From tbooth at ceh.ac.uk  Wed Jun  1 04:52:14 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 01 Jun 2011 09:52:14 +0100
Subject: [Bio-linux-dev] [Fwd: Re: Non-digit version numbers with Ubuntu
	natty]
Message-ID: <1306918334.2783.9411.camel@barsukas>

Hi,

I've just renumbered several of the packages, as we'd apparently been
using illegal version numbers (starting with "bl").  The new version
numbers are a bit ugly but solve the problem described below.

The packages are unchanged.

Cheers,

TIM

-------- Forwarded Message --------
From: Brad Chapman <chapmanb at 50mail.com>
To: Booth, Timothy G. <tbooth at ceh.ac.uk>
Subject: Re: Non-digit version numbers with Ubuntu natty
Date: Fri, 20 May 2011 12:12:07 +0100

Tim;
Thanks for digging into this and coming up with a quick fix. 
I'm not surprised people are upset; this seems like kind of an
arbitrary restriction. Thanks again,
Brad

> Hi Brad,
> 
> Hmmm - there is a fairly long thread on the Debian mailing list with
> people complaining about this change being added suddenly, but it looks
> like I can renumber as, eg., "1:1bl-0" so that should be OK.  I'll try
> and do it in the next few days.
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2011-05-19 at 20:38 +0100, Brad Chapman wrote:
> > Tim;
> > I was working on ugrading to the latest Ubuntu and apt is unhappy
> > about some of the version numbers in Bio-Linux packages. They start
> > with bl instead of numbers, so apt-get errors out with:
> > 
> > error in Version string 'bl1-0': version number does not start with digit
> > 
> > At least these packages are affected:
> > 
> > bio-linux-clustal
> > bio-linux-sequin
> > bio-linux-jalview
> > 
> > If there is a better place to send bug reports to than you just let
> > me know and I can forward there. Thanks,
> > Brad
> 
> -- 
> 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
> 
> -- 
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
> 

-- 
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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From a.travis at abdn.ac.uk  Fri Jun 10 05:57:32 2011
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Fri, 10 Jun 2011 10:57:32 +0100
Subject: [Bio-linux-dev] MrBayes and OpenMPI
Message-ID: <4DF1EA8C.4040800@abdn.ac.uk>

Hi, Tim.

I've created an OpenMPI version of bio-linux-mrbayes-multi:

Bye,

   Tony.

> aptitude download bio-linux-mrbayes-multi
> dpkg-unpack bio-linux-mrbayes-multi_3.1.2-1_amd64.deb
> cd bio-linux-mrbayes-multi_3.1.2-1_amd64/usr/local/bioinf/mrbayes/mrbayes-multi-3.1.2
> make
> cd ../../../DEBIAN
> vim control # see patch below
> cd ../..
> mv -i bio-linux-mrbayes-multi_3.1.2-1_amd64 bio-linux-mrbayes-multi_3.1.2-2_amd64
> dpkg-repack bio-linux-mrbayes-multi_3.1.2-2_amd64

You can download the deb at:

> http://bioinformatics.rri.sari.ac.uk/download/bio-linux-mrbayes-multi_3.1.2-2_amd64.deb

Patch to remove mpich2 dependency:

--- bio-linux-mrbayes-multi_3.1.2-1_amd64/DEBIAN/control	2010-03-23 
16:00:24.000000000 +0000
+++ bio-linux-mrbayes-multi_3.1.2-2_amd64/DEBIAN/control	2011-06-09 
15:24:59.403563781 +0100
@@ -1,11 +1,11 @@
  Package: bio-linux-mrbayes-multi
-Version: 3.1.2-1
+Version: 3.1.2-2
  Section: science
  Priority: optional
-Depends: bio-linux-base-directories (>= 1.0-1), mpich2, libopenmpi-dev
+Depends: bio-linux-base-directories (>= 1.0-1), libopenmpi-dev
  Architecture: amd64
  Installed-Size: 7436
-Maintainer: Oliver Buckley <helpdesk at nebc.nox.ac.uk>
+Maintainer: Tony Travis <a.travis at abdn.ac.uk>
  Provides: bio-linux-mrbayes-multi
-Description: Multiprocessor version of MrBayes.
+Description: OpenMPI version of MrBayes.
   Bayesian inference of phylogeny is based upon a quantity called the 
posterior probability distribution of trees, which is the probability of 
a tree conditioned on the observations. This version has been compiled 
to run on multiple processors.

Here are my easy-to-remember dpkg-unpack/dpkg-repack scripts:

#!/bin/sh
# @(#)dpkg-unpack  2007-07-12  A.J.Travis

#
# Unpack Debian package ready to rebuild
#
package=$1
extract=`basename $package .deb`
dpkg-deb -x ${package} ${extract}
dpkg-deb -e ${package} ${extract}/DEBIAN

#!/bin/sh
# @(#)dpkg-repack  2007-03-29  A.J.Travis

#
# Re-pack unpacked Debian package
#
package=$1
dpkg-deb -b ${package}

-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk


From tbooth at ceh.ac.uk  Thu Jun 16 12:04:17 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 16 Jun 2011 17:04:17 +0100
Subject: [Bio-linux-dev] MrBayes and OpenMPI
In-Reply-To: <4DF1EA8C.4040800@abdn.ac.uk>
References: <4DF1EA8C.4040800@abdn.ac.uk>
Message-ID: <1308240257.4584.8821.camel@barsukas>

Hi Tony,

> I've created an OpenMPI version of bio-linux-mrbayes-multi:

Thanks - I'd been a bit naive regarding how OpenMPI and MPICH
interacted, or failed to interact.  It looks like my ApliconNoise
package is suffering from similar problems and I'll need to fix that
too.
I've rebuilt mb-multi as per your instructions, so I can now type:

mpirun.openmpi -np 4 mb-multi

I don't think we need the -dev dependency for OpenMPI so I've opted for.

