[Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

[Martin Morgan]

On 10/20/2013 10:36 PM, Gordon K Smyth wrote:
> Hi Martin,
>
> Thanks for the heads-up.  I think I've made the changes necessary, but am having
> trouble confirming whether the changes are correct on a Windows machine.
>
> Could you tell me hows Bioconductor builds the Windows binaries of Bioconductor
> packages?
>
> To see how things work, I am playing around with Biobase on svn.  I can build
> Biobase from the svn source including the pdfs of the vignettes using
>
>    R CMD build Biobase
>
> on my Windows machine.  This gives me a tar.gz file of Biobase with an inst/doc
> directory containing Rnws and pdfs of all the vignettes.  This shows that my
> LaTeX etc is working fine.
>
> However when I run
>
>    R CMD INSTALL --build Biobase
>
> which is the recommended way to install a package under Windows, I get a zip
> file containing no sign of any vignette.  In fact there is no doc or inst or
> vignette directory in the zip file.
>
> What else do I need to do to install the package from source with the vignettes
> build under Windows?
>
> No doubt the answer is somewhere in one of the R manuals (writing R extensions
> or admin and installation perhaps) but I cannot find it.

The build machines run

     R CMD INSTALL --build Biobase_2.23.1.tar.gz

i.e., on the file created by R CMD build Biobase. This is not inconsistent with 
1.3.3 of Writing R Extensions:

"R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in 
the usual .tar.gz format) or the location of the directory of the package source 
to be built. "

although there really seems to be only one way to build complete binaries. The 
Bioconductor build system reports what it's doing in the 'Summary' section 
'Command' line at

 
http://bioconductor.org/checkResults/devel/bioc-LATEST/Biobase/moscato2-buildbin.html

Martin

>
> Thanks
> Gordon
>
> PS.  I am running Rtools3.1 with:
>
>> sessionInfo()
> R Under development (unstable) (2013-10-18 r64076)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252
> [2] LC_CTYPE=English_Australia.1252
> [3] LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils
> [6] datasets  methods   base
>
> other attached packages:
> [1] Biobase_2.23.1     BiocGenerics_0.9.0
>
>
>
>
>> Date: Fri, 18 Oct 2013 14:58:52 -0700
>> From: Martin Morgan <mtmorgan at fhcrc.org>
>> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
>> Subject: [Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/
>>
>> Bioconductor developers,
>>
>> Thank you for your contributions to our last release, with a total of 749
>> packages! This is a great resource for the bioninformatics community.
>>
>> No good deed goes unpunished. The 'devel' version of R no longer builds
>> vignettes in the inst/doc directory. Vignette sources (.Rnw or perhaps .Rmd
>> files) must be in the vignettes/ directory. There's a lot of work to be done to
>> make this happen, and we'd really like your help with this. Here's one recipe
>> for the neccessary changes, illustrtated with Biobase
>>
>> 1. Find the url of your package in the devel version of the Bioconductor svn
>> repository, e.g., for Biobase
>>
>>    https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase
>>
>> 2. Make a clean check-out of the source into a directory where `Biobase' does
>> not already exist
>>
>>    svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase
>>
>> 3. Re-name the inst/doc directory. Using svn rename preserves the commit history
>>
>>    svn rename Biobase/inst/doc Biobase/vignettes
>>
>> 4. Increase the least significant part of the package version number in
>> Biobase/DESCRIPTION. I changed Biobase from 2.23.0 to 2.23.1.
>>
>> 5. Build the package, using the latest devel version of R
>>
>>    R CMD build Biobase
>>
>> 6. Check that the built version contains .Rnw, .R, and .pdf files in the
>> inst/doc directory, e.g.,
>>
>>    tar tzf Biobase_2.23.1.tar.gz |grep inst/doc
>>
>> 7. Make sure the built package passes R CMD check
>>
>>    R CMD check Biobase_2.23.1.tar.gz
>>
>> 8. Review and check in your changes
>>
>>    svn st Biobase
>>    svn diff Biobase/DESCRIPTION
>>    svn ci
>>
>> This will work for many cases, but if you have problems please do not hesitate
>> to bring up issues on the mailing list.
>>
>> If things go smoothly, you might wish to follow the instructions in the
>> BiocStyle vignette
>>
>>
>> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.pdf
>>
>>
>> for creating vignettes with a consistent look-and-feel. The text is wider, for
>> instance, so code generally formats better, and packages are easily linked to
>> their 'landing page' on the Bioconductor web site
>>
>> Please don't hesitate to ask if there are any questions, and thanks in advance
>> for your continued effort to support the project.
>>
>> Martin
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>
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