From plummerm at iarc.fr  Thu Mar 26 14:50:47 2015
From: plummerm at iarc.fr (Martyn Plummer)
Date: Thu, 26 Mar 2015 13:50:47 +0000
Subject: [Rd] vignette checking woes
In-Reply-To: <85544E7F-4A52-46B1-AEEE-1AC5130D3F6F@illinois.edu>
References: <9D62BF42-5AB3-4600-A6F1-66C56426304D@illinois.edu>
	<ba2481dbbbd94d8aa33f09b482e7ac2a@CHIHT3.ad.uillinois.edu>
	<85544E7F-4A52-46B1-AEEE-1AC5130D3F6F@illinois.edu>
Message-ID: <1427377847.18388.63.camel@iarc.fr>

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?

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
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[Rd] vignette checking woes
Martyn Plummer