[R] Updating packages for R 2.6.0
pietr007 at mc.duke.edu
Thu Oct 4 15:54:26 CEST 2007
I must be making some really basic mistake, since I keep getting an
error message when using update.packages(checkBuilt=TRUE, ask=FALSE) -
an example for MASS is below. I am running ubuntu 7.04, with a clean
install done today of version 2.6.0 straight from the R repository.
here is the message:
* Installing *source* package 'MASS' ...
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-fpic -g -O2 -c lqs.c -o lqs.o
In file included from lqs.c:31:
/usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory
/usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory
In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
limits.h: No such file or directory
In file included from lqs.c:31:
/usr/share/R/include/R.h:32:18: error: math.h: No such file or directory
/usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory
In file included from /usr/share/R/include/R.h:50,
/usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file
lqs.c: In function 'lqs_fitlots':
lqs.c:222: warning: implicit declaration of function 'fabs'
lqs.c:222: warning: incompatible implicit declaration of built-in
lqs.c:238: warning: implicit declaration of function 'sqrt'
lqs.c:238: warning: incompatible implicit declaration of built-in
lqs.c:239: warning: incompatible implicit declaration of built-in
lqs.c: In function 'do_one':
lqs.c:319: warning: implicit declaration of function 'log'
lqs.c:319: warning: incompatible implicit declaration of built-in function 'log'
lqs.c:319: warning: incompatible implicit declaration of built-in
lqs.c: In function 'mve_fitlots':
lqs.c:376: warning: incompatible implicit declaration of built-in function 'log'
make: *** [lqs.o] Error 1
ERROR: compilation failed for package 'MASS'
** Removing '/usr/local/lib/R/site-library/MASS'
** Removing '/usr/local/lib/R/site-library/class'
** Removing '/usr/local/lib/R/site-library/nnet'
** Removing '/usr/local/lib/R/site-library/spatial'
The downloaded packages are in
In install.packages() :
installation of package 'VR' had non-zero exit status
any thoughts appreciated
On 10/4/07, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> Since this has come up already:
> It is a good idea to re-install all packages for a minor-version increment
> of R, e.g. 2.5.1 -> 2.6.0 (it is major.minor.patchlevel). This is most
> easily done by
> > update.packages(checkBuilt=TRUE, ask=FALSE)
> However, if you don't want to do that yet, be aware that
> - Certain S4-using packages must be reinstalled, and using old versions
> can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and
> - Any S4 package that makes an existing function S4-generic will grab that
> function as it existed in the version of R under which they were
> installed. If it has changed, there is potential trouble.
> - Packages that create or change character strings at C level will have
> needed to be updated for R 2.6.0 (and some have not yet been). Using such
> a package can in principle result in other character data being changed
> (since most character strings now share storage).
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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