From shou at ceh.ac.uk  Fri Jun  8 10:17:41 2007
From: shou at ceh.ac.uk (Stewart Houten)
Date: Fri, 8 Jun 2007 15:17:41 +0100
Subject: [Bio-Linux] Bio-Linux Upgrade
Message-ID: <20070608141741.GA17321@ivpcp068.nerc-oxford.ac.uk>

Dear All,

The base-system underlying Bio-Linux was recently upgraded making
Debian GNU/Linux 4.0, codenamed "Etch", the new stable release.  This
upgrade provides support for a greater range of hardware and makes
available many new and updated software packages including R v2.4,
OpenOffice v2.0 and more [1].

The upgrade will *not* be done automatically via the nightly update
mechanism and will need to be performed by the systems administrator.
To help with this we have put together a detailed set of upgrade
instructions specific to Bio-Linux which will hopefully catch any
pitfalls that might be encountered.  Alternatively, if you wish to
reinstall your machine with our updated image then please contact us
and request a new installation CD. 

For further information visit our website[2].

Please take the time to perform the upgrade and let us know via the
helpdesk <helpdesk at nebc.nox.ac.uk> if you have any problems or queries.

Regards,
Stewart

[1] http://www.us.debian.org/News/2007/20070408
[2] http://envgen.nox.ac.uk/envgen/software/archives/000576.html


--
Dr Stewart Houten, Bio-Linux Developer
NEBC, CEH, Mansfield Road, Oxford, OX1 3SR
http://nebc.nox.ac.uk/ 



From ajt at rri.sari.ac.uk  Fri Jun  8 11:31:35 2007
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Fri, 08 Jun 2007 16:31:35 +0100
Subject: [Bio-Linux] Bio-Linux Upgrade
In-Reply-To: <20070608141741.GA17321@ivpcp068.nerc-oxford.ac.uk>
References: <20070608141741.GA17321@ivpcp068.nerc-oxford.ac.uk>
Message-ID: <46697657.5040704@rri.sari.ac.uk>

Stewart Houten wrote:
> [...]
> pitfalls that might be encountered.  Alternatively, if you wish to
> reinstall your machine with our updated image then please contact us
> and request a new installation CD. 

Hello, Stewart.

Yes, I would like to upgrade my Bio-Linux4 reference machine at RRI:

	143.234.32.16 rri16.rri.sari.ac.uk rri16 kitcat

I've rebuilt this machine recently and it's currently running Ubuntu. 
I'll use another machine in future, because this one is part of our 
openMosix Beowulf cluster, but its IP address is in your firewall.

Please send me an updated CD image - thanks.

Re: 'biobuntu' I could kick myself for taking so long to discover why my 
'live' DVD wasn't working! Well, I have been busy with other things 
recently too. In short, it was because doing:

	aptitude dist-upgrade

In the 'chroot' before remastering the CD/DVD breaks the Casper boot 
because, despite the fact Casper's i386 kernel is outside the 'squashfs' 
it still has dependencies on the CD/DVD compressed root filesystem...

I've now fixed the problem by 'holding' the i386 kernel at the version 
used to create the 6.06.1 LTS 'live' CD. I've read instructions about 
how to 'expert' a custom kernel from the 'chroot', but not done it yet.

When it's a bit more stable, I'll put an iso image of the DVD on:

	http://bioinformatics.rri.sari.ac.uk/~ajt/biobuntu

It boots OK now, but it still needs more work before it's ready :-)

Good luck with the upgrade to Etch!

Best wishes,

	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



From J.Hadfield at ed.ac.uk  Mon Jun 11 05:18:42 2007
From: J.Hadfield at ed.ac.uk (Jarrod Hadfield)
Date: Mon, 11 Jun 2007 10:18:42 +0100
Subject: [Bio-Linux] biolinux wont boot
Message-ID: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk>

Hi,

I've jsut got back from holiday, to find I ca no longer log onto my  
biolinux machine.  I get the message 'fsck died with exit status 4"   
I get prompted for the root password for maintenance, but get no joy  
= "unable to read inode block".  As far as I'm aware, the only thing  
that happened since I've been away, is that soemone tried to drag  
some stuff off onto a USB  stick.  Could this be the cause of the  
problem.

