Yeah, this is not very clear, although repeated posts on R-devel suggests
that R-core believes it ought to be common knowledge to always run R CMD
INSTALL/check on a tarball produced by R CMD build.

I see Martin is reporting this on R-devel.

Best,
Kasper


On Mon, Oct 21, 2013 at 2:37 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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<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@fhcrc.org>
>>>> To: "bioc-devel@r-project.org" <bioc-devel@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<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<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<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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