emerging mod_php 4.3.1 fails: .... checking for Java support... yes checking Java Jar location... configure: error: Unable to locate /opt/blackdown-jre-1.4.1/bin but this directory exists: pegasus root # ls -la /opt/blackdown-jre-1.4.1/bin/ total 336 drwxr-xr-x 2 joerg 1000 4096 Apr 18 22:43 . drwxr-xr-x 6 root root 4096 Apr 18 22:43 .. -rwxr-xr-x 1 root root 5477 May 31 16:02 JavaPluginControlPanel -rwxr-xr-x 1 root root 24644 May 31 16:02 java -rwxr-xr-x 1 root root 10540 May 31 16:02 java_vm -rwxr-xr-x 1 root root 26612 May 31 16:02 keytool -rwxr-xr-x 1 root root 26676 May 31 16:02 kinit -rwxr-xr-x 1 root root 26676 May 31 16:02 klist -rwxr-xr-x 1 root root 26676 May 31 16:02 ktab -rwxr-xr-x 1 root root 26972 May 31 16:02 orbd -rwxr-xr-x 1 root root 26612 May 31 16:02 policytool -rwxr-xr-x 1 root root 26612 May 31 16:02 rmid -rwxr-xr-x 1 root root 26612 May 31 16:02 rmiregistry -rwxr-xr-x 1 root root 26572 May 31 16:02 servertool -rwxr-xr-x 1 root root 26572 May 31 16:02 tnameserv emerge info tells me: USE="x86 oss 3dnow apm avi encode gif jpeg libg++ mikmod mpeg quicktime spell gdbm berkdb readline arts svga java guile sdl gpm tcpd pam libwww perl esd motif mozilla dvd X gtk gnome -alsa bonobo cdr crypt cups flash gtk2 gtkhtml imlib mbox mmx ncurses nls opengl oggvorbis pdflib png python qt kde slang tetex truetype usb xml xml2 xmms xv zlib ssl" Look at the ebuild of mod_php-4.3.1.ebuild: There is a line: use java && myconf="${myconf} --with-java=${JAVA_HOME}" So the user which calls this emerge should not have selected a jre, but the jdk (only the jdks contains the jar utility).
Use java-config to select your JDK. I've added some fixes for this now.