Cheers,

Jarrod





From tbooth at ceh.ac.uk  Mon Jun 11 05:36:53 2007
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 11 Jun 2007 10:36:53 +0100
Subject: [Bio-Linux] biolinux wont boot
In-Reply-To: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk>
References: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk>
Message-ID: <1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>

Hi Jarrod,

The error "unable to read inode block" suggests to me that your disk is
failing.  The only other reason for getting a serious error like this
out of the blue would be if the machine had lost power suddenly, but
unless you know that has happened it is likely that you are going to
need to replace the drive.

The first thing to do is to boot from a recovery CD and take a look.  I
generally use Knoppix (knopper.net).  You'll need to download and burn a
CD image.

The second thing is to see what data you can access from the recovery CD
and tar it up to somewhere safe like a network share or removable disk.

Then see which partition or partitions cannot be mounted via Knoppix.
Once you have got any data you need off the good partitions, you can try
running fsck on the problem partitions.  Fsck may fail, or it may fix
things completely, or it may work but you will still have problems
reading the disk.  If things are fixed completely you should be able to
reboot back into Bio-Linux, but remember that your disk may still be on
the verge of packing in.

If Knoppix can't fix the disk you will have to get a replacement disk
from Dell and recover from the disaster recovery partition on the second
hard drive.  We'll cross that bridge when we come to it.

If you need and help with the above then give me a call on 018656 281
975.

I'll copy this mail thread into the helpdesk system to keep track of it.

Cheers,

TIM

On Mon, 2007-06-11 at 10:18 +0100, Jarrod Hadfield wrote:
> Hi,
> 
> I've jsut got back from holiday, to find I ca no longer log onto my  
> biolinux machine.  I get the message 'fsck died with exit status 4"   
> I get prompted for the root password for maintenance, but get no joy  
> = "unable to read inode block".  As far as I'm aware, the only thing  
> that happened since I've been away, is that soemone tried to drag  
> some stuff off onto a USB  stick.  Could this be the cause of the  
> problem.
> 
> Cheers,
> 
> Jarrod
> 
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975




From J.Hadfield at ed.ac.uk  Mon Jun 11 10:21:06 2007
From: J.Hadfield at ed.ac.uk (Jarrod Hadfield)
Date: Mon, 11 Jun 2007 15:21:06 +0100
Subject: [Bio-Linux] biolinux wont boot
In-Reply-To: <1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>
References: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk>
	<1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>
Message-ID: <286D823E-E88E-4957-8CCD-B2D22AA98C6D@ed.ac.uk>

Hi Tim,

Sorry to bother you again.  For files in many directories I was  
getting the error "cannot stat"  and the final message on finishing  
was "tar: Error exit delayed from previous errors".  I'm guessing  
these files may be unbackupable?

Cheers,

Jarrod
On 11 Jun 2007, at 10:36, Tim Booth wrote:

> Hi Jarrod,
>
> The error "unable to read inode block" suggests to me that your  
> disk is
> failing.  The only other reason for getting a serious error like this
> out of the blue would be if the machine had lost power suddenly, but
> unless you know that has happened it is likely that you are going to
> need to replace the drive.
>
> The first thing to do is to boot from a recovery CD and take a  
> look.  I
> generally use Knoppix (knopper.net).  You'll need to download and  
> burn a
> CD image.
>
> The second thing is to see what data you can access from the  
> recovery CD
> and tar it up to somewhere safe like a network share or removable  
> disk.
>
> Then see which partition or partitions cannot be mounted via Knoppix.
> Once you have got any data you need off the good partitions, you  
> can try
> running fsck on the problem partitions.  Fsck may fail, or it may fix
> things completely, or it may work but you will still have problems
> reading the disk.  If things are fixed completely you should be  
> able to
> reboot back into Bio-Linux, but remember that your disk may still  
> be on
> the verge of packing in.
>
> If Knoppix can't fix the disk you will have to get a replacement disk
> from Dell and recover from the disaster recovery partition on the  
> second
> hard drive.  We'll cross that bridge when we come to it.
>
> If you need and help with the above then give me a call on 018656 281
> 975.
>
> I'll copy this mail thread into the helpdesk system to keep track  
> of it.
>
> Cheers,
>
> TIM
>
> On Mon, 2007-06-11 at 10:18 +0100, Jarrod Hadfield wrote:
>> Hi,
>>
>> I've jsut got back from holiday, to find I ca no longer log onto my
>> biolinux machine.  I get the message 'fsck died with exit status 4"
>> I get prompted for the root password for maintenance, but get no joy
>> = "unable to read inode block".  As far as I'm aware, the only thing
>> that happened since I've been away, is that soemone tried to drag
>> some stuff off onto a USB  stick.  Could this be the cause of the
>> problem.
>>
>> Cheers,
>>
>> Jarrod
>>
>>
>>
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at envgen.nox.ac.uk
>> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> -- 
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
> at CEH Oxford
> +44 1865 281 975
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>




