Etchevers:Notebook/STRA6 in eye development/2009/09/01

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Problems compiling newest FindPeaks 4.0.*

Finally back in lab and want to start using FP again, but can't compile newest version:

heather@embryo:~$ sudo rm -rf trunk/

heather@embryo:~$ svn co http://vancouvershortr.svn.sourceforge.net/svnroot/vancouvershortr/trunk

  A    trunk/jars
  A    trunk/.classpath
  A    trunk/.project
  A    trunk/Changelog.txt
  A    trunk/lib
  A    trunk/lib/postgresql-8.4-701.jdbc4.jar
  A    trunk/lib/constants.conf
  A    trunk/lib/mysql-connector-java-5.1.6-bin.jar
  A    trunk/lib/PSQL.conf
  A    trunk/lib/ensj-39.2.jar
  A    trunk/lib/junit.jar
  A    trunk/lib/sam-1.03.jar
  A    trunk/lib/picard-1.03.jar
  A    trunk/src
  A    trunk/src/unittests
  A    trunk/src/unittests/VSRAPTestSuite.java
  A    trunk/src/unittests/Test_maq_iterator.java
  A    trunk/src/lib
  A    trunk/src/lib/IterableIterator.java
  A    trunk/src/lib/mysql_wrapper.java
  A    trunk/src/lib/SNPDB.java
  A    trunk/src/lib/RandomAlignedReadGenerator.java
  A    trunk/src/lib/objects
  A    trunk/src/lib/objects/AlignedRead.java
  A    trunk/src/lib/objects/SNP.java
  A    trunk/src/lib/objects/SliderSNP.java
  A    trunk/src/lib/objects/SeqReducedAlignedRead.java
  A    trunk/src/lib/objects/Aberation.java
  A    trunk/src/lib/objects/FFInt.java
  A    trunk/src/lib/objects/MAQRyanMap.java
  A    trunk/src/lib/objects/SNPLine.java
  A    trunk/src/lib/objects/SimpleAlignedRead.java
  A    trunk/src/lib/objects/MAQinner.java
  A    trunk/src/lib/objects/CounterArray.java
  A    trunk/src/lib/objects/Counter.java
  A    trunk/src/lib/objects/MinimalLocation.java
  A    trunk/src/lib/objects/PSNP.java
  A    trunk/src/lib/objects/PETLocation.java
  A    trunk/src/lib/objects/PETRead.java
  A    trunk/src/lib/objects/Aberation_SNP.java
  A    trunk/src/lib/objects/SETLocation.java
  A    trunk/src/lib/objects/Aberation_Deletion.java
  A    trunk/src/lib/objects/Tuple.java
  A    trunk/src/lib/objects/ReducedAlignedRead.java
  A    trunk/src/lib/objects/MAQouter.java
  A    trunk/src/lib/objects/Aberation_Insertion.java
  A    trunk/src/lib/Utilities.java
  A    trunk/src/lib/Chromosome.java
  A    trunk/src/lib/StatisticsTools.java
  A    trunk/src/lib/Constants.java
  A    trunk/src/lib/ConstantsFile.java
  A    trunk/src/lib/Error_handling
  A    trunk/src/lib/Error_handling/PSQLInterfaceException.java
  A    trunk/src/lib/Error_handling/UnexpectedCharacterException.java
  A    trunk/src/lib/Error_handling/CommandLineProcessingException.java
  A    trunk/src/lib/Error_handling/OverflowException.java
  A    trunk/src/lib/Error_handling/UnexpectedResultException.java
  A    trunk/src/lib/Error_handling/MysqlInterfaceException.java
  A    trunk/src/lib/Error_handling/DoesNotMatchException.java
  A    trunk/src/lib/Error_handling/GenericProcessingException.java
  A    trunk/src/lib/Error_handling/CanNotConnectException.java
  A    trunk/src/lib/FloatingPoint.java
  A    trunk/src/lib/ReducedAlignedReads.java
  A    trunk/src/lib/Graphics
  A    trunk/src/lib/Graphics/HistogramImage.java
  A    trunk/src/lib/Graphics/BasicImage.java
  A    trunk/src/lib/Graphics/GraphImage.java
  A    trunk/src/lib/BitOperations.java
  A    trunk/src/lib/analysisTools
  A    trunk/src/lib/analysisTools/Exon_Junction_Map.java
  A    trunk/src/lib/analysisTools/CoreFunctions.java
  A    trunk/src/lib/analysisTools/Exon_Overlap.java
  A    trunk/src/lib/analysisTools/Process_SNPs.java
