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

[Gordon K Smyth]

Thanks, setting pkg to be the tar.gz file instead of the directory does 
the job.  I had not appreciated the difference.

The code on checkResults is very clear now.  I hadn't appreciated that the 
BUILD and the BUILDBIN steps were cumulative.

Thanks
Gordon


On Sun, 20 Oct 2013, Martin Morgan wrote:

> 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
>>> 
>> 
>
>
> -- 
> 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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