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
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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
UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way [W] http://www.ucl.ac.uk/~ucfagls/
London. WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
What you are doing is not building the recommended packages. We not guarantee that the examples will work if you do not. (I was aware this would happen but have not yet put in a workaround.) *WHY* are you not building the recommended packages? On Wed, 6 Apr 2005, 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 > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > 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 > UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ > 26 Bedford Way [W] http://www.ucl.ac.uk/~ucfagls/ > London. WC1H 0AP. > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > ______________________________________________ > R-devel@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >-- Brian D. Ripley, ripley@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
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