I was doing a fresh install, and noticed that gnu-jaxp-1.3's dependencies are a bit broken. In particular, it needs =dev-libs/libxml2-2* and dev-libs/libxslt. Also, DEPEND should have >=jdk-1.3, and RDEPEND should have >=jre-1.3. So, it should be something like: DEPEND=">=virtual/jdk-1.3 app-arch/unzip" RDEPEND=">=virtual/jre-1.3 =dev-libs/libxml2-2* dev-libs/libxslt"
they are build time deps too: RDEPEND=">=virtual/jre-1.3 =dev-libs/libxml2-2* dev-libs/libxslt" DEPEND=">=virtual/jdk-1.3 app-arch/unzip ${RDEPEND}" fixed thanks