compile error

[lindenb]

compile error

[lindenb]

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.

Uncommenting the #berkeleydb.jar does not help. I guess i have to install it first.

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] ^

[lindenb]

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...

Sorted the paths! Thanks!
BUILD SUCCESSFUL
Total time: 5 seconds