …………………… ok
t/Tools/Lucy.t ……………………. ok
t/Tools/Match.t …………………… ok
t/Tools/Phylo/Gerp.t ………………. ok
t/Tools/Phylo/Molphy.t …………….. ok
t/Tools/Phylo/PAML.t ………………. ok
t/Tools/Phylo/Phylip/ProtDist.t …….. ok
t/Tools/Primer3.t …………………. ok
t/Tools/Promoterwise.t …………….. ok
t/Tools/Pseudowise.t ………………. ok
t/Tools/QRNA.t ……………………. ok
t/Tools/RandDistFunctions.t ………… ok
t/Tools/RepeatMasker.t …………….. ok
t/Tools/Run/RemoteBlast.t ………….. skipped: The optional module LWP (or dependencies thereof) was not installed
t/Tools/Run/RemoteBlast_rpsblast.t ….. skipped: The optional module LWP (or dependencies thereof) was not installed
t/Tools/Run/StandAloneBlast.t ………. ok
t/Tools/Run/WBCommandExts.t ………… skipped: The optional module Bio::Tools::Run::WrapperBase::CommandExts (or dependencies thereof) was not installed
t/Tools/Run/WrapperBase.t ………….. ok
t/Tools/Seg.t …………………….. ok
t/Tools/SiRNA.t …………………… ok
t/Tools/Sigcleave.t ……………….. ok
t/Tools/Signalp.t …………………. ok
t/Tools/Signalp/ExtendedSignalp.t …… ok
t/Tools/Sim4.t ……………………. ok
t/Tools/Spidey/Spidey.t ……………. ok
t/Tools/TandemRepeatsFinder.t ………. ok
t/Tools/TargetP.t …………………. ok
t/Tools/Tmhmm.t …………………… ok
t/Tools/ePCR.t ……………………. ok
t/Tools/pICalculator.t …………….. ok
t/Tools/rnamotif.t ………………… skipped: These modules are now probably deprecated
t/Tools/tRNAscanSE.t ………………. ok
t/Tree/Compatible.t ……………….. skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
t/Tree/Node.t …………………….. ok
t/Tree/PhyloNetwork/Factory.t ………. skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.t ……… skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ……… ok
t/Tree/PhyloNetwork/PhyloNetwork.t ….. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory.t …. skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t …… skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.t …………. ok
t/Tree/Tree.t …………………….. ok
t/Tree/TreeIO.t …………………… ok
t/Tree/TreeIO/lintree.t ……………. ok
t/Tree/TreeIO/newick.t …………….. ok
t/Tree/TreeIO/nexml.t ……………… skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nexus.t ……………… ok
t/Tree/TreeIO/nhx.t ……………….. ok
t/Tree/TreeIO/phyloxml.t …………… skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/Tree/TreeIO/svggraph.t …………… ok
t/Tree/TreeIO/tabtree.t ……………. ok
t/Tree/TreeStatistics.t ……………. ok
t/Variation/AAChange.t …………….. ok
t/Variation/AAReverseMutate.t ………. ok
t/Variation/Allele.t ………………. ok
t/Variation/DNAMutation.t ………….. ok
t/Variation/RNAChange.t ……………. ok
t/Variation/SNP.t …………………. ok
t/Variation/SeqDiff.t ……………… ok
t/Variation/Variation_IO.t …………. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/nexml.t ………………………… skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
Test Summary Report
——————-
t/LocalDB/Fasta.t (Wstat: 512 Tests: 95 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 107 tests but ran 95.
t/SeqIO/Splicedseq.t (Wstat: 512 Tests: 1 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 19 tests but ran 1.
Files=334, Tests=17147, 94 wallclock secs ( 2.98 usr 0.67 sys + 86.88 cusr 6.43 csys = 96.96 CPU)
Result: FAIL #测试结果是失败的
——————-
t/LocalDB/Fasta.t (Wstat: 512 Tests: 95 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 107 tests but ran 95.
t/SeqIO/Splicedseq.t (Wstat: 512 Tests: 1 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 19 tests but ran 1.
Files=334, Tests=17147, 94 wallclock secs ( 2.98 usr 0.67 sys + 86.88 cusr 6.43 csys = 96.96 CPU)
Result: FAIL #测试结果是失败的
Failed 2/334 test programs. 0/17147 subtests failed.
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build test — NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-1.6.924.tar.gz
Failed during this command:
CJFIELDS/BioPerl-1.6.924.tar.gz : make_test NO