[R-sig-Debian] updating r-cran- packages on a new Ubuntu lucid system

Michael Friendly friendly at yorku.ca
Mon Jan 31 15:04:40 CET 2011

I'm not any further ahead in trying to update vcd from 1.2-7 to 1.2-9. 
How can I resolve this?

- Tried removing r-cran-colorspace, but aborted that because apt was 
going to remove other packages
that depend on colorspace. It also tells me that r-cran-effects is BROKEN

labtest: /usr/lib # aptitude remove r-cran-colorspace
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading extended state information
Initializing package states... Done
The following packages are BROKEN:
The following packages will be REMOVED:
0 packages upgraded, 0 newly installed, 1 to remove and 3 not upgraded.
Need to get 0B of archives. After unpacking 885kB will be freed.
The following packages have unmet dependencies:
r-cran-effects: Depends: r-cran-colorspace but it is not installable
The following actions will resolve these dependencies:

Remove the following packages:

Score is 188

Accept this solution? [Y/n/q/?] q
Abandoning all efforts to resolve these dependencies.

- Tried again to update.packages(). Works for car, but not vcd because 
colorspace was built for R 2.9.2

labtest: /usr/lib # R

R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
 > update.packages(ask=TRUE)
car :
Version 2.0-8 installed in /usr/lib/R/site-library
Version 2.0-9 available at http://probability.ca/cran
Update (y/N/c)? y
rgl :
Version 0.89 installed in /usr/lib/R/site-library
Version 0.92.798 available at http://probability.ca/cran
Update (y/N/c)? n
vcd :
Version 1.2-7 installed in /usr/lib/R/site-library
Version 1.2-9 available at http://probability.ca/cran
Update (y/N/c)? y
trying URL 'http://probability.ca/cran/src/contrib/car_2.0-9.tar.gz'
Content type 'application/x-gzip' length 358907 bytes (350 Kb)
opened URL
downloaded 350 Kb

trying URL 'http://probability.ca/cran/src/contrib/vcd_1.2-9.tar.gz'
Content type 'application/x-gzip' length 1104510 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb

* installing *source* package ‘car’ ...
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (car)
* installing *source* package ‘vcd’ ...
** R
** data
** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Error : package 'colorspace' was built before R 2.10.0: please re-install it
ERROR: lazy loading failed for package ‘vcd’
* removing ‘/usr/lib/R/site-library/vcd’
* restoring previous ‘/usr/lib/R/site-library/vcd’

The downloaded packages are in
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = 
contriburl, :
installation of package 'vcd' had non-zero exit status

On 1/30/2011 9:40 PM, Dirk Eddelbuettel wrote:
> For what it's worth, I use the scriipt below (via ~/bin/update.r) which is
> also an example script in the littler package.
> It _explicitly_ restricts the update to
>      /usr/local/lib/R/site-library
> so that the update from R is kept separate from the update via the Debian or
> Ubuntu package manager.
> Hope this helps,  Dirk
> #!/usr/bin/r -t
> #
> # a simple example to update packages in /usr/local/lib/R/site-library
> # parameters are easily adjustable
> ## adjust as necessary, see help('download.packages')
> repos<- "http://cran.r-project.org"
> ## or use BioC's repo list if Biobase is installed:
> suppressMessages(rc<- require(Biobase))
> if (rc) {
>    repos<- Biobase:::biocReposList()
> }
> ## this makes sense on Debian where no package touch /usr/local
> lib.loc<- "/usr/local/lib/R/site-library"
> ## simply unrolling of all unlink over all files 'repos*' in $TMP
> clearCache<- function() {
>    sapply(list.files(path=tempdir(), pattern="libloc*", full.names=TRUE), unlink)
> }
> ## Always clear caches of remote and local packages
> clearCache()
> ## r use requires non-interactive use
> update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc)
> ## Always clear caches of remote and local packages
> clearCache()

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

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