[Bioperl-l] Blast returns result, but does not return hits

Raghunath Verabelli iamvela at yahoo.com
Wed Feb 22 17:32:08 EST 2006


Chris,

Please see my response below.

--- Chris Fields <cjfields at uiuc.edu> wrote:

> You know, I assumed you were using ActivePerl b/c of
> the older version of
> Bioperl (and since it’s the most commonly used Perl
> for Windows build).  My
> goof.  It looks like you're using
> Apache/mod_perl/perl, right?  The only
> Perl/Apache/mod_perl combos for Windows I know of
> are listed here:


I am using ActivePerl 5.8.7 downloaded from
activeperl.com. I just happened to install it under
c:\mod_perl\Perl directory (application has hardcoded
dependencies for this directory). I am not using
apache/mod_perl/perl.

Please see below version string returned by perl
exectutable.

 
C:\bioperl-live\bioperl-live>perl -version

This is perl, v5.8.7 built for
MSWin32-x86-multi-thread
(with 14 registered patches, see perl -V for more
detail)

Copyright 1987-2005, Larry Wall

Binary build 815 [211909] provided by ActiveState
http://www.ActiveState.com
ActiveState is a division of Sophos.
Built Nov  2 2005 08:44:52


> 
>
http://perl.apache.org/docs/2.0/os/win32/install.html
> 
> The only Perl for Windows we have actively supported
> is ActivePerl AFAIK,
> but maybe we can walk through this.  Anything
> learned here can be added to
> the installation instructions in case this comes up
> again.
> 
> To start, what mod_perl/Perl version are you using,
> and from what
> distributor (IndigoStar, Apache, etc)?  Each
> distribution should have some
> documentation for installing CPAN modules or
> prebuilt/pretested packages,
> like ActiveState's PPM or IndigoStar's GPM.  I think
> Apache's Perl build is
> from ActiveState's source code so should come with
> PPM.
> 



I used 'ppm' to install packages (DBI, Oracle-DBD,
bioperl etc) before, so this is the first time I tried
to install it using 'nmake' utility.

After downloading the latest bioperl tar ball and
replacing the blast.pm file, can I just do ppm install
bioperl instead of doing nmake?


> Next: you obviously have installed Bioperl before
> (v1.2.3); did you use
> 'make' or 'nmake', or was it from a repository (like
> IndigoPerl's GPM)?
> AFAIK, you would install it like you would any other
> perl module; there
> should be no problem with 'make/nmake', though
> 'make/nmake test' will not
> pass completely (it should pass most tests, though,
> otherwise something is
> seriously wrong).
> 
> The other option, though not as nice, is setting the
> PERL5LIB variable to
> include the bioperl-live directory; it works for me
> while I'm developing. 

I tried setting PERL5LIB, but it did not make any
difference. I am still getting the same errors.


I wanted to a clean install, i tried 'nmake clean',
but looks like there is no 'rm' utility installed on
my machine.

