From dswan at ceh.ac.uk  Mon Aug 11 06:51:33 2003
From: dswan at ceh.ac.uk (Dr Dan Swan)
Date: 11 Aug 2003 11:51:33 +0100
Subject: [Bio-Linux] Correcting time issues under Bio-Linux
Message-ID: <1060599093.28551.1036.camel@ivpcp032.nerc-oxford.ac.uk>

Hello Bio-Linux users.

We have been aware for some time that the time on Bio-Linux machines is
highly prone to drifting (actually this is an annoying RedHat/Linux
issue as it also occurs on my laptop).  If you are suffering from this
then please apply the fix below:

As manager create a file called time.sh with the following information:

#!/bin/sh

echo "Resetting ntpd"
/etc/init.d/ntpd stop
ntpdate ntp2.ja.net
/etc/init.d/ntpd start

save it and then:

sudo cp time.sh /etc/cron.daily
sudo chown root:root /etc/cron.daily/time.sh
sudo chmod 755 /etc/cron.daily/time.sh

This makes things a little more useable - each day at around 4am
the time daemon will sync to the ntp server ntp2.ja.net which keeps the
correct UK time - the clock may drift a couple of minutes during the day
but should be ok as it is reset daily.

If you're outside the UK then you should approach your IT Staff for an NTP server
appropriate to your timezone.

regards,

Dan

-- 
Dr Dan Swan - 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  Mon Aug 11 08:54:12 2003
From: dswan at ceh.ac.uk (Dr Dan Swan)
Date: 11 Aug 2003 13:54:12 +0100
Subject: [Bio-Linux] RedCarpet update issues fglrx and freetype2.
Message-ID: <1060606452.28551.1078.camel@ivpcp032.nerc-oxford.ac.uk>

If you have updated your machine via RedCarpet recently you may have
seen an error:  

"XFree86-ligb-4.2.1-13.73.3 conflicts fglrx-glc22-4.2.0-2.5.1" 

then take the following action as :

sudo rpm -e fglrx-glc22-4.2.0-2.5.1

You should then be able to apply the XFree86 updates.

You will probably now get an error (if you are saying all updates and
not just the XFree86 ones):

"unmet dependecies.  nautilus-1.0.6-16.ximian.16 conflicts with
freetype2"

Freetype2 is an essential dependency for GD, which is an essential
dependency for some features of Bioperl.  As this is extremely tricky to
configure do not apply the updates - a fix is being investigated.  We
will inform the list and update the FAQ when a fix is available.

Please note that all fixes posted to the list will also be added to the
User FAQ at http://envgen.nox.ac.uk/envgen/software/archives/000337.html

Also note that if you find a bug/issue with Bio-Linux you can report it
to the helpdesk (helpdesk at envgen.nox.ac.uk), but cc'ing it via the
Bio-Linux list will allow others to come forward if they have also had
the same issue, or have fixed the issue already.

regards,

Dan

-- 
Dr Dan Swan - 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