Le Tue, Aug 28, 2012 at 12:49:59PM +0200, [email protected] 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: 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 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 ? Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
