安装Bioperl最基本模块Bio::SeqIO


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
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
ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions

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.
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
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

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