[Bio-Linux] bio-linux-emboss breaks debsums
Tony Travis
ajt at rri.sari.ac.uk
Mon May 8 19:23:47 EDT 2006
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
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