From tbooth at ceh.ac.uk  Thu Apr  4 11:56:15 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 4 Apr 2013 16:56:15 +0100
Subject: [Bio-Linux] Is your system freezing? Could be caused by Intel
	driver regression
Message-ID: <1365090975.3557.13.camel@balisaur>

Dear Bio-Linux Users,

I don't know if anyone else has hit this bug but it seems quite likely
it will affect a number of modern laptops:

https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1140716

In brief, the latest kernel update just before Easter can cause frequent
crashes on certain hardware.  If you think your Bio-Linux system has
suddenly started freezing, the easiest workaround is to hold the Shift
key during each boot-up and select the previous kernel from the menu.

The issue is flagged by the Ubuntu maintainers as critical so it should
be sorted out soon with another update.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From tbooth at ceh.ac.uk  Wed Apr 10 10:28:38 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 10 Apr 2013 15:28:38 +0100
Subject: [Bio-Linux] USb stick booting
In-Reply-To: <CABwDX3DjO07fOympzxTkVpZ1uemtvLhvDV3P5erc7RVSJWyG0g@mail.gmail.com>
References: <CABwDX3DjO07fOympzxTkVpZ1uemtvLhvDV3P5erc7RVSJWyG0g@mail.gmail.com>
Message-ID: <1365604118.25083.72.camel@balisaur>

Hi Enrique,

Sorry you are having trouble making the USB sticks.

The error you are seeing suggests that you made the USB sticks on a
machine with an older version of Syslinux, but then you say that regular
Ubuntu 12.04 works OK, so I may be wrong.  What happens if you type
"live" (without the quotes) at the boot prompt after the error and hit
return? (note you will need to have the keyboard connected in such a way
that it is visible to the BIOS, not via a USB hub).

Cheers,

TIM

On Wed, 2013-04-10 at 09:37 +0100, Enrique Ortega wrote:
> 
> Hello,
> I have been trying to use a home made Memory stick to use Biolinux 7
> on a live system to show it to my peers (and initiate them to the
> awesomeness of bioinformatics).
> So far, in different computers (old and new) and memory sticks created
> with different computers, the system wont boot. Once I modify the boot
> menu to boot from the usb key, it blocks immediatly after and shows
> the following lines:
> 
> 
> "SYSLINUX 3.63 Debian-2000-05-15 EBIOS copyright (C) 1994-2008 H.
> Peter Anvin
> Unknown keyword in configurtation file.
> boot : "
> 
> 
> In the same computers in which the boot blocks, the live system from a
> memory stick for standard releases of ubuntu (10.04 and 12.04) and
> other systems works OK.
> 
> 
> I haven't tried the boot from CD, since some of this computers have a
> broken CD tray.
> If I can help to fix this, please let me know.
> 
> 
> Best regards,
> Enrique Ortega-Abboud, PhD student BGPI-Cirad
> Monptellier, France
> 
> 
> 
> 
> --
> The contact from the website is broken too
> (http://nebc.nerc.ac.uk/contact-info) here's the error:
> Error
>         Unable to send mail: SMTP AUTH extension not supported by
>         server.
> 
> 
> -- 
> Cordialement
> 
> Enrique ORTEGA-ABBOUD
> Mobile : 06.49.61.10.08

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From kumar4ushakti at gmail.com  Tue Apr 23 08:11:58 2013
From: kumar4ushakti at gmail.com (kumar4ushakti .)
Date: Tue, 23 Apr 2013 17:41:58 +0530
Subject: [Bio-Linux] package fetch problem
Message-ID: <CAJbm36BerAOaUHhHwGqUA_-dzEyXxC62pPhshvZxnjhZ9U1naw@mail.gmail.com>

Respected Sir/Madam,
I am sending a error after editing source.list file by adding
following three lines:

deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main

when I typed sudo apt-get update
It runs but atlast it is showing following error

Failed to fetch
http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/Packages
404  Not Found

please help me.

