[Bioperl-l] (no subject)

Roy Chaudhuri roy.chaudhuri at gmail.com
Fri Jan 6 08:28:07 EST 2012


Hi Labrini.

Please ensure you copy replies to the mailing list, that way others can 
contribute to the discussion.

I'm afraid I don't use BioPerl on Windows, so I'm not sure about the 
specific error messages you are getting. Note that the latest version is 
BioPerl-1.6.901 not 1.6.1. Also, for the attempted manual build you 
appear to be typing perl Build.PL at the root of your C drive, it needs 
to be entered in the BioPerl directory.

If you are new to Perl and not familiar with using the command line I'd 
suggest that you start with something simple, not a complex package like 
BioPerl. There is a chapter in the O'Reilly "Learning Perl" book that 
introduces installing and using simple Perl modules.

Roy.

On 06/01/2012 03:13, Labrini Tziamourani wrote:
> Thank you for your answer
> I did according to :INSTALLING BIOPERL THE EASY WAY USING CPAN
> c:> cpan
>
> cpan> d /bioperl/
> ...
> cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz
> .....
> .....
> BioPerl-1.6.1/t/RemoteDB/BioFetch.t
> BioPerl-1.6.1/t/RemoteDB/CUTG.t
> BioPerl-1.6.1/t/RemoteDB/EMBL.t
> BioPerl-1.6.1/t/RemoteDB/EntrezGene.t
> BioPerl-1.6.1/t/RemoteDB/EUtilities.t
> BioPerl-1.6.1/t/RemoteDB/GenBank.t
> BioPerl-1.6.1/t/RemoteDB/GenPept.t
> BioPerl-1.6.1/t/RemoteDB/MeSH.t
> BioPerl-1.6.1/t/RemoteDB/RefSeq.t
> BioPerl-1.6.1/t/RemoteDB/SeqHound.t
> BioPerl-1.6.1/t/RemoteDB/SeqRead_fail.t
> BioPerl-1.6.1/t/RemoteDB/SeqVersion.t
> BioPerl-1.6.1/t/RemoteDB/SwissProt.t
> BioPerl-1.6.1/t/RemoteDB/Taxonomy.t
> BioPerl-1.6.1/t/RemoteDB/HIV
> BioPerl-1.6.1/t/RemoteDB/HIV/HIV.t
> BioPerl-1.6.1/t/RemoteDB/HIV/HIVAnnotProcessor.t
> BioPerl-1.6.1/t/RemoteDB/HIV/HIVQuery.t
> BioPerl-1.6.1/t/RemoteDB/HIV/HIVQueryHelper.t
> BioPerl-1.6.1/t/RemoteDB/Query
> BioPerl-1.6.1/t/RemoteDB/Query/GenBank.t
> BioPerl-1.6.1/t/Restriction
> BioPerl-1.6.1/t/Restriction/Analysis-refac.t
> BioPerl-1.6.1/t/Restriction/Analysis.t
> BioPerl-1.6.1/t/Restriction/Gel.t
> BioPerl-1.6.1/t/Restriction/IO.t
> BioPerl-1.6.1/t/Root
> BioPerl-1.6.1/t/Root/Exception.t
> BioPerl-1.6.1/t/Root/RootI.t
> BioPerl-1.6.1/t/Root/RootIO.t
> BioPerl-1.6.1/t/Root/Storable.t
> BioPerl-1.6.1/t/Root/Tempfile.t
> BioPerl-1.6.1/t/Root/Utilities.t
> BioPerl-1.6.1/t/SearchIO
> BioPerl-1.6.1/t/SearchIO/blast.t
> BioPerl-1.6.1/t/SearchIO/blast_pull.t
> BioPerl-1.6.1/t/SearchIO/blasttable.t
> BioPerl-1.6.1/t/SearchIO/blastxml.t
> BioPerl-1.6.1/t/SearchIO/CigarString.t
