[R-sig-Debian] dependency errors upgrading to 2.2.1-0sarge1

[Michael Friendly]

Running a current, standard debian stable, I added
deb http://cran.R-project.org/bin/linux/debian stable/
to /apt/sources.list to get the current backport stable distro.

When I installed r-base, apt-get wanted to remove all my previous 
r-cran-* packages
and I let it, but encountered conflicts with things in r-recommended 
that I've been
unable to resolve.  It first showed up as (complete transcript below):

dpkg: r-cran-foreign: dependency problems, but removing anyway as you 
request:
 r-recommended depends on r-cran-foreign (>= 0.7-2).
Removing r-cran-foreign ...

----- transcript ------
euclid: ~ # su - root
euclid:~# apt-get install r-base
Reading Package Lists... Done
Building Dependency Tree... Done
The following extra packages will be installed:
  r-base-core r-recommended
Suggested packages:
  r-doc-info r-mathlib
Recommended packages:
  r-base-html r-base-dev
The following packages will be REMOVED:
  r-cran-boot r-cran-cluster r-cran-design r-cran-effects r-cran-foreign
  r-cran-hmisc r-cran-kernsmooth r-cran-lattice r-cran-mgcv r-cran-nlme
  r-cran-rcmdr r-cran-rpart r-cran-survival r-cran-vr
The following packages will be upgraded:
  r-base r-base-core r-recommended
3 upgraded, 0 newly installed, 14 to remove and 37 not upgraded.
Need to get 14.0MB of archives.
After unpacking 4391kB disk space will be freed.
Do you want to continue? [Y/n] y
Get:1 http://cran.R-project.org stable/ r-base 2.2.1-0sarge1 [21.3kB]
Get:2 http://cran.R-project.org stable/ r-recommended 2.2.1-0sarge1 [6143kB]
Get:3 http://cran.R-project.org stable/ r-base-core 2.2.1-0sarge1 [7854kB]
Fetched 14.0MB in 56s (247kB/s)
(Reading database ... 129141 files and directories currently installed.)
Removing r-cran-rcmdr ...
Removing r-cran-design ...
Removing r-cran-hmisc ...
Removing r-cran-effects ...
dpkg: r-cran-foreign: dependency problems, but removing anyway as you 
request:
 r-recommended depends on r-cran-foreign (>= 0.7-2).
Removing r-cran-foreign ...
dpkg: r-cran-kernsmooth: dependency problems, but removing anyway as you 
request:
 r-recommended depends on r-cran-kernsmooth (>= 2.2.14); however:
  Package r-cran-kernsmooth is to be removed.
Removing r-cran-kernsmooth ...
dpkg: r-cran-mgcv: dependency problems, but removing anyway as you request:
 r-recommended depends on r-cran-mgcv (>= 1.1.5); however:
  Package r-cran-mgcv is to be removed.
Removing r-cran-mgcv ...
dpkg: r-cran-vr: dependency problems, but removing anyway as you request:
 r-cran-relimp depends on r-cran-vr.
 r-recommended depends on r-cran-vr (>= 7.2.8); however:
  Package r-cran-vr is to be removed.
Removing r-cran-vr ...
dpkg: r-cran-nlme: dependency problems, but removing anyway as you request:
 r-recommended depends on r-cran-nlme (>= 3.1.52); however:
  Package r-cran-nlme is to be removed.
Removing r-cran-nlme ...
dpkg: r-cran-lattice: dependency problems, but removing anyway as you 
request:
 r-recommended depends on r-cran-lattice (>= 0.10.11); however:
  Package r-cran-lattice is to be removed.
Removing r-cran-lattice ...
dpkg: r-cran-rpart: dependency problems, but removing anyway as you request:
 r-recommended depends on r-cran-rpart (>= 3.1.20); however:
  Package r-cran-rpart is to be removed.
Removing r-cran-rpart ...
dpkg: r-cran-survival: dependency problems, but removing anyway as you 
request:
 r-recommended depends on r-cran-survival (>= 2.13.2-1); however:
  Package r-cran-survival is to be removed.
 r-cran-boot depends on r-cran-survival.
Removing r-cran-survival ...
dpkg: r-cran-boot: dependency problems, but removing anyway as you request:
 r-recommended depends on r-cran-boot (>= 1.2.19).
Removing r-cran-boot ...
(Reading database ... 125008 files and directories currently installed.)
Preparing to replace r-base 2.1.0-1 (using 
.../r-base_2.2.1-0sarge1_all.deb) ...Unpacking replacement r-base ...
dpkg: r-cran-cluster: dependency problems, but removing anyway as you 
request:
 r-recommended depends on r-cran-cluster (>= 1.9.6-2); however:
  Package r-cran-cluster is to be removed.
(Reading database ... 125008 files and directories currently installed.)
Removing r-cran-cluster ...
(Reading database ... 124781 files and directories currently installed.)
Preparing to replace r-recommended 2.1.0-1 (using 
.../r-recommended_2.2.1-0sarge1_i386.deb) ...
Unpacking replacement r-recommended ...
dpkg: error processing 
/var/cache/apt/archives/r-recommended_2.2.1-0sarge1_i386.deb (--unpack):
 trying to overwrite `/usr/lib/R/library/grid/R/grid', which is also in 
package r-base-core
dpkg-deb: subprocess paste killed by signal (Broken pipe)
Preparing to replace r-base-core 2.1.0-1 (using 
.../r-base-core_2.2.1-0sarge1_i386.deb) ...
Unpacking replacement r-base-core ...
Errors were encountered while processing:
 /var/cache/apt/archives/r-recommended_2.2.1-0sarge1_i386.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

