From ligges at statistik.tu-dortmund.de  Thu Apr 12 09:15:41 2012
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Thu, 12 Apr 2012 09:15:41 +0200
Subject: [Rd] Vignette questions
In-Reply-To: <4F8610DA.80908@gmail.com>
References: <4F85EC88.8070604@mayo.edu> <4F8610DA.80908@gmail.com>
Message-ID: <4F86811D.5040201@statistik.tu-dortmund.de>



On 12.04.2012 01:16, Paul Gilbert wrote:
>
>
> On 12-04-11 04:41 PM, Terry Therneau wrote:
>> Context: R2.15-0 on Ubuntu.
>>
>> 1. I get a WARNING from CMD check for "Package vignette(s) without
>> corresponding PDF:
>> In this case the vignettes directory had both the pdf and Rnw; do I need
>> to move the pdf to inst/doc?
>
> Yes, you need to put the pdf in the inst/doc directory if it cannot be
> built by R-forge and CRAN check machines, but leave the Rnw in the
> vignettes directory.

No, this is all done automatically by R CMD build, hence you do not need 
to worry.


>>
>> I'm reluctant to add the pdf to the svn source on Rforge, per the usual
>> rule that a code management system should not have both a primary source
>> and a object dervived from it under version control. However, if this is
>> the suggested norm I could do so.
>
> Yes, I think this is the norm if the vignette cannot be built on CRAN
> and R-forge,

Well, yours are that specific that they rely on third party software. 
Vignettes "only" depending on R and installed packages that are declared 
as dependencies can be build by CRAN.


> even though it does seem a bit strange. However, you do not
> necessarily need to update the vignette pdf in inst/doc every time you
> make a change to the package even though, in my opinion, the correct
> logic is to test remaking the vignette when you make a change to the
> package. You should do this testing, of course, you just do not need to
> put the new pdf in inst/doc and commit it to svn each time. (But you
> should probably do that before you build the final package to put on CRAN.)

R CMD build will rebuild vignettes unless you ask R not to do so.

Uwe


>>
>> 2. Close reading of the paragraph about vignette sources shows the
>> following -- I think? If I have a vignette that should not be rebuilt by
>> "check" or "BUILD" I should put the .Rnw source and pdf in /inst/doc,
>> and have the others that should be rebuilt in /vignettes. This would
>> include any that use "private R packages, screen snapshots, ...", or in
>> my case one that takes just a little short of forever to run.
>
> I don't think it is intended to say that, and I didn't read it that way.
> I think putting the Rnw in inst/doc is supported (temporarily?) for
> historical reasons only. If it is not in vignettes/ and is found in
> inst/doc/, it is treated the same way as if it were in vignettes/.
>
> You can include screen snapshots, etc, in either case. For your
> situation, what you probably do need to do is specify "BuildVignettes:
> false" in the DESCRIPTION file. This prevents the pdf for inst/doc from
> being generated by the the Rnw. However, it does not prevent R CMD check
> from checking that the R code extracted from the Rnw actually runs, and
> generating an error if it does not. To prevent testing of the R code,
> you have to appeal directly to the CRAN and R-forge maintainers, and
> they will put the package on a special list. You do need to give them a
> good reason why the code should not be tested. I think they are
> sympathetic with "takes forever to run" and not very sympathetic with
> "does not work anymore". Generally, I think they want to consider doing
> this only in exceptional cases, so they do not get in a situation of
> having lots of broken vignettes. (One should stick with journal articles
> for recording broken code.)
>
>> 3. Do these unprocessed package also contribute to the index via
>> \VignetteIndexEntry lines, or will I need to create a custom index?
>
> I'm not sure of the answer to this, but would be curious to know. You
> may need to rely on voodoo.
>
> Paul
>>
>> Terry Therneau
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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[Rd] Vignette questions
Uwe Ligges