[Bioc-devel] To use knitr, how to write the right Makefile for bioconductor devel and released branch?

Dan Tenenbaum dtenenba at fhcrc.org
Thu Sep 27 17:08:50 CEST 2012

On Wed, Sep 26, 2012 at 11:41 PM, Tengfei Yin <yintengfei at gmail.com> wrote:
> Dear maintainers and developers,
> I am wondering, is there a way to use knitr to built my vignette, I am
> trying to write a Makefile under my inst/doc, something like
> # Makefile to use knitr for package vignettes
> # put all PDF targets here, separated by spaces
> PDFS= ggbio.pdf
> all: $(PDFS)
> clean:
> rm -f *.tex *.bbl *.blg *.aux *.out *.log *.spl *tikzDictionary
> %.pdf: %.Rnw
> $(R_HOME)/bin/Rscript -e "library(knitr); knit2pdf('ggbio.Rnw')"
> Then I realize the bioc maintained two branch, released and development, so
> the R version it used to check each branch must be different, I don't
> really know how to specify those in my Makefile, especially after next
> Monday, the devel-branch become released version automatically, there must
> be a problem if I set up a fixed point to some */bin/Rscript?
> I don't really know how it works with bioconductor, the example above
> should work for cran, but I guess things are very different between cran
> and bioc.

If you use "$(R_HOME)/bin/R" in your Makefile, as you do, the correct
R will be used.

> thanks a lot!
> Tengfei
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
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