[R] Output from make check

Patrick Connolly p.connolly at hortresearch.co.nz
Thu Jun 27 00:05:59 CEST 2002

On Wed, 26-Jun-2002 at 07:50AM +0100, ripley at stats.ox.ac.uk wrote:

|> On Wed, 26 Jun 2002, Patrick Connolly wrote:
|> > These are probably very basic questions, but I don't know how one
|> > reads output such as this:
|> >
|> > [hrapgc at biomat1 R-1.5.1]$ make check
|> > make[1]: Entering directory `/home/hrapgc/local/R-1.5.1/tests'

[ ... ]

|> > Just what do Error 1 and Error 2 refer to?
|> Return codes from programs called by your make.  In this case the first is
|> forced by the line
|> 	@$(R) < $< > $@ || (mv $@ $@.fail && exit 1)
|> so the command has return code 1.

[ .... ]

|> You need to look at the file base-Ex.Rout.fail to see the actual problem,

Thanks for that information.

It falls over here (which corresponds to about half-way through the
base-Ex.R file):

> if(require(survival)){
+   oT <- T; oF <- F; T <- TRUE; F <- FALSE # survival fails otherwise
+   faketime <- rep(42,nrow(infert))
+   model3 <- coxph(Surv(faketime,case)~spontaneous+induced+strata(stratum),
+                 data=infert,method="exact")
+   summary(model3)
+   detach()# survival (conflicts)
+   T <- oT; F <- oF
+ }
Loading required package: survival 
Error in .Defunct() : `.Alias' is defunct.
See ?Defunct.
Execution halted

If I remove that section, all the other tests succeed.

I'm puzzled as to how that could have happened.  Is it finding an
older version of the survival package instead?  Can't imagine how it
could be doing that.  Could it have anything to do with the fact that
R is built as a shared library?

I gather this is what happens with Error 2.  Just how is it different
from Error 1?


Patrick Connolly
Mt Albert
New Zealand 
Ph: +64-9 815 4200 x 7188
I have the world`s largest collection of seashells. I keep it on all
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