From hpages at fhcrc.org  Mon May  2 08:29:44 2011
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Sun, 01 May 2011 23:29:44 -0700
Subject: [Rd] R CMD build processes inst/doc/Makefile only if there are
 vignette files?
In-Reply-To: <alpine.LFD.2.02.1104300630100.15222@gannet.stats.ox.ac.uk>
References: <BANLkTinYAyuKfHy74QKkqOBFfT3tiF8t5g@mail.gmail.com>
	<alpine.LFD.2.02.1103300946510.20705@gannet.stats.ox.ac.uk>
	<4DBB4191.80809@fhcrc.org>
	<alpine.LFD.2.02.1104300630100.15222@gannet.stats.ox.ac.uk>
Message-ID: <4DBE4F58.70801@fhcrc.org>

On 11-04-29 10:36 PM, Prof Brian Ripley wrote:
> On Fri, 29 Apr 2011, Herv? Pag?s wrote:
>
>> On 11-03-30 01:55 AM, Prof Brian Ripley wrote:
>>> What R CMD build (and check) does is to call tools::buildVignettes.
>>> That has been true for a while, and buildVignettes() returns if no
>>> vignettes are found. The docs are out-of-date.
>>>
>>> My view is that you are misusing inst/doc: it is intended *only* for
>>> files which are going to be installed and hence report.tex should not
>>> really be there. So you should be doing this in another source directory
>>> and copying report.pdf to inst/doc. Use configure to arrange this.
>>>
>>> Shortly vignettes to be built will be moved out of inst/doc.
>>
>> Could you please elaborate on this? I just found this in the NEWS for
>> R 2.14.0:
>>
>> o The preferred location for vignette sources is now the directory
>> ?vignettes? and not ?inst/doc?: R CMD build will now re-build
>> vignettes in ?vignettes? and copy the ?.Rnw? (etc) files and
>> the corresponding PDFs to ?inst/doc?.
>>
>> Sounds like an important move. What are the long term plans: keep
>> both inst/doc/ and vignettes/ as places for vignettes to be built?
>> Or drop inst/doc/ at some point?
>
> Drop inst/doc at some point.

May I ask when?

> It doesn't make much difference to the
> codebase: all the work is done in pkgVignettes().

Maybe but it will make a big difference from our side: about 450 BioC
packages will need to be modified.

Thanks,
H.


>
>>
>> Thanks!
>> H.
>>
>>
>>>
>>> On Tue, 29 Mar 2011, Henrik Bengtsson wrote:
>>>
>>>> Hi,
>>>>
>>>> in Section 'Writing package vignettes' of 'Writing R Extensions' it
>>>> says:
>>>>
>>>> "Whenever a Makefile is found, then R CMD build will try to run make
>>>> after the Sweave runs, so PDF manuals can be created from arbitrary
>>>> source formats (plain LaTeX files, ...). [...] Note that the make step
>>>> is executed even if there are no files in Sweave format, [...]".
>>>>
>>>> In my package, inst/doc/ file contains two files: Makefile, and
>>>> report.tex. However, when running 'Rcmd build' on Windows with R
>>>> v2.13.0 alpha (2011-03-27 r55091) I can only get 'make' to run
>>>> (process inst/doc/Makefile) if I add a inst/doc/dummy.Rnw file,
>>>> otherwise nothing happens. My Makefile contains:
>>>>
>>>> all: pdf
>>>>
>>>> pdf: report.tex
>>>> texi2dvi --pdf report.tex
>>>>
>>>> clean:
>>>> rm dummy.Rnw dummy.tex
>>>> rm *.aux *.log *.toc
>>>>
>>>> Is it really necessary to add dummy.Rnw? Am I missing something?
>>>>
>>>> /Henrik
>>>>
>>>>> sessionInfo()
>>>> R version 2.13.0 alpha (2011-03-27 r55091)
>>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_United States.1252
>>>> [2] LC_CTYPE=English_United States.1252
>>>> [3] LC_MONETARY=English_United States.1252
>>>> [4] LC_NUMERIC=C
>>>> [5] LC_TIME=English_United States.1252
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.13.0
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>
>>
>> --
>> Herv? Pag?s
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
>>
>


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] R CMD build processes inst/doc/Makefile only if there are vignette files?
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