> BioPerl-1.6.1/t/SearchIO/cross_match.t
> BioPerl-1.6.1/t/SearchIO/erpin.t
> BioPerl-1.6.1/t/SearchIO/exonerate.t
> BioPerl-1.6.1/t/SearchIO/fasta.t
> BioPerl-1.6.1/t/SearchIO/gmap_f9.t
> BioPerl-1.6.1/t/SearchIO/hmmer.t
> BioPerl-1.6.1/t/SearchIO/hmmer_pull.t
> BioPerl-1.6.1/t/SearchIO/infernal.t
> BioPerl-1.6.1/t/SearchIO/megablast.t
> BioPerl-1.6.1/t/SearchIO/psl.t
> BioPerl-1.6.1/t/SearchIO/rnamotif.t
> BioPerl-1.6.1/t/SearchIO/SearchIO.t
> BioPerl-1.6.1/t/SearchIO/sim4.t
> BioPerl-1.6.1/t/SearchIO/SimilarityPair.t
> BioPerl-1.6.1/t/SearchIO/Tiling.t
> BioPerl-1.6.1/t/SearchIO/waba.t
> BioPerl-1.6.1/t/SearchIO/wise.t
> BioPerl-1.6.1/t/SearchIO/Writer
> BioPerl-1.6.1/t/SearchIO/Writer/GbrowseGFF.t
> BioPerl-1.6.1/t/SearchIO/Writer/HitTableWriter.t
> BioPerl-1.6.1/t/SearchIO/Writer/HSPTableWriter.t
> BioPerl-1.6.1/t/SearchIO/Writer/HTMLWriter.t
> BioPerl-1.6.1/t/Seq
> BioPerl-1.6.1/t/Seq/DBLink.t
> BioPerl-1.6.1/t/Seq/EncodedSeq.t
> BioPerl-1.6.1/t/Seq/LargeLocatableSeq.t
> BioPerl-1.6.1/t/Seq/LargePSeq.t
> BioPerl-1.6.1/t/Seq/LocatableSeq.t
> BioPerl-1.6.1/t/Seq/MetaSeq.t
> BioPerl-1.6.1/t/Seq/PrimaryQual.t
> BioPerl-1.6.1/t/Seq/PrimarySeq.t
> BioPerl-1.6.1/t/Seq/PrimedSeq.t
> BioPerl-1.6.1/t/Seq/Quality.t
> BioPerl-1.6.1/t/Seq/Seq.t
> BioPerl-1.6.1/t/Seq/WithQuality.t
> BioPerl-1.6.1/t/SeqFeature
> BioPerl-1.6.1/t/SeqFeature/FeatureIO.t
> BioPerl-1.6.1/t/SeqFeature/Location.t
> BioPerl-1.6.1/t/SeqFeature/LocationFactory.t
> BioPerl-1.6.1/t/SeqFeature/Primer.t
> BioPerl-1.6.1/t/SeqFeature/Range.t
> BioPerl-1.6.1/t/SeqFeature/RangeI.t
> BioPerl-1.6.1/t/SeqFeature/SeqAnalysisParser.t
> BioPerl-1.6.1/t/SeqFeature/SeqFeatAnnotated.t
> BioPerl-1.6.1/t/SeqFeature/SeqFeatCollection.t
> BioPerl-1.6.1/t/SeqFeature/SeqFeature.t
> BioPerl-1.6.1/t/SeqFeature/SeqFeaturePrimer.t
> BioPerl-1.6.1/t/SeqFeature/Unflattener.t
> BioPerl-1.6.1/t/SeqFeature/Unflattener2.t
> BioPerl-1.6.1/t/SeqIO
> BioPerl-1.6.1/t/SeqIO/abi.t
> BioPerl-1.6.1/t/SeqIO/ace.t
> BioPerl-1.6.1/t/SeqIO/agave.t
> BioPerl-1.6.1/t/SeqIO/alf.t
> BioPerl-1.6.1/t/SeqIO/asciitree.t
> BioPerl-1.6.1/t/SeqIO/bsml.t
> BioPerl-1.6.1/t/SeqIO/bsml_sax.t
> BioPerl-1.6.1/t/SeqIO/chadoxml.t
> BioPerl-1.6.1/t/SeqIO/chaos.t
> BioPerl-1.6.1/t/SeqIO/chaosxml.t
> BioPerl-1.6.1/t/SeqIO/ctf.t
> BioPerl-1.6.1/t/SeqIO/embl.t
> BioPerl-1.6.1/t/SeqIO/entrezgene.t
> BioPerl-1.6.1/t/SeqIO/excel.t
> BioPerl-1.6.1/t/SeqIO/exp.t
> BioPerl-1.6.1/t/SeqIO/fasta.t
> BioPerl-1.6.1/t/SeqIO/fastq.t
> BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t
> BioPerl-1.6.1/t/SeqIO/game.t
> BioPerl-1.6.1/t/SeqIO/gcg.t
> BioPerl-1.6.1/t/SeqIO/genbank.t
> BioPerl-1.6.1/t/SeqIO/Handler.t
> BioPerl-1.6.1/t/SeqIO/interpro.t
> BioPerl-1.6.1/t/SeqIO/kegg.t
> BioPerl-1.6.1/t/SeqIO/largefasta.t
> BioPerl-1.6.1/t/SeqIO/lasergene.t
> BioPerl-1.6.1/t/SeqIO/locuslink.t
> BioPerl-1.6.1/t/SeqIO/metafasta.t
> BioPerl-1.6.1/t/SeqIO/MultiFile.t
> BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t
> BioPerl-1.6.1/t/SeqIO/phd.t
> BioPerl-1.6.1/t/SeqIO/pir.t
> BioPerl-1.6.1/t/SeqIO/pln.t
> BioPerl-1.6.1/t/SeqIO/qual.t
> BioPerl-1.6.1/t/SeqIO/raw.t
> BioPerl-1.6.1/t/SeqIO/scf.t
> BioPerl-1.6.1/t/SeqIO/SeqBuilder.t
> BioPerl-1.6.1/t/SeqIO/Splicedseq.t
> BioPerl-1.6.1/t/SeqIO/strider.t
> BioPerl-1.6.1/t/SeqIO/swiss.t
> BioPerl-1.6.1/t/SeqIO/tab.t
> BioPerl-1.6.1/t/SeqIO/table.t
> BioPerl-1.6.1/t/SeqIO/tigr.t
> BioPerl-1.6.1/t/SeqIO/tigrxml.t
> BioPerl-1.6.1/t/SeqIO/tinyseq.t
> BioPerl-1.6.1/t/SeqIO/ztr.t
> BioPerl-1.6.1/t/SeqTools
> BioPerl-1.6.1/t/SeqTools/Backtranslate.t
> BioPerl-1.6.1/t/SeqTools/CodonTable.t
> BioPerl-1.6.1/t/SeqTools/ECnumber.t
> BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t
> BioPerl-1.6.1/t/SeqTools/OddCodes.t
> BioPerl-1.6.1/t/SeqTools/SeqPattern.t
> BioPerl-1.6.1/t/SeqTools/SeqStats.t
> BioPerl-1.6.1/t/SeqTools/SeqUtils.t
> BioPerl-1.6.1/t/SeqTools/SeqWords.t
> BioPerl-1.6.1/t/Structure
> BioPerl-1.6.1/t/Structure/IO.t
> BioPerl-1.6.1/t/Structure/Structure.t
> BioPerl-1.6.1/t/Tools
> BioPerl-1.6.1/t/Tools/ePCR.t
> BioPerl-1.6.1/t/Tools/Est2Genome.t
> BioPerl-1.6.1/t/Tools/FootPrinter.t
> BioPerl-1.6.1/t/Tools/Geneid.t
> BioPerl-1.6.1/t/Tools/Genewise.t
> BioPerl-1.6.1/t/Tools/Genomewise.t
> BioPerl-1.6.1/t/Tools/Genpred.t
> BioPerl-1.6.1/t/Tools/GFF.t
> BioPerl-1.6.1/t/Tools/Hmmer.t
> BioPerl-1.6.1/t/Tools/IUPAC.t
> BioPerl-1.6.1/t/Tools/Lucy.t
> BioPerl-1.6.1/t/Tools/Match.t
> BioPerl-1.6.1/t/Tools/pICalculator.t
> BioPerl-1.6.1/t/Tools/Primer3.t
> BioPerl-1.6.1/t/Tools/Promoterwise.t
> BioPerl-1.6.1/t/Tools/Pseudowise.t
> BioPerl-1.6.1/t/Tools/QRNA.t
> BioPerl-1.6.1/t/Tools/RandDistFunctions.t
> BioPerl-1.6.1/t/Tools/RepeatMasker.t
> BioPerl-1.6.1/t/Tools/rnamotif.t
> BioPerl-1.6.1/t/Tools/Seg.t
> BioPerl-1.6.1/t/Tools/Sigcleave.t
> BioPerl-1.6.1/t/Tools/Signalp.t
> BioPerl-1.6.1/t/Tools/Sim4.t
> BioPerl-1.6.1/t/Tools/SiRNA.t
> BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t
> BioPerl-1.6.1/t/Tools/TargetP.t
> BioPerl-1.6.1/t/Tools/Tmhmm.t
> BioPerl-1.6.1/t/Tools/tRNAscanSE.t
