From gavin.simpson at ucl.ac.uk  Wed Apr  6 16:42:44 2005
From: gavin.simpson at ucl.ac.uk (Gavin Simpson)
Date: Wed Apr  6 16:42:54 2005
Subject: [Rd] make error in R devel
Message-ID: <4253F564.4090706@ucl.ac.uk>

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
-- 
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Gavin Simpson                     [T] +44 (0)20 7679 5522
ENSIS Research Fellow             [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC                 [E] gavin.simpsonATNOSPAMucl.ac.uk
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[Rd] make error in R devel
Gavin Simpson