thanks for all your help,
Raghu

> I
> don’t know how this may affect other
> mod_perl-related functions, though.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 
> 
> 
> > -----Original Message-----
> > From: Raghunath Verabelli
> [mailto:iamvela at yahoo.com]
> > Sent: Wednesday, February 22, 2006 3:07 PM
> > To: Chris Fields; bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Blast returns result, but
> does not return hits
> > 
> > Thanks Chris. I am getting below mentioned errors
> with
> > nmake.
> > 
> > As suggested, I downloaded the nmake utility from
> > Microsoft website and the bioperl-live tarball.
> > 
> > After untaring, I replaced the blast.pm file
> (under
> > bioperl-live\Bio\SearchIO) with the blast.pm (86
> KB
> > size) attached to the bug report 1934.
> > 
> > I then did the following to install packages using
> > nmake:
> > 
> > 1) perl Makefile.pl was successful without any
> errors.
> > 
> > 
> > 2) 'c:\nmake' results in following errors
> > 
> >         pl2bat.bat blib\script\bp_unflatten_seq.pl
> >         C:\mod_perl\Perl\bin\perl.exe
> > -MExtUtils::Command -e cp ./scripts_temp/b
> > p_taxid4species.pl blib\script\bp_taxid4species.pl
> >         pl2bat.bat blib\script\bp_taxid4species.pl
> >         C:\mod_perl\Perl\bin\perl.exe
> > -MExtUtils::Command -e cp ./scripts_temp/b
> > p_seqret.pl blib\script\bp_seqret.pl
> >         pl2bat.bat blib\script\bp_seqret.pl
> >         C:\mod_perl\Perl\bin\perl.exe
> "-Iblib\arch"
> > "-Iblib\lib" doc/makedoc.PL
> > bioscripts.pod
> > Can't open bioscripts.pod: No such file or
> directory.
> >         C:\mod_perl\Perl\bin\perl.exe
> "-Iblib\arch"
> > "-Iblib\lib" doc/makedoc.PL
> > biodatabases.pod
> > Can't open biodatabases.pod: No such file or
> > directory.
> >         C:\mod_perl\Perl\bin\perl.exe
> "-Iblib\arch"
> > "-Iblib\lib" doc/makedoc.PL
> > biodesign.pod
> > Can't open biodesign.pod: No such file or
> directory.
> >         C:\mod_perl\Perl\bin\perl.exe
> "-Iblib\arch"
> > "-Iblib\lib" doc/makedoc.PL
> > bioperl.pod
> > Can't open bioperl.pod: No such file or directory.
> > 
> > 
> > 3) 'c:\nmake test' fails with following errors:
> > 
> > NMAKE : fatal error U1095: expanded command line
> > 'C:\mod_perl\Perl\bin\perl.exe
> > "-MExtUtils::Command::MM" "-e" "test_harness(0,
> > 'blib\lib', 'blib\arch')" t\AACh
> > ange.t t\AAReverseMutate.t t\abi.t t\ace.t
> t\AlignIO.t
> > t\AlignStats.t t\AlignUti
> > l.t t\alignUtilities.t t\Allele.t t\Alphabet.t
> > t\Annotation.t t\AnnotationAdapto
> > r.t t\asciitree.t t\Assembly.t t\Biblio.t
> > t\Biblio_biofetch.t t\Biblio_eutils.t
> > t\BiblioReferences.t t\BioDBGFF.t t\BioFetch_DB.t
> > t\BioGraphics.t t\BlastIndex.t
> >  t\BPbl2seq.t t\BPlite.t t\BPpsilite.t
> t\bsml_sax.t
> > t\Chain.t t\chaosxml.t t\cig
> > arstring.t t\ClusterIO.t t\Coalescent.t
> t\CodonTable.t
> > t\Compatible.t t\consed.t
> >  t\CoordinateGraph.t t\CoordinateMapper.t
> > t\Correlate.t t\ctf.t t\CytoMap.t t\DB
> > .t t\DBCUTG.t t\DBFasta.t t\DNAMutation.t
> t\Domcut.t
> > t\ECnumber.t t\ELM.t t\embl
> > .t t\EMBL_DB.t t\EMBOSS_Tools.t t\EncodedSeq.t
> > t\entrezgene.t t\ePCR.t t\ESEfind
> > er.t t\est2genome.t t\Exception.t t\Exonerate.t
> > t\exp.t t\fasta.t t\FeatureIO.t
> > t\flat.t t\FootPrinter.t t\game.t t\GbrowseGFF.t
> > t\gcg.t t\GDB.t t\Gel.t t\genba
> > nk.t t\GeneCoordinateMapper.t t\Geneid.t
> t\Genewise.t
> > t\Genomewise.t t\Genpred.t
> >  t\GFF.t t\GOR4.t t\GOterm.t t\GraphAdaptor.t
> > t\GuessSeqFormat.t t\hmmer.t t\HNN
> > .t t\HtSNP.t t\Index.t t\InstanceSite.t
> t\interpro.t
> > t\InterProParser.t t\IUPAC.
> > t t\kegg.t t\largefasta.t t\LargeLocatableSeq.t
> > t\largepseq.t t\LinkageMap.t t\L
> > iveSeq.t t\LocatableSeq.t t\Location.t
> > t\LocationFactory.t t\LocusLink.t t\lucy.
> > t t\Map.t t\MapIO.t t\masta.t t\Matrix.t
> t\Measure.t
> > t\MeSH.t t\metafasta.t t\Me
> > taSeq.t t\MicrosatelliteMarker.t t\MiniMIMentry.t
> > t\MitoProt.t t\Molphy.t t\Mult
> > iFile.t t\multiple_fasta.t t\Mutation.t
> t\Mutator.t
> > t\NetPhos.t t\Node.t t\OddCo
> > des.t t\OMIMentry.t t\OMIMentryAllelicVariant.t
> > t\OMIMparser.t t\Ontology.t t\On
> > tologyEngine.t t\OntologyStore.t t\PAML.t t\Perl.t
> > t\phd.t t\Phenotype.t t\Phyli
> > pDist.t t\PhysicalMap.t t\pICalculator.t
> t\Pictogram.t
> > t\pir.t t\pln.t t\PopGen.
> > t t\PopGenSims.t t\primaryqual.t t\PrimarySeq.t
> > t\primedseq.t t\Primer.t t\prime
> > r3.t t\Promoterwise.t t\ProtDist.t t\protgraph.t
> > t\ProtMatrix.t t\ProtPsm.t t\Ps
> > eudowise.t t\psm.t t\QRNA.t t\qual.t
> > t\RandDistFunctions.t t\RandomTreeFactory.t
> >  t\Range.t t\RangeI.t t\raw.t t\RefSeq.t
> t\Registry.t
> > t\Relationship.t t\Relatio
> > nshipType.t t\RemoteBlast.t t\RepeatMasker.t
> > t\RestrictionAnalysis.t t\Restricti
> > onEnzyme.t t\RestrictionIO.t t\RNAChange.t
> > t\Root-Utilities.t t\RootI.t t\RootIO
> > .t t\RootStorable.t t\Scansite.t t\scf.t
> > t\SearchDist.t t\SearchIO.t t\Seq.t t\s
> > eq_quality.t t\SeqAnalysisParser.t t\SeqBuilder.t
> > t\SeqDiff.t t\SeqFeatCollectio
> > n.t t\SeqFeature.t t\seqfeaturePrimer.t
> > t\SeqHound_DB.t t\SeqIO.t t\SeqPattern.t
> >  t\seqread_fail.t t\SeqStats.t t\SequenceFamily.t
> > t\sequencetrace.t t\SeqUtils.t
> >  t\SeqVersion.t t\seqwithquality.t t\SeqWords.t
> > t\Sigcleave.t t\Sim4.t t\Similar
> > ityPair.t t\SimpleAlign.t t\simpleGOparser.t
> 
=== message truncated ===


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