安装Bioperl最基本模块Bio::SeqIO
2016-02-27 17:50
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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
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
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