stable backport apt problem (solved)

Hi Dirk,

This is my attempt to re-create the problem.  I'm not so sure it is just 
a dependency problem now.  I think there is possibly an apt problem on 
my machine, combined with a problem with the dependencies where 
r-recommended is wanting its old dependencies at the same time as trying 
to replace them.

I removed all the r-\* packages, removed the backports line from 
/etc/apt/source.list, installed
r-base-core r-recommended r-base-dev r-mathlib
which went OK, then added the backport URL to sources.list again:

tolstoy:/home/king# apt-get upgrade
Reading Package Lists... Done
Building Dependency Tree... Done
The following packages have been kept back:
   kernel-image-2.6-686 r-base-dev
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.

tolstoy:/home/king# apt-get install r-base-dev
Reading Package Lists... Done
Building Dependency Tree... Done
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.

Since you only requested a single operation it is extremely likely that
the package is simply not installable and a bug report against
that package should be filed.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
   r-base-dev: Depends: r-base-core (= 2.3.0-0sarge1) but 2.1.0-1 is to 
be installed
E: Broken packages

tolstoy:/home/king# apt-get install r-base-core=2.3.0-0sarge1
Reading Package Lists... Done
Building Dependency Tree... Done
E: Version '2.3.0-0sarge1' for 'r-base-core' was not found

tolstoy:/home/king# apt-cache show r-base-core
shows the following versions of r-base-core available

Version: 2.1.0-1
Version: 2.2.1-6

Even though 
/var/lib/apt/lists/cran.au.r-project.org_bin_linux_debian_stable_Packages
shows version 2.3.0-0sarge1
and I can download it with wget

tolstoy:/home/king# grep 'Package: r-base-core' /var/lib/apt/lists/*
/var/lib/apt/lists/cran.au.r-project.org_bin_linux_debian_stable_Packages:Package: 
r-base-core
(has Version: 2.3.0-0sarge1)
/var/lib/apt/lists/ftp.au.debian.org_debian_dists_stable_main_binary-i386_Packages:Package: 
r-base-core
(has Version: 2.1.0-1)
/var/lib/apt/lists/ftp.au.debian.org_debian_dists_testing_main_binary-i386_Packages:Package: 
r-base-core
(has Version: 2.2.1-6)

Even if I remove the testing line from the sources.list, apt-cache and 
apt-get will only see the stable version

Then to the manual-download solution:

# dpkg -i r-base-core_2.3.0-0sarge1_i386.deb
(Reading database ... 62319 files and directories currently installed.)
Preparing to replace r-base-core 2.1.0-1 (using 
.../r-base-core_2.3.0-0sarge1_i386.deb) ...
Unpacking replacement r-base-core ...
Setting up r-base-core (2.3.0-0sarge1) ...
Installing new version of config file /etc/R/Makeconf ...

Configuration file `/etc/R/Renviron'
  ==> Modified (by you or by a script) since installation.
  ==> Package distributor has shipped an updated version.
    What would you like to do about it ?  Your options are:
     Y or I  : install the package maintainer's version
     N or O  : keep your currently-installed version
       D     : show the differences between the versions
       Z     : background this process to examine the situation
  The default action is to keep your current version.
*** Renviron (Y/I/N/O/D/Z) [default=N] ?

# dpkg -i /nfs/r-mathlib_2.3.0-0sarge1_i386.deb
(Reading database ... 62472 files and directories currently installed.)
Preparing to replace r-mathlib 2.1.0-1 (using 
.../r-mathlib_2.3.0-0sarge1_i386.deb) ...
Unpacking replacement r-mathlib ...
Setting up r-mathlib (2.3.0-0sarge1) ...

# dpkg -i /nfs/r-recommended_2.3.0-0sarge1_i386.deb
dpkg: considering removing r-cran-boot in favour of r-recommended ...
dpkg: no, cannot remove r-cran-boot (--auto-deconfigure will help):
  r-recommended depends on r-cran-boot (>= 1.2.19)
   r-cran-boot is to be removed.
dpkg: regarding .../r-recommended_2.3.0-0sarge1_i386.deb containing 
r-recommended:
  r-recommended conflicts with r-cran-boot
   r-cran-boot (version 1.2.22-1) is installed.
dpkg: error processing /nfs/r-recommended_2.3.0-0sarge1_i386.deb 
(--install):
  conflicting packages - not installing r-recommended
Errors were encountered while processing:
  /nfs/r-recommended_2.3.0-0sarge1_i386.deb

Try auto-deconfigure as recommended:

tolstoy:/home/king# dpkg -i --auto-deconfigure 
/nfs/r-recommended_2.3.0-0sarge1_i386.deb
dpkg: considering removing r-cran-boot in favour of r-recommended ...
dpkg: yes, will remove r-cran-boot in favour of r-recommended.
(Reading database ... 62468 files and directories currently installed.)
Preparing to replace r-recommended 2.1.0-1 (using 
.../r-recommended_2.3.0-0sarge1_i386.deb) ...
De-configuring r-recommended, so that we can remove r-cran-boot ...
Unpacking replacement r-recommended ...
Replacing files in old package r-cran-kernsmooth ...
Replacing files in old package r-cran-vr ...
Replacing files in old package r-cran-cluster ...
Replacing files in old package r-cran-foreign ...
Replacing files in old package r-cran-lattice ...
Replacing files in old package r-cran-mgcv ...
Replacing files in old package r-cran-nlme ...
Replacing files in old package r-cran-rpart ...
Replacing files in old package r-cran-survival ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
More than one copy of package r-recommended has been unpacked
  in this run !  Only configuring it once.
Setting up r-recommended (2.3.0-0sarge1) ...

tolstoy:/home/king# apt-get -f install
Reading Package Lists... Done
Building Dependency Tree... Done
Correcting dependencies... Done
The following extra packages will be installed:
   r-base-dev
The following packages will be REMOVED:
   r-cran-cluster r-cran-foreign r-cran-kernsmooth r-cran-lattice 
r-cran-mgcv
   r-cran-nlme r-cran-rpart r-cran-survival r-cran-vr
The following packages will be upgraded:
   r-base-dev
1 upgraded, 0 newly installed, 9 to remove and 1 not upgraded.
Need to get 0B/2208B of archives.
After unpacking 19.0MB disk space will be freed.
Do you want to continue? [Y/n]
Removing r-cran-kernsmooth ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
Removing r-cran-mgcv ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
Removing r-cran-vr ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
Removing r-cran-nlme ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
Removing r-cran-lattice ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
Removing r-cran-rpart ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
Removing r-cran-survival ...
Ignoring deprecated call to build-help.pl from postinst or postrm script.
(Reading database ... 62787 files and directories currently installed.)
Preparing to replace r-base-dev 2.1.0-1 (using 
.../r-base-dev_2.3.0-0sarge1_all.deb) ...
Unpacking replacement r-base-dev ...
Setting up r-base-dev (2.3.0-0sarge1) ...
tolstoy:/home/king# apt-get install r-base
Reading Package Lists... Done
Building Dependency Tree... Done
Suggested packages:
   ess r-doc-info r-doc-pdf r-doc-html
Recommended packages:
   r-base-html r-base-latex
The following NEW packages will be installed:
   r-base
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 0B/22.8kB of archives.
After unpacking 57.3kB of additional disk space will be used.
Selecting previously deselected package r-base.
(Reading database ... 62789 files and directories currently installed.)
Unpacking r-base (from .../r-base_2.3.0-0sarge1_all.deb) ...
Setting up r-base (2.3.0-0sarge1) ...

stable backport apt problem (solved)

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