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 _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
