JNA JAR has duplicate manifest (two different manifest files): $ jar tf /chroot/usr/lib/java/jna.jar |grep -i mani META-INF/MANIFEST.MF META-INF/MANIFEST.MF JAR file format requires manifest to be the very first entry. Upstream build.xml creates JAR using Ant <zip> task, which is not aware of JAR file format and breaks it by adding META-INF/ directory entry before manifest file. This causes %mvn_install to add second copy of the manifest.
Fixed in jna-4.4.0-4
I believe that this bug is fixed in jna-4.4.0-4, which is available in Fedora Rawhide, so I am closing this bug now. The build containing the fix can be found at Koji: http://koji.fedoraproject.org/koji/buildinfo?buildID=916874