  A    trunk/src/lib/analysisTools/Transcript_Bias.java
  A    trunk/src/lib/analysisTools/Process_Exons.java
  A    trunk/src/lib/Ensembl.java
  A    trunk/src/lib/CommandLine.java
  A    trunk/src/lib/Coverage.java
  A    trunk/src/lib/ioInterfaces
  A    trunk/src/lib/ioInterfaces/MAQJunctionMapIterator.java
  A    trunk/src/lib/ioInterfaces/ElandExtUtilities.java
  A    trunk/src/lib/ioInterfaces/BowtieIterator.java
  A    trunk/src/lib/ioInterfaces/BedIterator.java
  A    trunk/src/lib/ioInterfaces/ExonerateIterator.java
  A    trunk/src/lib/ioInterfaces/FileOut.java
  A    trunk/src/lib/ioInterfaces/MultiMemberGZIPInputStream.java
  A    trunk/src/lib/ioInterfaces/FastaIterator.java
  A    trunk/src/lib/ioInterfaces/BedGraphWriter.java
  A    trunk/src/lib/ioInterfaces/GSC_Aberation_Iterator.java
  A    trunk/src/lib/ioInterfaces/VulgarIterator.java
  A    trunk/src/lib/ioInterfaces/SnpIterator.java
  A    trunk/src/lib/ioInterfaces/Log_Buffer.java
  A    trunk/src/lib/ioInterfaces/PushBackIteratorWrapper.java
  A    trunk/src/lib/ioInterfaces/GffIterator.java
  A    trunk/src/lib/ioInterfaces/PSNPwriter.java
  A    trunk/src/lib/ioInterfaces/ElandExtIterator.java
  A    trunk/src/lib/ioInterfaces/MapviewMAQIterator.java
  A    trunk/src/lib/ioInterfaces/Wigwriter.java
  A    trunk/src/lib/ioInterfaces/AceWriter.java
  A    trunk/src/lib/ioInterfaces/MAQmapIterator.java
  A    trunk/src/lib/ioInterfaces/Bedwriter.java
  A    trunk/src/lib/ioInterfaces/MapviewMAQPETIterator.java
  A    trunk/src/lib/ioInterfaces/PSNPIterator.java
  A    trunk/src/lib/ioInterfaces/SAMIterator.java
  A    trunk/src/lib/ioInterfaces/Generic_AlignRead_Iterator.java
  A    trunk/src/lib/ioInterfaces/AlignedReadsIterator.java
  A    trunk/src/lib/ioInterfaces/SliderIterator.java
  A    trunk/src/lib/ioInterfaces/ElandIterator.java
  A    trunk/src/lib/Histogram.java
  A    trunk/src/projects
  A    trunk/src/projects/findFeatures
  A    trunk/src/projects/findFeatures/FindFeatures.java
  A    trunk/src/projects/SNP_Database
  A    trunk/src/projects/SNP_Database/PSQLInterface.java
  A    trunk/src/projects/SNP_Database/dbSNPimport.java
  A    trunk/src/projects/SNP_Database/objects
  A    trunk/src/projects/SNP_Database/objects/Library.java
  A    trunk/src/projects/SNP_Database/LibraryDetails.java
  A    trunk/src/projects/SNP_Database/AlignmentScrape.java
  A    trunk/src/projects/SNP_Database/SNP_Parser.java
  A    trunk/src/projects/SNP_Database/SnpIterators
  A    trunk/src/projects/SNP_Database/SnpIterators/dbSNPIterator.java
  A    trunk/src/projects/SNP_Database/SnpIterators/WTSSPipelineSNPIterator.java
  A    trunk/src/projects/SNP_Database/SnpIterators/Generic_SNP_Iterator.java
  A    trunk/src/projects/SNP_Database/SnpIterators/AndySnpIterator.java
  A    trunk/src/projects/SNP_Database/SnpIterators/MaqSnpIterator.java
  A    trunk/src/projects/SNP_Database/SnpIterators/SNPIterator.java
  A    trunk/src/projects/SNP_Database/schema.txt
  A    trunk/src/projects/findPeaks
  A    trunk/src/projects/findPeaks/Distribution.java
  A    trunk/src/projects/findPeaks/filewriters
  A    trunk/src/projects/findPeaks/filewriters/RegionWriter.java
  A    trunk/src/projects/findPeaks/filewriters/PeakWriter.java
  A    trunk/src/projects/findPeaks/PeakDataSetParent.java
  A    trunk/src/projects/findPeaks/FPConstants.java
  A    trunk/src/projects/findPeaks/tests
  A    trunk/src/projects/findPeaks/tests/test_linear_regressionPerpendicular.java
  A    trunk/src/projects/findPeaks/tests/test_linear_regression.java
