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 <[email protected]>
To: "[email protected]" <[email protected]>
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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