you got it. works perfectly now. thanks On 10/4/07, Gabor Csardi <[EMAIL PROTECTED]> wrote: > You need to install the libc6-dev ubuntu package to be able > to compile programs. > > sudo apt-get install libc6-dev > > Gabor > > On Thu, Oct 04, 2007 at 09:54:26AM -0400, Ricardo Pietrobon wrote: > > 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. > > -- > Csardi Gabor <[EMAIL PROTECTED]> MTA RMKI, ELTE TTK >
-- Ricardo Pietrobon, MD, PhD, MBA Associate Vice Chair and Assistant Professor, Department of Surgery Director of Biomedical Informatics, Duke Translational Medicine Institute http://www.dtmi.duke.edu/ my calendar is available at http://www.google.com/calendar/embed?src=pietr007%40gmail.com&mode=MONTH to view start and end times, click on the specific hyperlink and then send me a time that best fits your schedule ______________________________________________ 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.
