[Bio-Linux] Red-Carpet Updates and Perl issues (Read this if you are using Perl on Bio-Linux)

[Dr Dan Swan]

Dear all,

It has come to our attention that RedCarpet has updated Perl 5.6.1 on
the Bio-Linux systems.  Bio-Linux 2.X comes with Perl 5.6.1 and Perl
5.8.0.

The Perl binaries are generally found in 2 locations:

/usr/bin/perl

/usr/local/bin/perl

When 5.8.0 was installed on the system a symbolic link was created
linking /usr/bin/perl to /usr/local/bin/perl.

When Red-Carpet attempts to update the existing installation of 5.6.1
(which has recently, like 5.8.0, had a bugfix release) it overwrites the
/usr/bin/perl symlink.

Consequently if your Perl scripts reference /usr/bin/perl instead of
/usr/local/bin/perl you may run into some problems.

We suggest 2 courses of action:

1) Use /usr/local/bin/perl in your shebang line - this is compatible
with Bio-Linux 2.0 and the upcoming 3.0 release (this issue will not
occur in 3.0 due to an improved update mechanism).
2) If you wish to restore the symlink, log in as manager:

sudo rm /usr/bin/perl
sudo ln -s /usr/local/bin/perl /usr/bin/perl

This will avoid you having to change any scripts. However if any
*further* Perl 5.6.X upgrades are released it is almost certain that
this issue will reappear.

Apologies to anyone who has been frustrated by this error,

regards,

Dan
-- 
Dr Dan Swan (RHCE) - Bio-Linux Developer
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 975 Fax: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk