On Thu, Sep 27, 2012 at 2:42 PM, Hervé Pagès wrote: > Hi Tengfei, > > Yes, as Dan said, that should work. Make sure you indent the Makefile > properly though (normally with a tab), or it won't work: > > ------------------------------**------------------------------** > ----------- > > PDFS= ggbio.pdf > > all: $(PDFS) > > clean: > rm -f *.tex *.bbl *.blg *.aux *.out *.log *.spl *tikzDictionary > > %.pdf: %.Rnw > $(R_HOME)/bin/Rscript -e "library(knitr); knit2pdf('$*.Rnw')" > ------------------------------**------------------------------** > ----------- > > Also note the use of a regexpr in the call to knit2pdf() so that all > Sweave files in the folder will be processed. > > I would suggest 3 more things: > > 1. Add *.toc to the rm command above. > > 2. Don't forget to add knitr to the Suggests field of your package. > > 3. If you've not done it already, add library(knitr) right before the > knit_hooks$... line in the set-options code chunk in each of your > Rnw files, so that people can still run Sweave() on them if they > want. > > Cheers, > H. > > Hi Hervé, Thanks a lot for your suggestion, I haven't done that yet, so I could make all those changes. Potential issues is that(actually as Martin just mentioned), if my Rnw won't be running through sweave(sweave first run on my Rnw) which because knitr-specified tag is included in my Rnw file, and Sweave won't recognize, for example, may be tag, fig.cap = " with quotes", there is no such tag and I guess I cannot use quotes, I guess I am hitting a potential problem like that, one solution could be that I have to put a fake Rnw first, then remove fake vignette and run knitr on real Rnw file somewhere and copy it to the right location to replace the fake vignette... I am experimenting on my machine now... hope that would work, I heard from knitr designer that Rcpp did similar things like that. Tengfei > > On 09/27/2012 08:08 AM, Dan Tenenbaum wrote: > >> On Wed, Sep 26, 2012 at 11:41 PM, Tengfei Yin >> 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. >> Dan >> >> >> >>> thanks a lot! >>> >>> Tengfei >>> >>> >>> >>> -- >>> Tengfei Yin >>> MCDB PhD student >>> 1620 Howe Hall, 2274, >>> Iowa State University >>> Ames, IA,50011-2274 >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/**listinfo/bioc-devel >>> >> >> ______________________________**_________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/**listinfo/bioc-devel >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alternative HTML version deleted]]