libnucleus error in fdnapars and others after updates

[wolfgang rumpf]

Binary package hint: emboss

I had a fully operational EMBOSS server with the embassy-phylip software package added on. All worked fine until a few days ago, when I did some software updates (e.g. Ubuntu 10.4 to 10.10 plus some security updates). Now when I run certain apps in EMBOSS, libnucleus causes errors like this:

fdnapars: symbol lookup error: /usr/lib/libnucleus.so.6: undefined symbol: ajSeqdbInit

This has happened on two separate Ubuntu 10.10 servers I am using - obviously the fdnapars app didn't execute at all.

Also:

apt-cache policy libnucleus6
libnucleus6:
  Installed: 6.2.0-2
  Candidate: 6.2.0-2
  Version table:
 *** 6.2.0-2 0
        500 http://us.archive.ubuntu.com/ubuntu/ maverick/universe i386 Packages
        100 /var/lib/dpkg/status

So - how do I get fdnapars and other apps that use libnucleus to work again? One of my boxes is an AMD-based system, the other is a Dell Mini-10, not sure why it failed at all - it worked fine prior to the updates.

ProblemType: Bug
DistroRelease: Ubuntu 10.10
Package: libnucleus6 6.2.0-2
ProcVersionSignature: Ubuntu 2.6.35-27.48-generic 2.6.35.11
Uname: Linux 2.6.35-27-generic i686
Architecture: i386
Date: Wed Mar 9 16:59:48 2011
InstallationMedia: Ubuntu 10.04.1 LTS "Lucid Lynx" - Release i386 (20100816.1)
ProcEnviron:
 LANG=en_US.UTF-8
 SHELL=/bin/bash
SourcePackage: emboss

[Charles Plessy (plessy)]

Hello Wolfgang,

the 6.2.0-2 packages and the accompanying EMBASSY packages were not well tied to each other. Sorry for this.

embassy-phylip 3.68-1 is to be used with emboss 6.1.0.
embassy-phylip 3.69-1 is to be used with emboss 6.2.0.
embassy-phylip 3.69+20100721 is to be used with emboss 6.3.1 (and is properly tied to it).

Maverick does not have the right combination, so you need to stay with EMBOSS 6.1.0, or upgrade to later versions. I would have liked to provide you a backport of embassy-phylip in Debian Med's PPA, but non-free software is not allowed in PPAs. How about the following:

 - Tell me which suite you are interested in, and I will upload a backport of emboss 6.3.1 there (https://launchpad.net/~debian-med/+archive/ppa)
 - Rebuild embassy-phylip by yourself if you do not mind installing extra packages. Something along these lines (not tested)

apt-get install build-essential devscripts
dget -x http://archive.ubuntu.com/ubuntu/pool/multiverse/e/embassy-phylip/embassy-phylip_3.69+20100721-3.dsc
cd embassy-phylip-3.69+20100721-3
sudo mk-build-deps -r -i
debuild -us -uc
cd ..
sudo dpkg -i embassy-phylip*deb

Cheers,

--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

[wolfgang rumpf (wolfgang-rumpf)]

Charles, I got everything to work with the files you sent me earlier. But I'm considering moving to Ubuntu 11.04 (Natty Narwhal); are all the dependencies checked out there? I've been hesitating on the upgrade, since once I got things working I didn't want to lose that status again... :)

Thanks again for all your help - hope you're doing well....

[Charles Plessy (plessy)]

Hi Wolfgang,

here in Yokohama things have settled down and life has returned to normal.

In Ubuntu 11.04 (Natty Narwhal), you will find the latest EMBOSS packages, properly tied with the EMBASSY packages. I have installed Natty on a friend's computer recently, and on the EMBOSS side, thinks looked to work well. GNOME 3 was a bit surprising, but the fallback mode seems to emulate well the look and feel of GNOME 2.

Have a nice day,