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

[Michael Friendly]

On 2/1/2011 11:35 PM, Dirk Eddelbuettel wrote:
> On 1 February 2011 at 10:56, Michael Friendly wrote:
> | On 1/31/2011 12:14 PM, Dirk Eddelbuettel wrote:
> |>  On 31 January 2011 at 09:04, Michael Friendly wrote:
> |>  | I'm not any further ahead in trying to update vcd from 1.2-7 to 1.2-9.
> |>  | How can I resolve this?
> | OK:   I used (as sudo)
> | install.packages("vcd"),
> | and it seemed to work;  however old.packages() still reports vcd at
> | 1.2-7.  Why is that?
>
> You supplied no information that would enable us to tell you.
>
> What does '.libPaths()' show?
>
Sorry about that:

 > .libPaths()
[1] "/home/friendly/lib/R/library"  "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"       "/usr/lib/R/library"
[5] "/usr/lib64/R/library"
 > old.packages()
     Package LibPath                   Installed Built    ReposVer
rgl "rgl"   "/usr/lib/R/site-library" "0.89"    "2.10.1" "0.92.798"
vcd "vcd"   "/usr/lib/R/site-library" "1.2-7"   "2.9.2"  "1.2-9"
     Repository
rgl "http://probability.ca/cran/src/contrib"
vcd "http://probability.ca/cran/src/contrib"
 > library(vcd)
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
 > sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)

...
attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] vcd_1.2-9        colorspace_1.0-1 MASS_7.3-9

loaded via a namespace (and not attached):
[1] tools_2.12.1

So, apparently from sudo R, install.packages("vcd") installed to 
/usr/local/lib/R/site-library,
but old.packages() only finds the copy installed by apt-get install 
r-cran-vcd in
/usr/lib/R/site-library.
According to the docs, old.packages() *should* search through all known 
trees in .libPaths


labtest: ~ % ll /usr/local/lib/R/site-library
total 12
drwxr-sr-x 8 root staff 4096 2011-01-30 13:01 colorspace
-rw-r--r-- 1 root staff 1179 2011-01-30 13:01 R.css
drwxr-sr-x 9 root staff 4096 2011-01-31 13:00 vcd


-- 
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