  A    trunk/src/projects/findPeaks/FindPeaks.java
  A    trunk/src/projects/findPeaks/PeakLocator.java
  A    trunk/src/projects/findPeaks/FP_Output.java
  A    trunk/src/projects/findPeaks/Functions.java
  A    trunk/src/projects/findPeaks/objects
  A    trunk/src/projects/findPeaks/objects/PeakStats.java
  A    trunk/src/projects/findPeaks/objects/Peakdesc.java
  A    trunk/src/projects/findPeaks/objects/PeakPairIdx.java
  A    trunk/src/projects/findPeaks/objects/SaturationDataHolder.java
  A    trunk/src/projects/findPeaks/objects/Map_f.java
  A    trunk/src/projects/findPeaks/objects/MinPeakDesc.java
  A    trunk/src/projects/findPeaks/objects/Parameters.java
  A    trunk/src/projects/findPeaks/objects/Map_i.java
  A    trunk/src/projects/findPeaks/objects/SeqStore.java
  A    trunk/src/projects/findPeaks/objects/PairDistance.java
  A    trunk/src/projects/findPeaks/objects/LinearRegressionPerpendicular.java
  A    trunk/src/projects/findPeaks/objects/MapStore.java
  A    trunk/src/projects/findPeaks/objects/LinearRegression.java
  A    trunk/src/projects/findPeaks/objects/PeakStore.java
  A    trunk/src/projects/findPeaks/PeakDataSetChild.java
  A    trunk/src/projects/findPeaks/RFunctions.java
  A    trunk/src/projects/findPeaks/FDR
  A    trunk/src/projects/findPeaks/FDR/LanderWatermanTheory.java
  A    trunk/src/projects/findPeaks/FDR/MC_Simulation.java
  A    trunk/src/projects/findPeaks/FDR/ApplyControl.java
  A    trunk/src/projects/findPeaks/FDR/ApplyCompare.java
  A    trunk/src/projects/findPeaks/DuplicateFiltering.java
  A    trunk/src/projects/findPeaks/PeakLocatorSaturation.java
  A    trunk/src/projects/maq_utilities
  A    trunk/src/projects/maq_utilities/ReadsUsed.java
  A    trunk/src/projects/maq_utilities/objects
  A    trunk/src/projects/maq_utilities/objects/ExonBoundaries.java
  A    trunk/src/projects/maq_utilities/objects/GeneMap.java
  A    trunk/src/projects/maq_utilities/objects/Exonboundary.java
  A    trunk/src/projects/genomeViewer
  A    trunk/src/projects/genomeViewer/AlignSlice.java
  A    trunk/src/fileUtilities
  A    trunk/src/fileUtilities/CombineFiles.java
  A    trunk/src/fileUtilities/BowtieToBedFormat.java
  A    trunk/src/fileUtilities/RegionToBed.java
  A    trunk/src/fileUtilities/MapHeaderInfo.java
  A    trunk/src/fileUtilities/SeparateReads.java
  A    trunk/src/fileUtilities/MaqToReadFormat.java
  A    trunk/src/fileUtilities/SortFiles.java
  A    trunk/src/fileUtilities/ConvertToAce.java
  A    trunk/src/fileUtilities/ConvertToBed.java
  A    trunk/src/fileUtilities/MaqPetToBedFormat.java
  A    trunk/src/fileUtilities/RegionToAberations.java
  A    trunk/src/transcriptome_analysis
  A    trunk/src/transcriptome_analysis/Genome_Alignment
  A    trunk/src/transcriptome_analysis/Genome_Alignment/GenomicAlignmentAnalysis.java
  A    trunk/src/transcriptome_analysis/Genome_Alignment/TranscriptBiasAnalysis.java
  A    trunk/src/transcriptome_analysis/Transcriptome_Alignment
  A    trunk/src/transcriptome_analysis/Transcriptome_Alignment/Transcript_analysis.java
  A    trunk/src/transcriptome_analysis/SNP_Detection
  A    trunk/src/transcriptome_analysis/SNP_Detection/SNPAnalysis.java
  A    trunk/src/transcriptome_analysis/SNP_Detection/evaluate_snps.java
  A    trunk/src/transcriptome_analysis/SNP_Detection/PSNPAnalysisPipeline.java
  A    trunk/testdata
  A    trunk/testdata/22.test.eland
  A    trunk/testdata/p53.map
  A    trunk/classes
  A    trunk/build.xml
   U   trunk
  RĂ©vision 1496 extraite.
  

