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

[Michael Rutter]

On 01/30/2011 02:30 PM, Michael Friendly wrote:
> 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"

<-- 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.

> 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?
> 

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().

That may solve your problem,
Michael



-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter