From keith.jolley at medawar.oxford.ac.uk Thu Oct 16 07:15:37 2003 From: keith.jolley at medawar.oxford.ac.uk (Keith Jolley) Date: Thu, 16 Oct 2003 12:15:37 +0100 Subject: [Bio-Linux] Problem with daylight-saving hours Message-ID: Following the upgrade of my Bio-Linux machine, ntpd was set up to synchronise with the University time servers. The time was one hour off though, even though the timezone was set correctly using redhat-config-date. The problem is mentioned in Redhat Bugzilla (http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=91228), and is due to a symlink to the timezone file pointing to an unmounted partition on reboot if there is a dedicated /usr partition. The problem is solved by copying rather than linking the timezone file, e.g. sudo cp /usr/share/zoneinfo/Europe/London /etc/localtime Hope this may be of use to someone. Keith -- Dr. Keith Jolley The Peter Medawar Building for Pathogen Research University of Oxford South Parks Road Oxford, OX1 3SY From dswan at ceh.ac.uk Fri Oct 17 05:15:58 2003 From: dswan at ceh.ac.uk (Dan Swan) Date: Fri, 17 Oct 2003 10:15:58 +0100 Subject: [Bio-Linux] OpenGL bug in Bio-Linux v 2.0 and 2.1 Message-ID: Dear Bio-Linux users, it has come to our attention from a user (thanks Luciane) that the OpenGL implementation (3D graphics libraries) in Bio-Linux is broken and applications such as PyMol will not run if installed. If you are experiencing problems with OpenGL applications: 1) Log in as manager 2) Open a terminal 3) Type: sudo rm -rf `locate libglx.so` The ` symbol is below the Esc key on the keyboard. This should fix the OpenGL issues which were due to stale NVIDIA drivers incompletely removed from the system when they were uninstalled. regards, Dan From dswan at ceh.ac.uk Wed Oct 22 04:50:55 2003 From: dswan at ceh.ac.uk (Dr Dan Swan) Date: 22 Oct 2003 09:50:55 +0100 Subject: [Bio-Linux] Red-Carpet update : iptables and iptables-v6 Message-ID: <1066812654.16071.30.camel@router.example.com> Dear Systems Administrators, A couple of people have recently brought up the fact that Red-Carpet is trying to update 2 packages (iptables and iptables-v6) on the system resulting in an error: "There are no installable providers of >=kernel-2.4.20 for iptables-1.2.8-8.72.3[Red Hat Linux 7.3]" The iptables package provides the firewalling functions of your Bio-Linux machine. Without a significant (and non-essential) upgrade of the system core (the kernel) these 2 packages cannot be installed. Ignoring these updates will not cause a problem for the operation of the Bio-Linux machines. 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 From dswan at ceh.ac.uk Wed Oct 22 11:18:18 2003 From: dswan at ceh.ac.uk (Dr Dan Swan) Date: 22 Oct 2003 16:18:18 +0100 Subject: [Bio-Linux] Red-Carpet Updates and Perl issues (Read this if you are using Perl on Bio-Linux) Message-ID: <1066835898.16071.58.camel@router.example.com> 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