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

[Michael Friendly]

On 1/30/2011 3:21 PM, Michael Rutter wrote:


<-- snip -->
> <-- Cut -->
>
>>> 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.
> Yes, perhaps that command does need to be updated on cran.  The best
> thing to do is run update.packages() with no arguments so all library
> locations can be checked for updates.
>
Yes, my thought too:  in the README, just say "A routine update can then 
be undertaken from R using ..."

update.packages()

<-- snip -->

>> 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?
>>
> When you first listed the installed packages, colorspace was not among
> them.  Not sure why that is.  My suggestion would be to remove
> colorspace via apt-get, then install it again from within R with
> install.packages().
>
>
r-cran-colorspace was actually installed via apt-get as a dependency of 
one of the other r-cran packages I
installed initially.  What I showed was that it wasn't listed among 
old.packages().  I'll try your suggestion,
but what made me suspicious was that vcd was the only r-cran package 
listed as Built: 2.9.2, so I think
this is a more likely source of the problem.



-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
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