[EMBOSS] Compiling EMBOSS: missing jni.h?

charles-listes-emboss at plessy.org charles-listes-emboss at plessy.org
Wed Nov 26 13:17:27 UTC 2008

Le Tue, Nov 25, 2008 at 10:22:52AM -0500, Sylvain Foisy a écrit :
> Thanks for the inputs on the paths toward java/javaos; make/make install now
> worked...kind of. I need the Jemboss interface to facilitate my students'
> interactions with EMBOSS, this is why I want to compile myself.
> Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to
> be related to the fact that libeplplot.so.3 is not found. I know that I have
> the libplplot9/libplplot-dev packages installed. Any pointers? Could I use
> your experimental package for emboss-libs to fix this?

Hi Sylvain,

EMBOSS uses a fork of libplplot, that was named libeplplot to allow both
libraries to be installed on the same system. (By the way, is the fork still
needed?) What seems to happen on your system is that it does not find the
nucleus and eplplot libraries. Although it is not really recommended to mix
local and packaged installs, the packages libajax6, libnucleus6 and emboss-lib
may provide you what you need.

I have started to implement support for jEMBOSS in the Debian packages, but it
will take time before it reaches Debian archives. What you can do if you would
like to try it is to unpack the emboss sources, and within them type
"debcheckout emboss". Then you can use the protocol I gave you before, with
mk-build-deps if still needed, and then debuild. On my amd64 system, I just
checked that something would appear whan running runJemboss, but did not verify
further that it functions correctly.

Lastly, if all you need is an interface, you can try the emboss-explorer
package, that provides a web frontend to EMBOSS.

Have a nice day,

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

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