[Bio-linux-dev] Problems upgrading Ubuntu 12.04.3 to Bio-Linux 7

[Tim Booth]

Hi Tony,

Thanks for that.  I renamed tigr-glimmer and forgot to change the
script, but have fixed it now.

With R, when Bio-Linux 7 came out it made sense that you could choose to
use either the R from Ubuntu or the latest one from CRAN, but now you
really need R 3.0 so the repo should always be installed.  I'll fix that
later.

Cheers,

TIM

On Sun, 2013-11-03 at 22:45 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> I encountered two problems today when upgrading a recent install of
> Ubuntu 12.04.3 LTS to Bio-Linux 7 on my server "kitcat". First, the CRAN
> repository is not added, but is preserved if it is found. Second, there
> is a conflict between bio-linux-glimmer3 and tigr-glimmer.
> 
> Here is a quick summary of how I installed Bio-Linux 7:
> 
> HTH,
> 
>   Tony.
> 
> > Upgrade "kitcat" to Bio-Linux 7
> > # login on "kitcat" and sudo -i
> > root at kitcat:~# mkdir upgrade
> > cd upgrade
> > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh
> > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log
> > ...
> > root at kitcat:~/upgrade# tail -20 bl_do_update_to7.log
> > Building dependency tree...
> > Reading state information...
> > Some packages could not be installed. This may mean that you have
> > requested an impossible situation or if you are using the unstable
> > distribution that some required packages have not yet been created
> > or been moved out of Incoming.
> > The following information may help to resolve the situation:
> >
> > The following packages have unmet dependencies.
> >  galaxy-server-all : Depends: r-cran-prettyr but it is not going to be installed
> >                      Depends: r-cran-leaps but it is not going to be installed
> >                      Depends: r-cran-tcltk2 but it is not going to be installed
> >                      Depends: r-cran-rwave but it is not going to be installed
> >                      Depends: r-cran-wavethresh but it is not going to be installed
> >                      Depends: r-cran-waveslim but it is not going to be installed
> >                      Depends: r-cran-bitops but it is not going to be installed
> >                      Recommends: ucsc-tools-non-free but it is not installable
> >                      Recommends: laj but it is not installable
> > E: Unable to correct problems, you have held broken packages.
> > Not all packages installed properly - exiting.
> >
> > # add CRAN mirror - preserved, but not added by bl_do_update_to7.sh
> > vim /etc/apt/sources.list.d/nebc-bio-linux-precise.list
> > ...
> > deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/
> > ...
> >
> > # re-run
> > bl_do_update_to7.sh
> > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log
> > ...
> > Reading package lists...
> > Building dependency tree...
> > Reading state information...
> > 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> >
> > Verifying that everything installed...
> > bio-linux-glimmer3 failed to install
> > Not all packages installed properly - exiting.
> >
> > # check package dependencies
> > apt-cache depends bio-linux-glimmer3
> > root at kitcat:~/upgrade# apt-cache depends bio-linux-glimmer3
> > bio-linux-glimmer3
> >   Depends: glimmer3
> >   Conflicts: <bio-linux-glimmer>
> >   Conflicts: <bio-linux-glimmer:i386>
> >   Replaces: <bio-linux-glimmer>
> >   Replaces: <bio-linux-glimmer:i386>
> >   Replaces: tigr-glimmer
> >     glimmer3
> >   Replaces: tigr-glimmer:i386
> >     glimmer3:i386
> >
> > # download
> > bl_master_package_list.sh
> > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh
> >
> > # remove tigr-glimmer
> > vim bl_master_package_list.sh
> >
> > ...
> > /tigr-glimmer
> > dd
> > :wq
> >
> > # edit update script to run bl_master_package_list.sh locally
> >
> > vim bl_do_update_to7.sh
> >
> > ...
> > root at kitcat:~/upgrade# diff -Naur bl_do_update_to7.sh bl_do_update_to7.sh.orig
> > --- bl_do_update_to7.sh       2013-11-03 14:08:25.072271905 +0000
> > +++ bl_do_update_to7.sh.orig  2012-12-03 11:54:38.000000000 +0000
> > @@ -165,8 +165,7 @@
> >  # Now the main upgrade - fetch the script and run
> >  # runurl should come from the PPA
> >  apt-get install runurl
> > -#runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh"
> > -bash bl_master_package_list.sh
> > +runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh"
> >  if [ $? != 0 ] ; then
> >      echo "Not all packages installed properly - exiting."
> >      exit 1
> >
> > # run again with local modified
> > bl_master_package_list.sh
> > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log
> >
> 
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> 
> 
> 
> 
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> _______________________________________________
> 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