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

{| width="800"
 * style="background-color: #EEE"|[[Image:C14.jpg|128px]] Genetics of human eye development
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


 * colspan="2"|
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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.


 * }