[R] Updating packages for R 2.6.0

[Dirk Eddelbuettel]

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.

>From source? Or as a binary?  Ubuntu backports of the R 2.6.0 package
should be at CRAN within a few days.

> here is the message:

You seem to be missing essential header files, so I'd start from

    $ sudo apt-get install r-base-dev

and try again. I don't see you could compile R if you can't build MASS.

Dirk

> 
> 
> * 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 <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
> > 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,                  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
> > 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 at 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.

-- 
Three out of two people have difficulties with fractions.