From H.J.NEWBURY at bham.ac.uk  Mon Jun 11 10:20:13 2007
From: H.J.NEWBURY at bham.ac.uk (John Newbury)
Date: Mon, 11 Jun 2007 15:20:13 +0100
Subject: [Bio-Linux] biolinux wont boot
In-Reply-To: <286D823E-E88E-4957-8CCD-B2D22AA98C6D@ed.ac.uk>
References: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk><1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>
	<286D823E-E88E-4957-8CCD-B2D22AA98C6D@ed.ac.uk>
Message-ID: <8BAA42D1298CA341BA5E80F938E76F9B54F72E@BIOEX2.adf.bham.ac.uk>

Do I really need to get this, and previous, messages?

John Newbury 

> -----Original Message-----
> From: bio-linux-bounces at envgen.nerc-oxford.ac.uk 
> [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf 
> Of Jarrod Hadfield
> Sent: 11 June 2007 15:21
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] biolinux wont boot
> 
> Hi Tim,
> 
> Sorry to bother you again.  For files in many directories I 
> was getting the error "cannot stat"  and the final message on 
> finishing was "tar: Error exit delayed from previous errors". 
>  I'm guessing these files may be unbackupable?
> 
> Cheers,
> 
> Jarrod
> On 11 Jun 2007, at 10:36, Tim Booth wrote:
> 
> > Hi Jarrod,
> >
> > The error "unable to read inode block" suggests to me that 
> your disk 
> > is failing.  The only other reason for getting a serious error like 
> > this out of the blue would be if the machine had lost power 
> suddenly, 
> > but unless you know that has happened it is likely that you 
> are going 
> > to need to replace the drive.
> >
> > The first thing to do is to boot from a recovery CD and 
> take a look.  
> > I generally use Knoppix (knopper.net).  You'll need to download and 
> > burn a CD image.
> >
> > The second thing is to see what data you can access from 
> the recovery 
> > CD and tar it up to somewhere safe like a network share or 
> removable 
> > disk.
> >
> > Then see which partition or partitions cannot be mounted 
> via Knoppix.
> > Once you have got any data you need off the good 
> partitions, you can 
> > try running fsck on the problem partitions.  Fsck may fail, 
> or it may 
> > fix things completely, or it may work but you will still 
> have problems 
> > reading the disk.  If things are fixed completely you 
> should be able 
> > to reboot back into Bio-Linux, but remember that your disk 
> may still 
> > be on the verge of packing in.
> >
> > If Knoppix can't fix the disk you will have to get a 
> replacement disk 
> > from Dell and recover from the disaster recovery partition on the 
> > second hard drive.  We'll cross that bridge when we come to it.
> >
> > If you need and help with the above then give me a call on 
> 018656 281 
> > 975.
> >
> > I'll copy this mail thread into the helpdesk system to keep 
> track of 
> > it.
> >
> > Cheers,
> >
> > TIM
> >
> > On Mon, 2007-06-11 at 10:18 +0100, Jarrod Hadfield wrote:
> >> Hi,
> >>
> >> I've jsut got back from holiday, to find I ca no longer 
> log onto my 
> >> biolinux machine.  I get the message 'fsck died with exit status 4"
> >> I get prompted for the root password for maintenance, but 
> get no joy 
> >> = "unable to read inode block".  As far as I'm aware, the 
> only thing 
> >> that happened since I've been away, is that soemone tried to drag 
> >> some stuff off onto a USB  stick.  Could this be the cause of the 
> >> problem.
> >>
> >> Cheers,
> >>
> >> Jarrod
> >>
> >>
> >>
> >> _______________________________________________
> >> Bio-Linux mailing list
> >> Bio-Linux at envgen.nox.ac.uk
> >> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > --
> > Tim Booth <tbooth at ceh.ac.uk>
> > NERC Environmental Bioinformatics Centre at CEH Oxford
> > +44 1865 281 975
> >
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at envgen.nox.ac.uk
> > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> >
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> 