Shakti Kumar
Bioinformatics Centre
North-Eastern Hill University
Shillong-793022 India
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From tbooth at ceh.ac.uk  Tue Apr 23 08:50:20 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 23 Apr 2013 13:50:20 +0100
Subject: [Bio-Linux] package fetch problem
In-Reply-To: <CAJbm36BerAOaUHhHwGqUA_-dzEyXxC62pPhshvZxnjhZ9U1naw@mail.gmail.com>
References: <CAJbm36BerAOaUHhHwGqUA_-dzEyXxC62pPhshvZxnjhZ9U1naw@mail.gmail.com>
Message-ID: <1366721420.20970.381.camel@balisaur>

Hi Shakti,

This indicates that you are trying to install Bio-Linux packages onto a
32-bit version of Ubuntu or Debian.  The Bio-Linux repository only
caters for 64-bit systems.  Have you tried running Ubuntu 12.04.2 64-bit
on your machine?  Virtually all PCs nowadays will support it.

If you really need to run things on a 32-bit system, I may be able to
help it there is a specific package you need but you will not be able to
use our main repository.

Cheers,

TIM

On Tue, 2013-04-23 at 13:11 +0100, kumar4ushakti . wrote:
> Respected Sir/Madam,
> I am sending a error after editing source.list file by adding 
> following three lines:
> 
> deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
> deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> 
> when I typed sudo apt-get update
> It runs but atlast it is showing following error
> 
> Failed to fetch
> http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/Packages  404  Not Found
> 
> please help me.
> 
> Shakti Kumar 
> Bioinformatics Centre
> North-Eastern Hill University
> Shillong-793022 India

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From kumar4ushakti at gmail.com  Wed Apr 24 01:05:23 2013
From: kumar4ushakti at gmail.com (kumar4ushakti .)
Date: Wed, 24 Apr 2013 10:35:23 +0530
Subject: [Bio-Linux] package fetch problem
In-Reply-To: <1366721420.20970.381.camel@balisaur>
References: <CAJbm36BerAOaUHhHwGqUA_-dzEyXxC62pPhshvZxnjhZ9U1naw@mail.gmail.com>
	<1366721420.20970.381.camel@balisaur>
Message-ID: <CAJbm36Bj1tpmZk5=w96w7euZG-hw0aj93_AsJ7uZZi+6e-wsxQ@mail.gmail.com>

Tim Sir,

Thank you for replying me.

Sir, I kindly inform you that I belongs to India and most student and
research scholar are still
using 32-bit system. Kindly provide use 32-bit of Biolinux repository.
I will be grateful and thankful you.


Your's sincerely
Shakti Kumar
Bioinformatics Centre
North-Eastern Hill University
Shillong-793022 India.

On Tue, Apr 23, 2013 at 6:20 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Shakti,
>
> This indicates that you are trying to install Bio-Linux packages onto a
> 32-bit version of Ubuntu or Debian.  The Bio-Linux repository only
> caters for 64-bit systems.  Have you tried running Ubuntu 12.04.2 64-bit
> on your machine?  Virtually all PCs nowadays will support it.
>
> If you really need to run things on a 32-bit system, I may be able to
> help it there is a specific package you need but you will not be able to
> use our main repository.
>
> Cheers,
>
> TIM
>
> On Tue, 2013-04-23 at 13:11 +0100, kumar4ushakti . wrote:
> > Respected Sir/Madam,
> > I am sending a error after editing source.list file by adding
> > following three lines:
> >
> > deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
> > deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> > deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> >
> > when I typed sudo apt-get update
> > It runs but atlast it is showing following error
> >
> > Failed to fetch
> >
> http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/Packages 404  Not Found
> >
> > please help me.
> >
> > Shakti Kumar
> > Bioinformatics Centre
> > North-Eastern Hill University
> > Shillong-793022 India
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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