> BioPerl-1.6.1/t/Tools/Alignment
> BioPerl-1.6.1/t/Tools/Alignment/Consed.t
> BioPerl-1.6.1/t/Tools/Analysis
> BioPerl-1.6.1/t/Tools/Analysis/DNA
> BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein
> BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t
> BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t
> BioPerl-1.6.1/t/Tools/EMBOSS
> BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t
> BioPerl-1.6.1/t/Tools/EUtilities
> BioPerl-1.6.1/t/Tools/EUtilities/egquery.t
> BioPerl-1.6.1/t/Tools/EUtilities/einfo.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t
> BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t
> BioPerl-1.6.1/t/Tools/EUtilities/epost.t
> BioPerl-1.6.1/t/Tools/EUtilities/esearch.t
> BioPerl-1.6.1/t/Tools/EUtilities/espell.t
> BioPerl-1.6.1/t/Tools/EUtilities/esummary.t
> BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t
> BioPerl-1.6.1/t/Tools/Phylo
> BioPerl-1.6.1/t/Tools/Phylo/Gerp.t
> BioPerl-1.6.1/t/Tools/Phylo/Molphy.t
> BioPerl-1.6.1/t/Tools/Phylo/PAML.t
> BioPerl-1.6.1/t/Tools/Phylo/Phylip
> BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t
> BioPerl-1.6.1/t/Tools/Run
> BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t
> BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t
> BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t
> BioPerl-1.6.1/t/Tools/Run/WrapperBase.t
> BioPerl-1.6.1/t/Tools/Signalp
> BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t
> BioPerl-1.6.1/t/Tools/Spidey
> BioPerl-1.6.1/t/Tools/Spidey/Spidey.t
> BioPerl-1.6.1/t/Tree
> BioPerl-1.6.1/t/Tree/Compatible.t
> BioPerl-1.6.1/t/Tree/Node.t
> BioPerl-1.6.1/t/Tree/RandomTreeFactory.t
> BioPerl-1.6.1/t/Tree/Tree.t
> BioPerl-1.6.1/t/Tree/TreeIO.t
> BioPerl-1.6.1/t/Tree/TreeStatistics.t
> BioPerl-1.6.1/t/Tree/PhyloNetwork
> BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t
> BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t
> BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t
> BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t
> BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t
> BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t
> BioPerl-1.6.1/t/Tree/TreeIO
> BioPerl-1.6.1/t/Tree/TreeIO/lintree.t
> BioPerl-1.6.1/t/Tree/TreeIO/newick.t
> BioPerl-1.6.1/t/Tree/TreeIO/nexus.t
> BioPerl-1.6.1/t/Tree/TreeIO/nhx.t
> BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t
> BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t
> BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t
