Perils of Debian unstable

So this is not exactly a bioinformatics post – but it’s been a while, so consider this a “day to day problems of working with computers” post, if you will.

Several of my machines are perilous experimental beasts – Debian unstable, CVS everything else (Bioperl and so on).  I know – I deserve everything I get.  In general though, I get very few
problems, though the daily updates are a bit tedious.

So today I’m running a perl script which includes a system call to a program named procheck and suddenly I see:

  unknown colorls variable `su’.

I realise that the perl is OK – so what’s going on?  A little research reveals that the LS_COLORS env variable, used to colour filenames using ‘ls’ is the culprit – it seems Debian unstable packages coreutils and fileutils have updated recently and the dircolors database includes this illegal option, ‘su’.

Recompiling procheck fails because the compilation script runs under csh, which is where the LS_COLORS problem lies.  So we edit the script, procomp.scr to ‘#!/bin/bash’ and it compiles fine.  As an aside – why are structural biologists so keen on csh?  Just wondered.  Then in our Perl script we add:

  $ENV{‘LS_COLORS’} = ”;

and procheck runs happily once more.  $ENV is a handy thing to know, by the way.