Andreas Tille <andr...@an3as.eu> writes: > Hi,
hello Andreas, > On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote: >> >> Thanks. This was pretty helpful. Now I need to package the >> remaining JAR which is not yet packaged from >> >> http://la4j.org/ > > I made some progress and also uploaded libla4j-java[1] to new. With > this I tried to build drop-seq[2] and stumbled upon two issues: > > At first a lintian issue: > > W: drop-seq-tools: classpath-contains-relative-path > usr/share/java/dropseq-2.3.0.jar: lib/FastInfoset-1.2.12.jar, > lib/FastInfoset.jar, lib/FastInf > N: > N: The classpath listed in the jar file refers to a potential missing jar > N: file. This could be the remnants of a build-time classpath that are not > N: relevant for a JAR bundled in a Debian package. > N: > N: Alternatively, the classpath may be correct, but the package is lacking > N: a jar file or a symlink to it. > N: > N: Note, Lintian assumes that all (relative) classpaths pointing to > N: /usr/share/java/ (but not subdirs thereof) are satisfied by dependencies > N: as long as there is at least one strong libX-java dependency. > N: > N: Severity: warning > N: > N: Check: languages/java > > I have no idea what this means. A `grep -Ri fastinfoset` inside the source > tree remains empty. > The (current) problem is this in the jar-executable target: <pathconvert property="classpath.manifest" refid="classpath" pathsep=" "> <chainedmapper> <flattenmapper/> <globmapper from="*.jar" to="lib/*.jar"/> </chainedmapper> </pathconvert> This causes the classpath for the runnable jar to be prefixed with lib/, but /usr/share/java/lib/... (or lib/...) does not exist. Please try to change it to: <pathconvert property="classpath.manifest" refid="classpath" pathsep=" "> <flattenmapper/> </pathconvert> > The other one is a runtime error of the wrapper script: > > $ drop-seq > Error: Could not find or load main class > org.broadinstitute.dropseqrna.cmdline.DropSeqMain > Caused by: java.lang.NoClassDefFoundError: > picard/cmdline/PicardCommandLine This is a likely consequence of the lintian above: the dropseq jar does not refer to the correct classpath entry for picard.jar. If it still does not work, please post the META-INF/MANIFEST.MF contents of the usr/share/java/dropseq-2.3.0.jar (you can rename it to .zip, then open it with an archiver). Cheers and Best Regards, -- Felix Natter debian/rules!
