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

[Dirk Eddelbuettel]

On 2 February 2011 at 08:48, Michael Friendly wrote:
| 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"

Ok, so you have a local per-user library entry. That should not block things,

However, it is the standard setup and not what I personally do, but that
shouldn't matter all that match.

|  > 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

I would try to identify which version of which library in which location you
think gets in your way, and then remove that.

If something was installed using apt / dpkg / aptitude / ... (ie in
/usr/lib/R or /usr/lib64/R [ which is the same ] then use that tool to remove
it. 

Then try installing _by specifying a target directory_.  I sent you two
scripts that help me; you can use R commands too of course by do specify a
target directory, make sure you have your build dependies set etc pp.

Good luck.

Dirk, snowed-in
 
| 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
| 
| 

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com