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Bug 549294

Summary: dev-java/ant-1.9.2 or dev-java/ant-core-1.9.2: no org.apache.tools.bzip2 installed
Product: Gentoo Linux Reporter: Martin Mokrejš <mmokrejs>
Component: Current packagesAssignee: Gentoo Linux bug wranglers <bug-wranglers>
Status: RESOLVED WONTFIX    
Severity: normal CC: fordfrog, jstein
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Martin Mokrejš 2015-05-12 19:01:59 UTC
It is weird that dev-java/ant-1.9.2 installs no files. Is this a virtual package?

In the jar files provided by ant-core I do not see anything related to org/apache/tools/bzip2 . I thought I do not have some USE flag set but which one would it be?

[ebuild   R    ] dev-java/ant-core-1.9.2::gentoo  USE="-doc -source" 0 KiB
[ebuild   R    ] dev-java/ant-commons-net-1.9.2::gentoo  0 KiB
[ebuild   R    ] dev-java/ant-contrib-1.0_beta3-r1::gentoo  USE="-doc -source" 0 KiB
[ebuild   R    ] dev-java/ant-ivy-2.3.0:2::gentoo  USE="-doc -examples -source {-test}" 0 KiB
[ebuild   R    ] dev-java/ant-1.9.2::gentoo  USE="X antlr bcel bsf commonslogging commonsnet javamail jdepend jsch log4j oro regexp resolver -jai -jmf -testutil" 0 KiB




My real pain is:

Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/tools/bzip2/CBZip2InputStream


This is from MarkDuplicates utility from sci-biology/picard-1.103 .
Comment 1 James Le Cuirot gentoo-dev 2015-05-14 14:23:48 UTC
dev-java/ant is indeed a virtual package. ant-core provides this class.

chewi@symphony % jar tf /usr/share/ant-core/lib/ant.jar | fgrep CBZip2InputStream
org/apache/tools/bzip2/CBZip2InputStream$Data.class
org/apache/tools/bzip2/CBZip2InputStream.class

I can't look into it now but it's probably a problem with the picard build itself.
Comment 2 Miroslav Šulc gentoo-dev 2021-04-15 14:00:15 UTC
this bug is pretty old. as well as sci-biology/picard-1.103. i suggest maintainers bump picard to the latest 2.25.2 from https://github.com/broadinstitute/picard. if the issue would not be fixedd with the latest release then we can try to fix it.
Comment 3 Martin Mokrejš 2021-04-15 17:37:32 UTC
Picard cannot be bumped to latest because they switched from apache ant to gradle. In the tree used to be the last version of picard and gatk which was using apache ant for building. If it is 1.103 I am not certain from top of my head but it was tracked in changelog or in ebuild comments.