"Depends: openmpi-bin"

I realise this may confuse anyone who is already happily using mpich and
mpd so I've held off releasing the package until I put a note on the
Bio-Linux list.

Cheers,

TIM

> Bye,
> 
>    Tony.
> 
> > aptitude download bio-linux-mrbayes-multi
> > dpkg-unpack bio-linux-mrbayes-multi_3.1.2-1_amd64.deb
> > cd bio-linux-mrbayes-multi_3.1.2-1_amd64/usr/local/bioinf/mrbayes/mrbayes-multi-3.1.2
> > make
> > cd ../../../DEBIAN
> > vim control # see patch below
> > cd ../..
> > mv -i bio-linux-mrbayes-multi_3.1.2-1_amd64 bio-linux-mrbayes-multi_3.1.2-2_amd64
> > dpkg-repack bio-linux-mrbayes-multi_3.1.2-2_amd64
> 
> You can download the deb at:
> 
> > http://bioinformatics.rri.sari.ac.uk/download/bio-linux-mrbayes-multi_3.1.2-2_amd64.deb
> 
> Patch to remove mpich2 dependency:
> 
> --- bio-linux-mrbayes-multi_3.1.2-1_amd64/DEBIAN/control	2010-03-23 
> 16:00:24.000000000 +0000
> +++ bio-linux-mrbayes-multi_3.1.2-2_amd64/DEBIAN/control	2011-06-09 
> 15:24:59.403563781 +0100
> @@ -1,11 +1,11 @@
>   Package: bio-linux-mrbayes-multi
> -Version: 3.1.2-1
> +Version: 3.1.2-2
>   Section: science
>   Priority: optional
> -Depends: bio-linux-base-directories (>= 1.0-1), mpich2, libopenmpi-dev
> +Depends: bio-linux-base-directories (>= 1.0-1), libopenmpi-dev
>   Architecture: amd64
>   Installed-Size: 7436
> -Maintainer: Oliver Buckley <helpdesk at nebc.nox.ac.uk>
> +Maintainer: Tony Travis <a.travis at abdn.ac.uk>
>   Provides: bio-linux-mrbayes-multi
> -Description: Multiprocessor version of MrBayes.
> +Description: OpenMPI version of MrBayes.
>    Bayesian inference of phylogeny is based upon a quantity called the 
> posterior probability distribution of trees, which is the probability of 
> a tree conditioned on the observations. This version has been compiled 
> to run on multiple processors.
> 
> Here are my easy-to-remember dpkg-unpack/dpkg-repack scripts:
> 
> #!/bin/sh
> # @(#)dpkg-unpack  2007-07-12  A.J.Travis
> 
> #
> # Unpack Debian package ready to rebuild
> #
> package=$1
> extract=`basename $package .deb`
> dpkg-deb -x ${package} ${extract}
> dpkg-deb -e ${package} ${extract}/DEBIAN
> 
> #!/bin/sh
> # @(#)dpkg-repack  2007-03-29  A.J.Travis
> 
> #
> # Re-pack unpacked Debian package
> #
> package=$1
> dpkg-deb -b ${package}
> 

-- 
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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From florent.angly at gmail.com  Fri Jun 17 20:18:28 2011
From: florent.angly at gmail.com (Florent Angly)
Date: Sat, 18 Jun 2011 10:18:28 +1000
Subject: [Bio-linux-dev] Problem with a package during update
Message-ID: <4DFBEED4.5070409@gmail.com>

Hi,

Today, I ran this command:
> sudo apt-get update
And got this error:
> Reading package lists... Error!
> E: Problem parsing dependency Depends
> E: Error occurred while processing bio-linux-mira-3rd-party (NewVersion2)
> E: Problem with MergeList 
> /var/lib/apt/lists/nebc.nox.ac.uk_bio-linux_dists_unstable_bio-linux_binary-amd64_Packages
> E: The package lists or status file could not be parsed or opened.
Apparently, something is wrong with the package 
bio-linux-mira-3rd-party, and it prevents apt-get update and upgrade to 
complete.

Florent


From tbooth at ceh.ac.uk  Mon Jun 20 04:57:30 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 20 Jun 2011 09:57:30 +0100
Subject: [Bio-linux-dev] Problem with a package during update
In-Reply-To: <4DFBEED4.5070409@gmail.com>
References: <4DFBEED4.5070409@gmail.com>
Message-ID: <1308560250.4584.13342.camel@barsukas>

Morning,

Oops - I only made a trivial change to the package, but when you are
writing out DEBIAN/control files manually it is very easy indeed to
upset APT.  Everything should be fixed again now.

TIM

On Sat, 2011-06-18 at 01:18 +0100, Florent Angly wrote:
> Hi,
> 
> Today, I ran this command:
> > sudo apt-get update
> And got this error:
> > Reading package lists... Error!
> > E: Problem parsing dependency Depends
> > E: Error occurred while processing bio-linux-mira-3rd-party (NewVersion2)
> > E: Problem with MergeList 
> > /var/lib/apt/lists/nebc.nox.ac.uk_bio-linux_dists_unstable_bio-linux_binary-amd64_Packages
> > E: The package lists or status file could not be parsed or opened.
> Apparently, something is wrong with the package 
> bio-linux-mira-3rd-party, and it prevents apt-get update and upgrade to 
> complete.
> 
> Florent
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.