[EMBOSS] Compiling EMBOSS: missing jni.h?

Charles Plessy charles-listes-emboss at plessy.org
Tue Nov 25 05:55:38 UTC 2008

Le Mon, Nov 24, 2008 at 04:20:13PM -0500, Sylvain Foisy a écrit :
> Hi,
> I'am trying to build a bioinfo workstation with Xubuntu and of course, I am
> trying to compile the latest EMBOSS (5.0 is the latest version of the
> pre-built package). I just hit a snag... After invoking make, it compiles
> for a while and then crashes with this (sorry for the length):

Hello Sylvain,

There is a Debian package ready for EMBOSS 6.0.1 in our experimental section.
If you do not need jEMBOSS (that is not yet supported by our packages), you can
either try to install directly the binary packages, or to compile them on your

 - Get the build tools: sudo aptitude install devscripts build-essential
 - Get the source package: dget -x http://ftp.de.debian.org/debian/pool/main/e/emboss/emboss_6.0.1-2.dsc
 - Get the build dependancies: cd emboss-6.0.1 ; sudo mk-build-deps -r -i
 - Make the binary packages: debuild
 - Install them: cd .. ; sudo dpkg -i emboss_6.0.1-2_*.deb emboss-data_6.0.1-2_all.deb emboss-doc_6.0.1-2_all.deb emboss-lib_6.0.1-2_*.deb libajax6_6.0.1-2_*.deb libnucleus6_6.0.1-2_*.deb

Another way is to contact the Ubuntu MOTUs and ask them to synchronise with the
Debian experimental package. The only reason why it is there is that Debian is
frozen now, preparing its release. It will be part of the main distribution
later (and the embassy packages will be rebuilt against it).

> Can anyone point me toward a solution? I have openjdk-6-jdk installed via
> apt-get but it seems that I am missing something...

Have you passed the following arguments to your configure script:

--with-java=/usr/lib/jvm/java-6-openjdk/include --with-javaos=/usr/lib/jvm/java-6-openjdk/include/linux

Have a nice day,

Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan

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