Re: snappy uploaded and picard-tools can be build against it
Le 8/29/12 7:07 AM, Charles Plessy a écrit :
> Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sallou@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
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