heather@embryo:~$ cd trunk

heather@embryo:~/trunk$ ant fpsuite

  Buildfile: build.xml
  cleanfp:
  initfp:
   [mkdir] Created dir: /home/heather/trunk/jars/fp4
  compile:
   [javac] Compiling 156 source files to /home/heather/trunk/classes
  FindPeaks:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/FindPeaks.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  SeparateReads:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SeparateReads.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  SortFiles:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SortFiles.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  GenomeViewer:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/AlignSlice.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  cleanfc:
  initfc:
   [mkdir] Created dir: /home/heather/trunk/jars/conversion_util
  ConvertToBed:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/conversion_util/ConvertToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  ConvertToAce:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/conversion_util/ConvertToAce.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  MaqPetToBed:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/conversion_util/MaqPetToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  BowtieToBedFormat:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/conversion_util/BowtieToBedFormat.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  buildfc:
  fcsuite:
  buildfp:
  fptestdata:
    [copy] Copying 2 files to /home/heather/trunk/jars/fp4
  changelog:
    [copy] Copying 1 file to /home/heather/trunk/jars
  fpsuite:
  BUILD SUCCESSFUL
  Total time: 4 seconds

  heather@embryo:~/trunk$ ant buildall
  Buildfile: build.xml
  clean:
  initfp:
   [mkdir] Created dir: /home/heather/trunk/jars/fp4
  inittr:
   [mkdir] Created dir: /home/heather/trunk/jars/transcripter
  initff:
   [mkdir] Created dir: /home/heather/trunk/jars/findfeatures
  initfc:
   [mkdir] Created dir: /home/heather/trunk/jars/conversion_util
  compile:
   [javac] Compiling 156 source files to /home/heather/trunk/classes
  FindPeaks:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/FindPeaks.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  SeparateReads:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SeparateReads.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  SortFiles:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SortFiles.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  GenomeViewer:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/AlignSlice.jar
  [delete] Deleting directory /home/heather/trunk/tmp
  cleanfc:
  ConvertToBed:
   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/conversion_util/ConvertToBed.jar

BUILD FAILED /home/heather/trunk/build.xml:312: Problem creating jar: /home/heather/trunk/jars/conversion_util/ConvertToBed.jar (No such file or directory) (and the archive is probably corrupt but I could not delete it)

Total time: 3 seconds

  • Heather 08:37, 1 September 2009 (EDT):

Will send Nicolas back the Dynal beads tomorrow morning.

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