[Bio-Linux] bio-linux-emboss breaks debsums

[Bela Tiwari]

Hi Tony

Thanks for the report and investigating the causes of the problem. The file scop.all is part of the EMBOSS release itself rather than something I have put in. I have updated the package, removing the space at the end of the filename. Can you install the latest bio-linux-emboss package and see what happens?

I wasn't sure what he problem was that you saw with the jemboss.desktop file. There didn't seem to be a space at the end of that filename. The jemboss.desktop file becomes X-Debian-Apps-Science-jemboss.desktop. This is on my machine. Can you check again to see if it is on yours?

cheers,

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> ajt at rri.sari.ac.uk 09/05/2006 00:23 >>>
I've noticed that "debsums" (used to verify the installation of Debian 
packages) is broken after installing bio-linux-emboss under Debian 
Sarge/Etch. The "debsums" package is not a standard part of Bio-Linux4, 
but it's a useful way of verifying system integrity. Unfortunately, a 
problem in the bio-linux-emboss package results in diagnostic errors 
being produced when subsequently installing *any* other packages! This 
is caused by trailing spaces in the filename:

"/usr/local/bioinf/EMBOSS/EMBOSS-3.0.0/test/data/structure/scop.all "
                                                                    ^
> ajt at wildcat:% debsums -ac bio-linux-emboss_3.0.0-3_i386.deb 
> debsums: can't open scop.all  (No such file or directory)
> Can't return to /tmp/YGGGLV8DjO/bio-linux-emboss/usr/local/bioinf/EMBOSS/EMBOSS-3.0.0/test/data/structure from /tmp/YGGGLV8DjO (No such file or directory) at /usr/share/perl/5.8/File/Temp.pm line 858
> END failed--call queue aborted.

The "debsums" program is a Perl script, and the perl library function 
open() automatically processes filenames to remove leading/trailing 
spaces. However, the "scop.all " file is created _with_ a trailing space 
when bio-linux-emboss is installed. I've extracted the contents of the 
NEBC package "bio-linux-emboss_3.0.0-3_i386.deb" and confirmed that the 
file in the package does indeed have a trailing space in its name.

Renaming the file "scop.all" (i.e. without a trailing space), then
rebuilding and installing the updated package cures this problem, but
there is also a problem with at least one other file in the package:

/var/lib/menu-xdg/applications/menu-xdg/jemboss.desktop

I've confirmed that this file is in the bio-linux-emboss package but it 
doesn't seem to be created when the package is installed, and I'm not 
sure why...

Any ideas?

	Tony.
-- 
Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk 
Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt 
Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687

_______________________________________________
Bio-linux mailing list
Bio-linux at envgen.nox.ac.uk 
http://envgen.nox.ac.uk/mailman/listinfo/bio-linux