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