[Bioperl-l] Bioperl-run malformed svndiff

Ben Bimber bimber at wisc.edu
Sun Mar 7 22:57:12 EST 2010


I recently tried to check out a complete version of bioperl-run and received
an error saying 'malformed svndiff'.  I've tried this on two different
machines, so unless I've doing something wrong, it should be reproducible.
I cannot say where updating an existing repository would throw the same
error or not.

Below is the log:

*** Check Out
svn checkout "svn://code.open-bio.org/bioperl/bioperl-run/trunk/lib/Bio@HEAD"
-r HEAD --depth infinity "C:\Projects\Bio"
    A C:/Projects/Bio/Tools
    A C:/Projects/Bio/Tools/Run
    A C:/Projects/Bio/Tools/Run/Genewise.pm
    A C:/Projects/Bio/Tools/Run/Analysis
    A C:/Projects/Bio/Tools/Run/Analysis/soap.pm
    A C:/Projects/Bio/Tools/Run/AssemblerBase.pm
    A C:/Projects/Bio/Tools/Run/BWA.pm
    A C:/Projects/Bio/Tools/Run/Phrap.pm
    A C:/Projects/Bio/Tools/Run/FootPrinter.pm
    A C:/Projects/Bio/Tools/Run/AnalysisFactory.pm
    A C:/Projects/Bio/Tools/Run/BEDTools.pm
    A C:/Projects/Bio/Tools/Run/EMBOSSApplication.pm
    A C:/Projects/Bio/Tools/Run/Genscan.pm
    A C:/Projects/Bio/Tools/Run/RNAMotif.pm
    A C:/Projects/Bio/Tools/Run/Phylo
    A C:/Projects/Bio/Tools/Run/Phylo/Phast
    A C:/Projects/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Semphy.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Hyphy
    A C:/Projects/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Hyphy/Base.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Hyphy/REL.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
    A C:/Projects/Bio/Tools/Run/Phylo/PhyloBase.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phyml.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/Base.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/Consense.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Njtree
    A C:/Projects/Bio/Tools/Run/Phylo/Njtree/Best.pm
    A C:/Projects/Bio/Tools/Run/Phylo/QuickTree.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Gerp.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Molphy
    A C:/Projects/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
    A C:/Projects/Bio/Tools/Run/Phylo/PAML
    A C:/Projects/Bio/Tools/Run/Phylo/PAML/Yn00.pm
    A C:/Projects/Bio/Tools/Run/Phylo/PAML/Evolver.pm
    A C:/Projects/Bio/Tools/Run/Phylo/PAML/Baseml.pm
    A C:/Projects/Bio/Tools/Run/Phylo/PAML/Codeml.pm
    A C:/Projects/Bio/Tools/Run/Phylo/SLR.pm
    A C:/Projects/Bio/Tools/Run/Phylo/Gumby.pm
    A C:/Projects/Bio/Tools/Run/Phylo/LVB.pm
    A C:/Projects/Bio/Tools/Run/Primer3.pm
    A C:/Projects/Bio/Tools/Run/StandAloneBlastPlus.pm
    A C:/Projects/Bio/Tools/Run/Meme.pm
    A C:/Projects/Bio/Tools/Run/RepeatMasker.pm
    A C:/Projects/Bio/Tools/Run/Analysis.pm
    A C:/Projects/Bio/Tools/Run/Cap3.pm
    A C:/Projects/Bio/Tools/Run/Vista.pm
    A C:/Projects/Bio/Tools/Run/Pseudowise.pm
    A C:/Projects/Bio/Tools/Run/Minimo.pm
    A C:/Projects/Bio/Tools/Run/Match.pm
    A C:/Projects/Bio/Tools/Run/Mdust.pm
    A C:/Projects/Bio/Tools/Run/Eponine.pm
    A C:/Projects/Bio/Tools/Run/Infernal.pm
    A C:/Projects/Bio/Tools/Run/BlastPlus
    A C:/Projects/Bio/Tools/Run/BlastPlus/Config.pm
    A C:/Projects/Bio/Tools/Run/EMBOSSacd.pm
    A C:/Projects/Bio/Tools/Run/Alignment
    A C:/Projects/Bio/Tools/Run/Alignment/Proda.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Kalign.pm
    A C:/Projects/Bio/Tools/Run/Alignment/StandAloneFasta.pm
    A C:/Projects/Bio/Tools/Run/Alignment/TCoffee.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Sim4.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Probalign.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Amap.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Lagan.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Blat.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Gmap.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Probcons.pm
    A C:/Projects/Bio/Tools/Run/Alignment/DBA.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Muscle.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Pal2Nal.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Exonerate.pm
    A C:/Projects/Bio/Tools/Run/Alignment/MAFFT.pm
    A C:/Projects/Bio/Tools/Run/Alignment/Clustalw.pm
    A C:/Projects/Bio/Tools/Run/StandAloneBlastPlus
    A C:/Projects/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
    A C:/Projects/Bio/Tools/Run/Hmmer.pm
    A C:/Projects/Bio/Tools/Run/BlastPlus.pm
    A C:/Projects/Bio/Tools/Run/ERPIN.pm
    A C:/Projects/Bio/Tools/Run/Maq.pm
    A C:/Projects/Bio/Tools/Run/Bowtie
    A C:/Projects/Bio/Tools/Run/Bowtie/Config.pm
    A C:/Projects/Bio/Tools/Run/Seg.pm
    A C:/Projects/Bio/Tools/Run/Prints.pm
    A C:/Projects/Bio/Tools/Run/MCS.pm
    A C:/Projects/Bio/Tools/Run/Tmhmm.pm
    A C:/Projects/Bio/Tools/Run/Ensembl.pm
    A C:/Projects/Bio/Tools/Run/Coil.pm
    A C:/Projects/Bio/Tools/Run/Samtools
    A C:/Projects/Bio/Tools/Run/Samtools/Config.pm
    A C:/Projects/Bio/Tools/Run/Genemark.pm
    A C:/Projects/Bio/Tools/Run/Bowtie.pm
    A C:/Projects/Bio/Tools/Run/Glimmer.pm
    A C:/Projects/Bio/Tools/Run/Signalp.pm
    A C:/Projects/Bio/Tools/Run/Simprot.pm
    A C:/Projects/Bio/Tools/Run/BWA
    A C:/Projects/Bio/Tools/Run/BWA/Config.pm
    A C:/Projects/Bio/Tools/Run/Newbler.pm
svn: Malformed svndiff data in representation
*** Error (took 00:07.184)


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