Michael Friendly
2011-Jan-30 19:30 UTC
[R-sig-Debian] updating r-cran- packages on a new Ubuntu lucid system
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"
ReposVer Repository
car "2.0-8" "http://probability.ca/cran/src/contrib"
gtools "2.6.2" "http://probability.ca/cran/src/contrib"
latticeExtra "0.6-14"
"http://probability.ca/cran/src/contrib"
lmtest "0.9-27" "http://probability.ca/cran/src/contrib"
multcomp "1.2-5" "http://probability.ca/cran/src/contrib"
mvtnorm "0.9-96" "http://probability.ca/cran/src/contrib"
Rcmdr "1.6-3" "http://probability.ca/cran/src/contrib"
relimp "1.0-2" "http://probability.ca/cran/src/contrib"
rgl "0.92.798" "http://probability.ca/cran/src/contrib"
sandwich "2.2-6" "http://probability.ca/cran/src/contrib"
sm "2.2-4.1" "http://probability.ca/cran/src/contrib"
strucchange "1.4-3" "http://probability.ca/cran/src/contrib"
vcd "1.2-9" "http://probability.ca/cran/src/contrib"
zoo "1.6-4" "http://probability.ca/cran/src/contrib"
class "7.3-3" "http://probability.ca/cran/src/contrib"
MASS "7.3-9" "http://probability.ca/cran/src/contrib"
class "7.3-3" "http://probability.ca/cran/src/contrib"
MASS "7.3-9" "http://probability.ca/cran/src/contrib"
But then I try:
> 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.
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?
--
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
Michael Rutter
2011-Jan-30 20:21 UTC
[R-sig-Debian] updating r-cran- packages on a new Ubuntu lucid system
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