From rkoenker at illinois.edu  Thu Mar 26 17:42:14 2015
From: rkoenker at illinois.edu (Roger Koenker)
Date: Thu, 26 Mar 2015 11:42:14 -0500
Subject: [Rd] vignette checking woes
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Message-ID: <9CC8E172-2E73-457D-9DBD-61AFED7833DB@illinois.edu>


> On Mar 26, 2015, at 8:50 AM, Martyn Plummer <plummerM at iarc.fr> wrote:
> 
> On Wed, 2015-03-25 at 15:12 -0500, Roger Koenker wrote:
>> Thierry,
>> 
>> I have this:
>> 
>> if (require(MatrixModels) && require(Matrix)) {
>>   X <- model.Matrix(Terms, m, contrasts, sparse = TRUE)
> 
> You have this in the current release, which does not show this problem
> in the CRAN tests. This, and the fact that you can build the vignette
> manually, suggests that there is a problem with your checking
> environment.
> 
> Did you set up a special checking environment in ~/.R/check.Renviron ?
> Does it set R_LIBS?

No, not that I can find.  But I agree that there seems to be something fishy.  Another
bit of evidence for this is fact that R CMD build gives me:

* creating vignettes ... ERROR
Rscript execution error: No such file or directory

so I've been building with the --no-build-vignettes flag...

Many thanks, for your suggestions,
Roger

> 
> Martyn
> 
>> in my function rqss()  I've tried variants of requireNamespace too without success.
>> If I understand properly model.Matrix is from MatrixModels but it calls 
>> sparse.model.matrix which is part of Matrix, and it is the latter function that I'm
>> not finding.  Maybe I should go back to the requireNamespace strategy again?
>> 
>> Roger
>> 
>> url:    www.econ.uiuc.edu/~roger            Roger Koenker
>> email    rkoenker at uiuc.edu            Department of Economics
>> vox:     217-333-4558                University of Illinois
>> fax:       217-244-6678                Urbana, IL 61801
>> 
>>> On Mar 25, 2015, at 2:54 PM, Thierry Onkelinx <thierry.onkelinx at inbo.be> wrote:
>>> 
>>> Dear Roger,
>>> 
>>> How is Matrix loaded?
>>> 
>>> If you use sparse.model.matrix() inside a function from your package you need to declare it as Matrix::sparse.model.matrix()
>>> 
>>> Best regards,
>>> 
>>> ir. Thierry Onkelinx
>>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest 
>>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance 
>>> Kliniekstraat 25
>>> 1070 Anderlecht
>>> Belgium
>>> 
>>> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>>> The plural of anecdote is not data. ~ Roger Brinner 
>>> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
>>> 
>>> 2015-03-25 19:59 GMT+01:00 Roger Koenker <rkoenker at illinois.edu>:
>>> I'm having trouble with R CMD check of my quantreg package.  All is well
>>> until I get to:
>>> 
>>> checking running R code from vignettes ...
>>> ?rq.Rnw? ... failed
>>> ERROR
>>> Errors in running code in vignettes:
>>> when running code in ?rq.Rnw?
>>> 
>>> when I see a snippet from the vignette code and then:
>>> 
>>> Loading required namespace: MatrixModels
>>> 
>>> When sourcing ?rq.R?:
>>> Error: could not find function "sparse.model.matrix"
>>> Execution halted
>>> 
>>> This is baffling to me since sparse.model.matrix is in the
>>> namespace of Matrix and it should be loaded at this stage
>>> since it is required by MatrixModels which has just been
>>> pronounced "loaded".
>>> 
>>> I've verified that I can Sweave("rq.Rnw")
>>> and texi2pdf("rq.tex", clean=TRUE) without any problem.
>>> 
>>> Any hints greatly appreciated, as always.
>>> 
>>> Roger
>>> 
>>> 
>>> url:    www.econ.uiuc.edu/~roger            Roger Koenker
>>> email    rkoenker at uiuc.edu            Department of Economics
>>> vox:     217-333-4558                University of Illinois
>>> fax:       217-244-6678                Urbana, IL 61801
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] vignette checking woes
Roger Koenker