virtual/jdk:1.6 adds icedtea which doesn't provide jni (at least jni.h). So, when a package needs jni.h, and depends on virtual/jdk, jni is not recognized. (it's even worst because icedtea is the defaurt virtual/jdk:1.6 choice) A possible fix is to add a jni USE flag which will remove icedtea choice when on. In my research I've also seen bug 172478 which have an issue with jni.h and gcc[gcj]. This is blocking java (jni) support in net-libs/opal-3.6.2.
Both icedtea6-bin and (at least my build) icedtea6 have jni.h, what exact version are you talking about, -bin or not, what flags etc. are you talking about?
(In reply to comment #1) > Both icedtea6-bin and (at least my build) icedtea6 have jni.h, what exact > version are you talking about, -bin or not, what flags etc. are you talking > about? > There is only icedtea6-bin in the tree. There is no icedtea6 package. The installed version is icedtea6-bin-1.4.1 (newest) with USE="X alsa".
(In reply to comment #2) > There is only icedtea6-bin in the tree. There is no icedtea6 package. > The installed version is icedtea6-bin-1.4.1 (newest) with USE="X alsa". Well, my installation contains this and I see no way how it could be missing: /opt/icedtea6-bin-1.4.1/include/jni.h
Sorry, my bad