From plummer at iarc.fr  Wed Apr  6 17:09:45 2005
From: plummer at iarc.fr (Martyn Plummer)
Date: Wed Apr  6 17:11:51 2005
Subject: [Rd] make error in R devel
In-Reply-To: <4253F564.4090706@ucl.ac.uk>
References: <4253F564.4090706@ucl.ac.uk>
Message-ID: <1112800185.26851.7.camel@seurat>

If you get the R source via svn, then you need to run tools/rsync-
recommended to get the recommended packages.  If you download the
tarball from CRAN then these are already included.

Martyn


On Wed, 2005-04-06 at 15:42 +0100, Gavin Simpson wrote:
> Dear list,
> 
> I just hit an error that stopped my make && make check-devel operation 
> on my linux box (FC3, i686 P4 2GB RAM). Just to note that I've been 
> building the development branch(?) for some time and this is the first 
> hint of a problem.
> 
> 1) updated the src tree using svn update
> 2) ran ../configure --with-recommended-package=no from my build directory
> 3) got:
> R is now configured for i686-pc-linux-gnu
> 
>    Source directory:          ../src
>    Installation directory:    /usr/local
> 
>    C compiler:                gcc  -O3 -g -march=i386 -mcpu=i686
>    C++ compiler:              g++  -O3 -g -march=i386 -mcpu=i686
>    Fortran compiler:          g77  -O3 -g -march=i386 -mcpu=i686
> 
>    Interfaces supported:      X11, tcltk
>    External libraries:        readline, BLAS(generic)
>    Additional capabilities:   PNG, JPEG, iconv, MBCS, NLS
>    Options enabled:           R profiling
> 
>    Recommended packages:      no
> 
> Note I've editted config.site to compile with optimisations -O3
> 4) did make && make check-devel and get this:
> ...
> make[5]: Entering directory `/home/gavin/R/devel/build/src/library'
>   >>> Building/Updating help pages for package 'graphics'
>       Formats: text html latex example
> make[5]: Leaving directory `/home/gavin/R/devel/build/src/library'
> running code in 'graphics-Ex.R' ... OK
> collecting examples for package 'stats' ...
> make[5]: Entering directory `/home/gavin/R/devel/build/src/library'
>   >>> Building/Updating help pages for package 'stats'
>       Formats: text html latex example
> make[5]: Leaving directory `/home/gavin/R/devel/build/src/library'
> running code in 'stats-Ex.R' ...make[4]: *** [stats-Ex.Rout] Error 1
> make[4]: Leaving directory `/home/gavin/R/devel/build/tests/Examples'
> make[3]: *** [test-Examples-Base] Error 2
> make[3]: Leaving directory `/home/gavin/R/devel/build/tests/Examples'
> make[2]: *** [test-Examples] Error 2
> make[2]: Leaving directory `/home/gavin/R/devel/build/tests'
> make[1]: *** [test-all-basics] Error 1
> make[1]: Leaving directory `/home/gavin/R/devel/build/tests'
> make: *** [check-devel] Error 2
> 
> 5) Looking at stats-Ex.Rout.fail I see this at the end:
>  >
>  > ### Name: confint
>  > ### Title: Confidence Intervals for Model Parameters
>  > ### Aliases: confint confint.default
>  > ### Keywords: models
>  >
>  > ### ** Examples
>  >
>  > fit <- lm(100/mpg ~ disp + hp + wt + am, data=mtcars)
>  > confint(fit)
>                     2.5 %      97.5 %
> (Intercept) -0.774822875 2.256118188
> disp        -0.002867999 0.008273849
> hp          -0.001400580 0.011949674
> wt           0.380088737 1.622517536
> am          -0.614677730 0.926307310
>  > confint(fit, "wt")
>         2.5 %   97.5 %
> wt 0.3800887 1.622518
>  >
>  > ## from example(glm)
>  > counts <- c(18,17,15,20,10,20,25,13,12)
>  > outcome <- gl(3,1,9); treatment <- gl(3,3)
>  > glm.D93 <- glm(counts ~ outcome + treatment, family=poisson())
>  > confint(glm.D93)
> Error in loadNamespace(name) : there is no package called 'MASS'
> Execution halted
> 
> But as there are no recommended packages this fails as indicated. So is 
> there something wrong with what I'm doing (i.e. something recent in the 
> last week has changed that I missed in NEWS) or is this a bug in the 
> tests or examples?
> 
> Cheers
> 
> Gav


[Rd] make error in R devel
Martyn Plummer