From ripley at stats.ox.ac.uk  Mon May  5 07:34:05 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 5 May 2008 06:34:05 +0100 (BST)
Subject: [Rd] troubles with R CMD check and examples under Ubuntu gutsy
In-Reply-To: <481E94DF.9000004@univ-fcomte.fr>
References: <481E94DF.9000004@univ-fcomte.fr>
Message-ID: <alpine.LFD.1.10.0805050630450.17584@gannet.stats.ox.ac.uk>

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).

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



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