Comments (5)
Last time I tested jvarkit, was with picard.version=1.100 (the picard.lib is subject to frequent changes)
you also need to uncomment the line "#berkeleydb.jar" as described in https://github.com/lindenb/jvarkit/wiki/Biostar92368#wiki-compilation
I hope it helps.
P.
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Uncommenting the #berkeleydb.jar does not help. I guess i have to install it first.
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build fails with picard-1.108
+ berkeleydb 5.0-103
configuration file
#bigwig.dir=/commun/data/packages/bigwig picard.version=1.108 picard.dir=/Users/george/picard-tools-${picard.version} picard.jar=${picard.dir}/picard-${picard.version}.jar sam.jar=${picard.dir}/sam-${picard.version}.jar variant.jar=${picard.dir}/variant-${picard.version}.jar tribble.jar=${picard.dir}/tribble-${picard.version}.jar berkeleydb.jar=/Users/george/je-5.0.103/lib/je-5.0.103.jar
Error synopsis
biostar92368: [echo] if the next javac statement fails, check that the 'build.properties' has been properly configured. See https://github.com/lindenb/jvarkit/wiki/Compilation [javac] Compiling 1 source file to /Users/george/Softwares/jvarkit/tmp [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:13: error: package org.broad.tribble.readers does not exist [javac] import org.broad.tribble.readers.LineIterator; [javac] ^ [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:15: error: package net.sf.picard does not exist [javac] import net.sf.picard.PicardException; [javac] ^ [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:16: error: package net.sf.samtools.util does not exist [javac] import net.sf.samtools.util.CloserUtil; [javac] ^ [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:99: error: cannot find symbol [javac] private void load(Transaction txn,LineIterator r) [javac] ^
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there is something wrong with your path(s): net.sf.samtools.util.CloserUtil is still available http://picard.sourceforge.net/javadoc/net/sf/samtools/util/CloserUtil.html as well as http://picard.sourceforge.net/javadoc/org/broad/tribble/readers/LineIterator.html etc...
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Sorted the paths! Thanks!
BUILD SUCCESSFUL
Total time: 5 seconds
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Related Issues (20)
- fixvcfmissinggenotypes.jar does not actually fix missing genotypes HOT 2
- [INFO][WGSCoveragePlotter]no valid chromosome was found in HOT 1
- biostar154220 removes too many reads when using with a bed file HOT 2
- installation issue HOT 1
- specify list of scaffolds for wgsCoveragePlotter HOT 2
- Minicaller OutOfBoundsException HOT 4
- BUILD FAILED HOT 17
- sam2tsv: limit output only the intersecting positions of reads HOT 2
- Does jvarkit provide official test cases? HOT 6
- Request to add a 'plot largest n contigs' for WGSCoveragePlotter HOT 1
- Error while installing -- Running Javac HOT 2
- strange biostar214299 results HOT 2
- vcf2tab HOT 2
- Randomized runs of Biostar154220.html HOT 1
- Test AssertionError HOT 2
- build failed and test failed
- Task :vcffilterjdk FAILED HOT 1
- ./gradlew mapuniprot install error HOT 3
- Is it possible to add the 'Gene' and peptide 'POSITION(S)' info corresponding to each genomic coordinate using MapUniProtFeatures HOT 5
- Task 'MapUniProtFeatures.main()' not found in root project 'jvarkit'. HOT 2
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