My next step wass to try aapt-get install -f, but this bombed too...

euclid:~# apt-get install -f
Reading Package Lists... Done
Building Dependency Tree... Done
Correcting dependencies... Done
The following extra packages will be installed:
  r-recommended
The following packages will be upgraded:
  r-recommended
1 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
2 not fully installed or removed.
Need to get 0B/6143kB of archives.
After unpacking 24.4MB of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 125000 files and directories currently installed.)
Preparing to replace r-recommended 2.1.0-1 (using 
.../r-recommended_2.2.1-0sarge1_i386.deb) ...
Unpacking replacement r-recommended ...
dpkg: error processing 
/var/cache/apt/archives/r-recommended_2.2.1-0sarge1_i386.deb (--unpack):
 trying to overwrite `/usr/lib/R/library/grid/latex/Grid.tex', which is 
also in package r-base-latex
dpkg-deb: subprocess paste killed by signal (Broken pipe)
Errors were encountered while processing:
 /var/cache/apt/archives/r-recommended_2.2.1-0sarge1_i386.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

Finally, I tried to reinstall some of the r-cran packages:

euclid:~# apt-get install  r-cran-boot r-cran-cluster r-cran-design 
r-cran-effects r-cran-foreign
Reading Package Lists... Done
Building Dependency Tree... Done
You might want to run `apt-get -f install' to correct these:
The following packages have unmet dependencies:
  r-base: Depends: r-recommended (= 2.2.1-0sarge1) but 2.1.0-1 is to be 
installed
  r-cran-boot: Depends: r-cran-survival
  r-cran-design: Depends: r-cran-hmisc but it is not going to be installed
                 Depends: r-cran-survival
  r-cran-effects: Depends: r-cran-lattice (>= 0.10.11)
  r-cran-relimp: Depends: r-cran-vr
  r-recommended: Depends: r-base-core (= 2.1.0-1) but 2.2.1-0sarge1 is 
to be installed
                 Depends: r-cran-kernsmooth (>= 2.2.14)
                 Depends: r-cran-lattice (>= 0.10.11)
                 Depends: r-cran-mgcv (>= 1.1.5)
                 Depends: r-cran-nlme (>= 3.1.52)
                 Depends: r-cran-rpart (>= 3.1.20)
                 Depends: r-cran-survival (>= 2.13.2-1)
                 Depends: r-cran-vr (>= 7.2.8)
E: Unmet dependencies. Try 'apt-get -f install' with no packages (or 
specify a solution).

At this point, I'm stumped.  How do I get everything back working again?

-- 
Michael Friendly     Email: friendly at yorku.ca 
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA