[Rd] troubles with R CMD check and examples under Ubuntu gutsy

Patrick Giraudoux patrick.giraudoux at univ-fcomte.fr
Mon May 5 08:09:25 CEST 2008

Prof Brian Ripley a écrit :
> It seems likely that the contents of 'pgirmess' under Linux are 
> incomplete.
> There's a recent version of pgirmess on CRAN, and that works under 
> Linux. I suggest you try that (start with the tarball, perhaps).
Sorry prof Ripley, but this is the same version as the one on CRAN (I am 
the developper)... Actually Kurt Hornik tried it and it went through 
with his debian yesterday (after some troubles -solved- about encoding 
and the new R 6.7.0), Uwe Ligges sent me an automated  message telling 
that it has also been built under Windows successfully (as it was under 
my own Windows version). I have also checked that PermTest was in the 
package. So I suppose that it has something to do with Ubuntu... but 
don't know how to debug this...

On Mon, 5 May 2008, Patrick Giraudoux wrote:
>> Dear listers,
>> I was used to package pgirmess under Windows with everything OK, but, 
>> for the first time, I had a trial this afternoon on Ubuntu 7.10 gutsy 
>> (I have a double boot computer and work more and more under unix) and 
>> R 2.7.0. Everything went OK except this:
>> sudo R CMD check pgirmess
> Do you really want to be doing this under root?  I see no reason to do 
> so -- just make sure you have a writeable current directory for your 
> account.
>> .....
>> * checking examples ... ERROR
>> Running examples in 'pgirmess-Ex.R' failed.
>> The error most likely occurred in:
>>> ### * PermTest
>>> flush(stderr()); flush(stdout())
>>> ### Name: PermTest
>>> ### Title: Permutation test for lm, lme and glm (binomial and Poisson)
>>> ###   objects
>>> ### Aliases: PermTest PermTest.lm PermTest.lme PermTest.glm 
>>> print.PermTest
>>> ### Keywords: htest
>>> ### ** Examples
>>> library(MASS)
>>> mylm<-lm(Postwt~Prewt,data=anorexia)
>>> PermTest(mylm,B=250)
>> Error: could not find function "PermTest"
>> Execution halted
>> If I run R CMD check --no-examples pgirmess, everything comes OK. 
>> Seems again that this check makes problem. I googled a bit on R-devel 
>> but did not find any understandable post on that...
>> Any idea about what happens ? (please consider if I can write some 
>> lines and build a package, I am *not* an advanced fellow in matter of 
>> packaging... and just know something about running the commands 'R 
>> CMD check' and R CMD build...)
>> Thanks in advance,
>> Patrick

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