R devel - Jan 2015 - R CMD check message: "The following files should probably not be installed"

Sorry.  This, and the description in the ?Writing R Extensions? manual,
leaves me completely mystified.  Is it that I have to remove the PDFs
that are created when I run ?R CMD build?, and somehow ensure that
they are rebuilt when the package is installed?  Do I need a Makefile?


John Maindonald             email: john.maindonald at
anu.edu.au<mailto:john.maindonald at anu.edu.au>

phone : +61 2 (6125)3473    fax  : +61 2(6125)5549

Centre for Mathematics & Its Applications, Room 1194,

John Dedman Mathematical Sciences Building (Building 27)

Australian National University, Canberra ACT 0200.


On 26 Jan 2015, at 22:00, <r-devel-request at
r-project.org<mailto:r-devel-request at r-project.org>>
<r-devel-request at r-project.org<mailto:r-devel-request at
r-project.org>> wrote:

From: Prof Brian Ripley <ripley at stats.ox.ac.uk<mailto:ripley at
stats.ox.ac.uk>>
Subject: Re: [Rd] R CMD check message: "The following files should probably
not be installed"
Date: 26 January 2015 19:52:12 AEDT
To: <r-devel at r-project.org<mailto:r-devel at r-project.org>>


On 25/01/2015 23:25, John Maindonald wrote:
I am doing [R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet?; Platform:
x86_64-apple-darwin10.8.0 (64-bit)]

R CMD build DAAGviz
R CMD check DAAGviz_1.0.3.tar.gz

Without a .Rinstignore file, I get:

<<<
The following files should probably not be installed:
  ?figs10.pdf?, ?figs11.pdf?, ?figs12.pdf?, ?figs13.pdf?, ?figs14.pdf?,
  ?figs5.pdf?, ?figs6.pdf?, ?figs9.pdf?

Consider the use of a .Rinstignore file: see ?Writing R Extensions?,
or move the vignette sources from ?inst/doc? to ?vignettes?.


The vignette sources were in ?vignettes? when DAAGviz_1.0.3.tar.gz was created. 
There was nothing in the ?inst/doc? directory.

If I have in my .Rinstignore file

  inst/doc/.*[.]pdf

That filters out more than the files warned about.  I guess you meant

inst/doc/figs.*[.]pdf

But the question has to be: how did the files get copied into inst/doc?  Maybe

'When R CMD build builds the vignettes, it copies these and the vignette
sources from directory vignettes to inst/doc. To install any other files from
the vignettes directory, include a file vignettes/.install_extras which
specifies these as Perl-like regular expressions on one or more lines. (See the
description of the .Rinstignore file for full details.)'

suggests how?

then I get:

<<<
* checking package vignettes in ?inst/doc? ... WARNING
Package vignettes without corresponding PDF/HTML:
. . .


What am I missing?  Can I ignore the "The following files should probably
not be installed? message?

Not if you want to submit the package to CRAN.



John Maindonald             email: john.maindonald at
anu.edu.au<mailto:john.maindonald at anu.edu.au>
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.

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