R devel - Jun 2012 - Requests for vignette clarification (re: Writing R Extensions)

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

I'll make a guess at some parts of this.

On 12-06-01 02:53 PM, Paul Johnson wrote:
> 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 :)
I think the idea is that a user looking at an installed version of the 
package will be able to see things that are in the doc/ directory of the 
installed package. This automatically includes the source files (eg 
*.Stex) from vignettes/ and also the generated *.pdf and the *.R files 
stripped from the *.Stex files. If you want them to have access to other 
files then you should put those somewhere so they get installed, such as 
in the source package /inst/doc directory so they get put in the doc/ 
directory of the installed package. That should probably include 
anything else that is important to reproduce the results in the 
vignette, but I do not count the .bib file in that list (so I have it in 
vignettes/ and users would need to look at the package source to find
it).
>
> 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.
There was at least one earlier R-devel discussion of this, in which I 
contributed an incorrect understanding, but was generally straightened 
out by Uwe. I hope I have a correct understanding now.

You can put a pdf file in inst/doc and specify "BuildVignettes: false"
in the DESCRIPTION file, in which case the already constructed pdf from 
inst/doc will be used. The purpose of this is to allow vignettes which 
would not be completely constructed from sources, for example, because 
certain data or other resources may not be generally available. However, 
R CMD check will still try to parse the Sweave file and run the R code, 
and fail if it does not run. So, when the resources to build the 
vignette are not generally available this does require some special 
attention, often with try(), in the code for your vignette.

It is possible to claim special exemption for a vignette. If the reasons 
seem valid then that package will be put on a special list which allows 
skipping the vignette when the package is tested for CRAN. The reason 
for somewhat tight control on this by CRAN maintainers is that the 
vignettes have proven to be a good check on problems with packages, so 
skipping them will reduce quality, and so CRAN maintainers do not want 
to provide an easy option to skip this check.

There have been a variety of mechanism suggested on R-devel for 
subverting the CRAN checks of the vignette code. My interpretation is 
that these should generally be considered contrary to the spirit of what 
CRAN maintainers are attempting to do, and package maintainers should 
expect continuing problems as the loopholes are removed.

Paul Gilbert
>
> 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
>