From tbooth at ceh.ac.uk  Mon Jun 11 10:33:10 2007
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 11 Jun 2007 15:33:10 +0100
Subject: [Bio-Linux] Use of the Bio-Linux list
In-Reply-To: <8BAA42D1298CA341BA5E80F938E76F9B54F72E@BIOEX2.adf.bham.ac.uk>
References: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk>
	<1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>
	<286D823E-E88E-4957-8CCD-B2D22AA98C6D@ed.ac.uk>
	<8BAA42D1298CA341BA5E80F938E76F9B54F72E@BIOEX2.adf.bham.ac.uk>
Message-ID: <1181572390.1307.96.camel@ivpcp044.nerc-oxford.ac.uk>

Hi John,

The Bio-Linux list is for open discussion of Bio-Linux related issues.
While the list has been quiet of late and most people send requests like
this directly to the helpdesk, there is no reason not to put technical
questions, comments, tips etc. over the Bio-Linux list.  

If you don't want to get these messages then you are probably better off
being unsubscribed from this list and just staying on our
'envgen-announce' list which only carries announcement postings from the
NEBC.  Let me know if you would rather do that.

In this case, I've continued the e-mails with Jarrod via the helpdesk as
they are getting quite involved and are probably not of interest to most
people.

Cheers,

TIM

On Mon, 2007-06-11 at 15:20 +0100, John Newbury wrote:
> Do I really need to get this, and previous, messages?
> 
> John Newbury 
> 
> > -----Original Message-----
> > From: bio-linux-bounces at envgen.nerc-oxford.ac.uk 
> > [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf 
> > Of Jarrod Hadfield
> > Sent: 11 June 2007 15:21
> > To: Bio-Linux help and discussion
> > Subject: Re: [Bio-Linux] biolinux wont boot
> > 
> > Hi Tim,
> > 
> > Sorry to bother you again.  For files in many directories I 
> > was getting the error "cannot stat"  and the final message on 
> > finishing was "tar: Error exit delayed from previous errors". 
> >  I'm guessing these files may be unbackupable?
> > 
> > Cheers,
> > 
> > Jarrod
> > On 11 Jun 2007, at 10:36, Tim Booth wrote:
> > 
> > > Hi Jarrod,
> > >
> > > The error "unable to read inode block" suggests to me that 
> > your disk 
> > > is failing.  The only other reason for getting a serious error like 
> > > this out of the blue would be if the machine had lost power 
> > suddenly, 
> > > but unless you know that has happened it is likely that you 
> > are going 
> > > to need to replace the drive.
> > >
> > > The first thing to do is to boot from a recovery CD and 
> > take a look.  
> > > I generally use Knoppix (knopper.net).  You'll need to download and 
> > > burn a CD image.
> > >
> > > The second thing is to see what data you can access from 
> > the recovery 
> > > CD and tar it up to somewhere safe like a network share or 
> > removable 
> > > disk.
> > >
> > > Then see which partition or partitions cannot be mounted 
> > via Knoppix.
> > > Once you have got any data you need off the good 
> > partitions, you can 
> > > try running fsck on the problem partitions.  Fsck may fail, 
> > or it may 
> > > fix things completely, or it may work but you will still 
> > have problems 
> > > reading the disk.  If things are fixed completely you 
> > should be able 
> > > to reboot back into Bio-Linux, but remember that your disk 
> > may still 
> > > be on the verge of packing in.
> > >
> > > If Knoppix can't fix the disk you will have to get a 
> > replacement disk 
> > > from Dell and recover from the disaster recovery partition on the 
> > > second hard drive.  We'll cross that bridge when we come to it.
> > >
> > > If you need and help with the above then give me a call on 
> > 018656 281 
> > > 975.
> > >
> > > I'll copy this mail thread into the helpdesk system to keep 
> > track of 
> > > it.
> > >
> > > Cheers,
> > >
> > > TIM
> > >
> > > On Mon, 2007-06-11 at 10:18 +0100, Jarrod Hadfield wrote:
> > >> Hi,
> > >>
> > >> I've jsut got back from holiday, to find I ca no longer 
> > log onto my 
> > >> biolinux machine.  I get the message 'fsck died with exit status 4"
> > >> I get prompted for the root password for maintenance, but 
> > get no joy 
> > >> = "unable to read inode block".  As far as I'm aware, the 
> > only thing 
> > >> that happened since I've been away, is that soemone tried to drag 
> > >> some stuff off onto a USB  stick.  Could this be the cause of the 
> > >> problem.
> > >>
> > >> Cheers,
> > >>
> > >> Jarrod
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Bio-Linux mailing list
> > >> Bio-Linux at envgen.nox.ac.uk
> > >> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > > --
> > > Tim Booth <tbooth at ceh.ac.uk>
> > > NERC Environmental Bioinformatics Centre at CEH Oxford
> > > +44 1865 281 975
> > >
> > >
> > > _______________________________________________
> > > Bio-Linux mailing list
> > > Bio-Linux at envgen.nox.ac.uk
> > > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > >
> > 
> > 
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at envgen.nox.ac.uk
> > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975




