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

[Michael Friendly]

I am setting up a new Ubuntu lucid system on a Dell Precision T3500, 
quad core, E5507, x86_64 box
and am having some difficulty updating r-cran packages as per the 
instructions at
http://cran.us.r-project.org/bin/linux/ubuntu
Perhaps the instructions are incomplete or wrong, or I've misunderstood 
something,
and/or I've run into a dependency problem among r-cran- packages, vcd in 
particular.

As per instructions, I installed r-base and r-base-dev via
sudo apt-get install r-base,
giving me R 2.12-1, then installed a bunch of my favorite r-cran 
packages. All OK

Starting R as root, I check for packages with available updates:

 > utils::old.packages()
Package LibPath Installed Built
car "car" "/usr/lib/R/site-library" "1.2-16" "2.10.0"
gtools "gtools" "/usr/lib/R/site-library" "2.6.1" "2.10.0"
latticeExtra "latticeExtra" "/usr/lib/R/site-library" "0.6-5" "2.10.1"
lmtest "lmtest" "/usr/lib/R/site-library" "0.9-26" "2.10.0"
multcomp "multcomp" "/usr/lib/R/site-library" "1.1-4" "2.10.1"
mvtnorm "mvtnorm" "/usr/lib/R/site-library" "0.9-8" "2.10.1"
Rcmdr "Rcmdr" "/usr/lib/R/site-library" "1.5-4" "2.10.1"
relimp "relimp" "/usr/lib/R/site-library" "1.0-1" "2.10.0"
rgl "rgl" "/usr/lib/R/site-library" "0.89" "2.10.1"
sandwich "sandwich" "/usr/lib/R/site-library" "2.2-5" "2.10.1"
sm "sm" "/usr/lib/R/site-library" "2.2-3" "2.10.0"
strucchange "strucchange" "/usr/lib/R/site-library" "1.3-7" "2.10.0"
vcd "vcd" "/usr/lib/R/site-library" "1.2-7" "2.9.2"
zoo "zoo" "/usr/lib/R/site-library" "1.6-2" "2.10.0"
class "class" "/usr/lib/R/library" "7.3-2" "2.11.0"
MASS "MASS" "/usr/lib/R/library" "7.3-5" "2.11.0"
class "class" "/usr/lib64/R/library" "7.3-2" "2.11.0"
MASS "MASS" "/usr/lib64/R/library" "7.3-5" "2.11.0"
ReposVer Repository
car "2.0-8" "http://probability.ca/cran/src/contrib"
gtools "2.6.2" "http://probability.ca/cran/src/contrib"
latticeExtra "0.6-14" "http://probability.ca/cran/src/contrib"
lmtest "0.9-27" "http://probability.ca/cran/src/contrib"
multcomp "1.2-5" "http://probability.ca/cran/src/contrib"
mvtnorm "0.9-96" "http://probability.ca/cran/src/contrib"
Rcmdr "1.6-3" "http://probability.ca/cran/src/contrib"
relimp "1.0-2" "http://probability.ca/cran/src/contrib"
rgl "0.92.798" "http://probability.ca/cran/src/contrib"
sandwich "2.2-6" "http://probability.ca/cran/src/contrib"
sm "2.2-4.1" "http://probability.ca/cran/src/contrib"
strucchange "1.4-3" "http://probability.ca/cran/src/contrib"
vcd "1.2-9" "http://probability.ca/cran/src/contrib"
zoo "1.6-4" "http://probability.ca/cran/src/contrib"
class "7.3-3" "http://probability.ca/cran/src/contrib"
MASS "7.3-9" "http://probability.ca/cran/src/contrib"
class "7.3-3" "http://probability.ca/cran/src/contrib"
MASS "7.3-9" "http://probability.ca/cran/src/contrib"

But then I try:

 > update.packages(lib.loc = "/usr/local/lib/R/site-library")

and nothing happens. This is contrary to the statement that "A routine 
update can then be undertaken from R using ..."
the above command.

Not mentioning lib.loc works, but I get errors for two packages: rgl and 
vcd.
rgl depends on an X11 server, and I'm installing remotely from a Windows 
terminal client, so I can understand
this. But I can't understand the error regarding vcd, or how to correct 
this.


 > update.packages(ask=TRUE)
car :
Version 1.2-16 installed in /usr/lib/R/site-library
Version 2.0-8 available at http://probability.ca/cran
Update (y/N/c)? y
gtools :
Version 2.6.1 installed in /usr/lib/R/site-library
Version 2.6.2 available at http://probability.ca/cran
Update (y/N/c)? y
...

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/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 ‘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
‘/tmp/RtmpihHKKK/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = 
contriburl, :
installation of package 'vcd' had non-zero exit status
 >

colorspace was initially installed via apt-get install. I also tried the 
following within R. It seemed to
work, but didn't make any difference in update.packages() for vcd.

 > install.packages("colorspace")
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://probability.ca/cran/src/contrib/colorspace_1.0-1.tar.gz'
Content type 'application/x-gzip' length 233865 bytes (228 Kb)
opened URL
==================================================
downloaded 228 Kb

* installing *source* package ‘colorspace’ ...
** libs
gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c colorspace.c 
-o colorspace.o
gcc -shared -o colorspace.so colorspace.o -L/usr/lib64/R/lib -lR
installing to /usr/local/lib/R/site-library/colorspace/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "colorspace"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (colorspace)

Relevant version information on vcd and colorspace:

 > packageDescription("vcd", fields = c("Package", "Version", "Depends"))
Package: vcd
Version: 1.2-7
Depends: R (>= 2.4.0), MASS, grid, colorspace

 > packageDescription("colorspace", fields = c("Package", "Version", 
"Depends"))
Package: colorspace
Version: 1.0-1
Depends: R (>= 2.0.0), methods

So, vcd 1.2-7 from r-cran-vcd was built for R 2.9.2. vcd 1.2-9 is 
available, but I can't install it.
How can I correct this?


-- 

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