> BioPerl-1.6.1/t/Variation
> BioPerl-1.6.1/t/Variation/AAChange.t
> BioPerl-1.6.1/t/Variation/AAReverseMutate.t
> BioPerl-1.6.1/t/Variation/Allele.t
> BioPerl-1.6.1/t/Variation/DNAMutation.t
> BioPerl-1.6.1/t/Variation/RNAChange.t
> BioPerl-1.6.1/t/Variation/SeqDiff.t
> BioPerl-1.6.1/t/Variation/SNP.t
> BioPerl-1.6.1/t/Variation/Variation_IO.t
> Catching error: "Couldn't move
> C:\\Perl\\cpan\\build\\tmp-3156\\BioPerl-1.6.1\\t
>   to C:\\Perl\\cpan\\build\\BioPerl-1.6.1-othMfb\\t: No such file or
> directory at
>   C:\\Perl\\site\\lib/CPAN/Distribution.pm line
> 524\cJ\cICPAN::Distribution::run_
> preps_on_packagedir('CPAN::Distribution=HASH(0xa201d94)') called at
> C:\\Perl\\si
> te\\lib/CPAN/Distribution.pm line
> 351\cJ\cICPAN::Distribution::get('CPAN::Distri
> bution=HASH(0xa201d94)') called at
> C:\\Perl\\site\\lib/CPAN/Distribution.pm line
>   1754\cJ\cICPAN::Distribution::make('CPAN::Distribution=HASH(0xa201d94)') called
>   at C:\\Perl\\site\\lib/CPAN/Distribution.pm line
> 3067\cJ\cICPAN::Distribution::
> test('CPAN::Distribution=HASH(0xa201d94)') called at
> C:\\Perl\\site\\lib/CPAN/Di
> stribution.pm <http://stribution.pm> line
> 3469\cJ\cICPAN::Distribution::install('CPAN::Distribution=HAS
> H(0xa201d94)') called at C:\\Perl\\site\\lib/CPAN/Shell.pm line
> 1797\cJ\cICPAN::
> Shell::rematein('CPAN::Shell', 'install',
> 'CJFIELDS/BioPerl-1.6.1.tar.gz') calle
> d at C:\\Perl\\site\\lib/CPAN/Shell.pm line
> 1977\cJ\cICPAN::Shell::__ANON__('CPA
> N::Shell', 'CJFIELDS/BioPerl-1.6.1.tar.gz') called at
> C:/Perl/site/lib/CPAN.pm l
> ine 376\cJ\cIeval {...} called at C:/Perl/site/lib/CPAN.pm line
> 373\cJ\cICPAN::s
> hell() called at C:/Perl/site/lib/App/Cpan.pm line
> 295\cJ\cIApp::Cpan::_process_
> options('App::Cpan') called at C:/Perl/site/lib/App/Cpan.pm line
> 364\cJ\cIApp::C
> pan::run('App::Cpan') called at C:\\Perl\\site\\bin/cpan line 8\cJ" at
> C:/Perl/s
> ite/lib/CPAN.pm line 392
>          CPAN::shell() called at C:/Perl/site/lib/App/Cpan.pm line 295
>          App::Cpan::_process_options('App::Cpan') called at
> C:/Perl/site/lib/App/
> Cpan.pm line 364
>          App::Cpan::run('App::Cpan') called at C:\Perl\site\bin/cpan line 8
>
> cpan> quit
> Lockfile removed.
> The other idea is to continue with " perl Build.PL"
> C:\>perl Build.PL
> Can't open perl script "Build.PL": No such file or directory
> C:\>
> Please let me know if i have to do sth else.
> Thank you,
> Labrini



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