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

[Prof Brian Ripley]

On Mon, 5 May 2008, Patrick Giraudoux wrote:

> 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

Yes, I do know (I solved them).

> 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...

I suggest you do as I suggest, for the most likely explanation is that 
this is not the same set of files.

> 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
>>> 
>>> 
>> 
>
>

-- 
Brian D. Ripley,                  ripley at 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