From pauljohn32 at gmail.com  Fri Jun  1 20:53:41 2012
From: pauljohn32 at gmail.com (Paul Johnson)
Date: Fri, 1 Jun 2012 13:53:41 -0500
Subject: [Rd] Requests for vignette clarification (re: Writing R Extensions)
Message-ID: <CAErODj90VWY19eWVtuVeLL8JpN0QxrKvWA+N5CQg-LcdALVsWQ@mail.gmail.com>

I apologize that these questions are stupid and literal.

I write to ask for clarification of comments in the R extensions
manual about vignettes.  I'm not great at LaTeX, but I'm not a
complete novice either, and some of the comments are puzzling to me.

1. I'm stumbling over this line:

"Make sure all files needed to run the R code in the vignette (data
sets, ...) are accessible by either placing them in the inst/doc
hierarchy of the source package or by using calls to system.file()."

Where it says "inst/doc", can I interpret it to mean "vignettes"?  The
vignette files are under vignettes. Why wouldn't those other files be
in there? Or does that mean I'm supposed to copy the style and bib
files from the vignettes folder to the inst/doc folder?  Or none of
the above :)

2. I'm also curious about the implications of the parenthesized
section of this comment:

"By default R CMD build will run Sweave on all files in Sweave format
in vignettes, or if that does not exist, inst/doc (but not in
sub-directories)."

At first I though that meant it will search vignettes and
subdirectories under vignettes, or it will look under inst/doc, but no
subdirectories under inst/doc.  So I created vignettes in
subdirectories under vignettes and they are ignored by the build
process, so that was obviously wrong.  For clarification, it would
help me if the manual said

"By default R CMD build will run Sweave on all files in Sweave format
in vignettes (but not in sub-directories), or if that does not exist,
inst/doc ."

In this list I've read several questions/complaints from people who
don't want their vignettes rebuild during the package check or build
process, and I wondered if there is a benefit to having vignettes in
subdirectories.   Could inclusion of troublesome vignettes in
subdirectories be a way that people can circumvent the rebuilding and
re-checking of vignettes during build, check, or install?  If I build
my vignettes manually and copy the pdf output over to inst/doc, will
those pdf files be "legitimate" vignette files as far as CRAN is
concerned?  The writeup in R Extensions is a little bit confusing on
that point.

"By including the PDF version in the package sources it is not
necessary that the vignette PDFs can be re-built at install time,
i.e., the package author can use private R packages, screen snapshots
and LaTeX extensions which are only available on his machine."

Its just confusing, that's all I can say about it.

I could learn how to do this from some examples of packages that
manage vignettes the "right way", if you could tell me which ones are
"right" :) I'd like to see one that has a Makefile, uses a bib file,
and, if possible, one that imports a pdf file from elsewhere.  If
there is one that uses subdirectories under vignettes to keep separate
 the content of vignettes, that would be extra helpful.

I'm eager to do this in the correct way, just point me at some that are proper.

pj

-- 
Paul E. Johnson
Professor, Political Science ? ?Assoc. Director
1541 Lilac Lane, Room 504 ? ? Center for Research Methods
University of Kansas ? ? ? ? ? ? ? University of Kansas
http://pj.freefaculty.org ? ? ? ? ? ?http://quant.ku.edu



[Rd] Requests for vignette clarification (re: Writing R Extensions)
Paul Johnson