From s.a.johns at sheffield.ac.uk  Tue Jun 12 04:12:05 2007
From: s.a.johns at sheffield.ac.uk (Sarah Johns)
Date: Tue, 12 Jun 2007 09:12:05 +0100
Subject: [Bio-Linux] Bio-Linux Upgrade
In-Reply-To: <20070608141741.GA17321@ivpcp068.nerc-oxford.ac.uk>
References: <20070608141741.GA17321@ivpcp068.nerc-oxford.ac.uk>
Message-ID: <1181635925.466e5555e024a@webmail.shef.ac.uk>

I treied to do the upgrade on friday, but realised I don't have a password for
root.  Can you help me?

Cheers
Sarah

Quoting Stewart Houten <shou at ceh.ac.uk>:

> Dear All,
> 
> The base-system underlying Bio-Linux was recently upgraded making
> Debian GNU/Linux 4.0, codenamed "Etch", the new stable release.  This
> upgrade provides support for a greater range of hardware and makes
> available many new and updated software packages including R v2.4,
> OpenOffice v2.0 and more [1].
> 
> The upgrade will *not* be done automatically via the nightly update
> mechanism and will need to be performed by the systems administrator.
> To help with this we have put together a detailed set of upgrade
> instructions specific to Bio-Linux which will hopefully catch any
> pitfalls that might be encountered.  Alternatively, if you wish to
> reinstall your machine with our updated image then please contact us
> and request a new installation CD. 
> 
> For further information visit our website[2].
> 
> Please take the time to perform the upgrade and let us know via the
> helpdesk <helpdesk at nebc.nox.ac.uk> if you have any problems or queries.
> 
> Regards,
> Stewart
> 
> [1] http://www.us.debian.org/News/2007/20070408
> [2] http://envgen.nox.ac.uk/envgen/software/archives/000576.html
> 
> 
> --
> Dr Stewart Houten, Bio-Linux Developer
> NEBC, CEH, Mansfield Road, Oxford, OX1 3SR
> http://nebc.nox.ac.uk/ 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> 


Dr Sarah Johns
Department of Animal & Plant Sciences
The University of Sheffield
Alfred Denny Building
Western Bank
Sheffield
S10 2TN
Lab: 0114 222 0109
Office: 0114 222 0113



From A.J.Pemberton at bham.ac.uk  Tue Jun 12 09:34:02 2007
From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton)
Date: Tue, 12 Jun 2007 14:34:02 +0100
Subject: [Bio-Linux] biolinux wont boot
In-Reply-To: <1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>
References: <383A68B5-19D2-470E-A9A6-CE5740653F1F@ed.ac.uk>
	<1181554613.1307.33.camel@ivpcp044.nerc-oxford.ac.uk>
Message-ID: <D39A1B623AED9D458065D38B8EA5278033EF74@BIOEX2.adf.bham.ac.uk>

