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 .
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.
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.
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.
