Le 8/29/12 7:07 AM, Charles Plessy a écrit : > Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr a écrit : >> Hi, >> I have uploaded libsnappy1.0.3-java package for picard-tools. >> I could successfully build picard-tools with this package. >> >> picard-tools still need to be updated to get latest release and use >> snappy1.0.3-java.jar file (update of the patch) > Hi Olivier, > > many thanks for all of this. > > I built and installed libsnappy1.0.3-java. It will need to conflict with > libsnappy-java, or the maven information will need to be renamed: I think maven info should be renamed, does not need to conflict. I will update package. Maven info should be:
/usr/share/maven-repo/org/xerial/snappy/snappy1.0.3-java/debian/snappy1.0.3-java-debian.pom > > Selecting previously unselected package libsnappy1.0.3-java. > (Reading database ... 312719 files and directories currently installed.) > Unpacking libsnappy1.0.3-java (from > libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb) ... > dpkg: error processing libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb > (--install): > trying to overwrite > '/usr/share/maven-repo/org/xerial/snappy/snappy-java/debian/snappy-java-debian.pom', > which is also in package libsnappy-java 1.0.4.1~dfsg-1 > Errors were encountered while processing: > libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb > > On the source pakcage side, can you push the pristine-tar branch that contain > the version 1.0.3-rc3~dfsg ? I will have a look. I updated the code Andreas put in git repo. I did not check for pristine etc... as I just updated the debian directory. > > I then build and installed picard tools, but all the command I try to run fail > with an errror like the following. > > $ picard-tools EstimateLibraryComplexity > I=testdata/net/sf/samtools/compressed.bam O=/dev/stdout > [Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity > INPUT=[testdata/net/sf/samtools/compressed.bam] OUTPUT=/dev/stdout > MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 > MAX_GROUP_RATIO=500 > READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* > OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false > VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 > CREATE_INDEX=false CREATE_MD5_FILE=false > [Wed Aug 29 14:06:35 JST 2012] Executing as charles@anx191 on Linux > 3.2.0-2-amd64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: > 1.75(exported) > [Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity > done. Elapsed time: 0.00 minutes. > Runtime.totalMemory()=189071360 > FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page > Exception in thread "main" java.lang.NoClassDefFoundError: > org/apache/tools/bzip2/CBZip2OutputStream > at > net.sf.picard.sam.EstimateLibraryComplexity.doWork(EstimateLibraryComplexity.java:217) > at > net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) > at > net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) > at > net.sf.picard.sam.EstimateLibraryComplexity.main(EstimateLibraryComplexity.java:208) > Caused by: java.lang.ClassNotFoundException: > org.apache.tools.bzip2.CBZip2OutputStream > at java.net.URLClassLoader$1.run(URLClassLoader.java:217) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:205) > at java.lang.ClassLoader.loadClass(ClassLoader.java:321) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) > at java.lang.ClassLoader.loadClass(ClassLoader.java:266) > ... 4 more > > Installing libjbzip2-java did not solve the problem. Do you have an idea ? Strange, I did not face this issue. libjbzip2-java should indeed solve CBZip2OutputStream. > > Have a nice day, > > > -- > gpg key id: 4096R/326D8438 (keyring.debian.org) > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/503db9f7.4070...@codeless.fr
