During the build process, jmol copies over classes from icedtea-web. Apart from general maintenance issues (a rebuild of jmol is needed to completely address icedtea-web bugs such as bug 1095309), this untracked dependency may cause Fedora to ship compiled Java code as part of the jmol packages, without shipping matching source code, against the licensing guidelines.
Although I'm the maintainer of both jspecview and JMol, I don't have much experience with Java. Could you aid me by telling what is the ant directive that causes the embedding?
Looks like the libjars target is the culprit. The build log says this: libjars: [mkdir] Created dir: /builddir/build/BUILD/jmol-14.0.13/build/appjars [unjar] Expanding: /usr/share/java/naga.jar into /builddir/build/BUILD/jmol-14.0.13/build/appjars [unjar] Expanding: /usr/share/java/commons-cli.jar into /builddir/build/BUILD/jmol-14.0.13/build/appjars [unjar] Expanding: /usr/share/java/jspecview.app.jar into /builddir/build/BUILD/jmol-14.0.13/build/appjars [unjar] Expanding: /usr/share/java/jspecview.applet.jar into /builddir/build/BUILD/jmol-14.0.13/build/appjars [delete] Deleting directory /builddir/build/BUILD/jmol-14.0.13/build/appjars/javajs [delete] Deleting directory /builddir/build/BUILD/jmol-14.0.13/build/appjars/org/jmol [delete] Deleting directory /builddir/build/BUILD/jmol-14.0.13/build/appjars/META-INF [touch] Creating /builddir/build/BUILD/jmol-14.0.13/build/libjars.timestamp As to why this is there, I don't know. In Fedora, we use wrapper scripts which set up an appropriate classpath, we don't copy the classes applications need.
Please check scratch build at http://koji.fedoraproject.org/koji/taskinfo?taskID=6823088
jmol-14.0.13-2.fc19 has been submitted as an update for Fedora 19. https://admin.fedoraproject.org/updates/jmol-14.0.13-2.fc19
jmol-14.0.13-2.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/jmol-14.0.13-2.fc20
(In reply to Susi Lehtola from comment #3) > Please check scratch build at > > http://koji.fedoraproject.org/koji/taskinfo?taskID=6823088 The files are gone, but I have not checked if functionality is impacted.
Package jmol-14.0.13-2.fc20: * should fix your issue, * was pushed to the Fedora 20 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing jmol-14.0.13-2.fc20' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2014-6150/jmol-14.0.13-2.fc20 then log in and leave karma (feedback).
jmol-14.0.13-2.fc20 has been pushed to the Fedora 20 stable repository. If problems still persist, please make note of it in this bug report.
jmol-14.0.13-2.fc19 has been pushed to the Fedora 19 stable repository. If problems still persist, please make note of it in this bug report.