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

[Tony Travis]

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.