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' ... ** libs 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, from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11, from /usr/share/R/include/R.h:30, from lqs.c:31: /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error: 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, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory 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 function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' 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 function 'fabs' 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 /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley <[EMAIL PROTECTED]> 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 > kappalab. > > - 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, [EMAIL PROTECTED] > 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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.