Hi All,

Just to add to what Tim said. There is a specific rescue CD now that
boots a live system from CD and has a number of useful tools for
diagnosis and disk rescue:

http://www.sysresccd.org/Main_Page

Regards,

Tony

> -----Original Message-----
> From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-
> bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Tim Booth
> Sent: 11 June 2007 10:37
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] biolinux wont boot
> 
> Hi Jarrod,
> 
> The error "unable to read inode block" suggests to me that your disk
is
> failing.  The only other reason for getting a serious error like this
> out of the blue would be if the machine had lost power suddenly, but
> unless you know that has happened it is likely that you are going to
> need to replace the drive.
> 
> The first thing to do is to boot from a recovery CD and take a look.
I
> generally use Knoppix (knopper.net).  You'll need to download and burn
> a
> CD image.
> 
> The second thing is to see what data you can access from the recovery
> CD
> and tar it up to somewhere safe like a network share or removable
disk.
> 
> Then see which partition or partitions cannot be mounted via Knoppix.
> Once you have got any data you need off the good partitions, you can
> try
> running fsck on the problem partitions.  Fsck may fail, or it may fix
> things completely, or it may work but you will still have problems
> reading the disk.  If things are fixed completely you should be able
to
> reboot back into Bio-Linux, but remember that your disk may still be
on
> the verge of packing in.
> 
> If Knoppix can't fix the disk you will have to get a replacement disk
> from Dell and recover from the disaster recovery partition on the
> second
> hard drive.  We'll cross that bridge when we come to it.
> 
> If you need and help with the above then give me a call on 018656 281
> 975.
> 
> I'll copy this mail thread into the helpdesk system to keep track of
> it.
> 
> Cheers,
> 
> TIM
> 
> On Mon, 2007-06-11 at 10:18 +0100, Jarrod Hadfield wrote:
> > Hi,
> >
> > I've jsut got back from holiday, to find I ca no longer log onto my
> > biolinux machine.  I get the message 'fsck died with exit status 4"
> > I get prompted for the root password for maintenance, but get no joy
> > = "unable to read inode block".  As far as I'm aware, the only thing
> > that happened since I've been away, is that soemone tried to drag
> > some stuff off onto a USB  stick.  Could this be the cause of the
> > problem.
> >
> > Cheers,
> >
> > Jarrod
> >
> >
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at envgen.nox.ac.uk
> > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
> at CEH Oxford
> +44 1865 281 975
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux



From NEBC at wpo.nerc.ac.uk  Fri Jun 15 10:34:08 2007
From: NEBC at wpo.nerc.ac.uk (NEBC)
Date: Fri, 15 Jun 2007 15:34:08 +0100
Subject: [Bio-Linux] Bio-Linux 4.0 upgrade to the Etch kernel.
Message-ID: <s672b198.080@wpo.nerc.ac.uk>

To all Bio-Linux system administrators,

Please be aware that there will be no upgrade support available from the NEBC office from Monday 18th June to Wednesday 20th June inclusive. This is because of conference commitments and annual leave. Please continue with your upgrades from 21st June onwards.

Sorry for the inconvenience
NEBC

NERC Environmental
Bioinformatics Centre, 
Centre for Ecology & Hydrology
Mansfield Road, Oxford, OX1 3SR
UK
Tel: +44 (0) 1865 281976 Fax: +44 (0) 1865 281 696
http://nebc.nox.ac.uk/ Email: admin at nebc.ac.uk

This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed.




From btiwari at ceh.ac.uk  Tue Jun 26 08:13:21 2007
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Tue, 26 Jun 2007 13:13:21 +0100
Subject: [Bio-Linux] New Partigene and Trace2dbest packages on Bio-Linux
Message-ID: <s6811106.094@wpo.nerc.ac.uk>

Hello all, 

This is just to let you know that the bio-linux-trace2dbest and bio-linux-partigene packages have been updated on the server. The versions now available are 3.01 and 3.03 respectively.

There are onlya couple of small changes in the bio-linux packages relative to the original distributions: 
    -The maximum length for a blast database name has been changed from under 10 to under 20 characters. 
    - The version of CLOBB installed can take in files with endings of .fsa or .fasta. 

In addition, there is a file called PartiGene_predb.pl_modified in /usr/local/bioinf/partigene/partigene.  This file contains an ugly, and only partially effective,  hack to get around a problem that sometimes (!), arises due to the names given to blast report files. 
Please see the information in /usr/local/bioinf/partigene/partigene/readme.biolinux  for further details after the upgraded packages are installed. By default, PartiGene_predb.pl_modified is not set up to run; it is only any use if you are generating html pages and run into this issue with blast report names. We have contacted the partigene developers about this issue.


cheers,

Bela 

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************