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

Genetics of human eye development

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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 Révision 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.