On Thu, Sep 27, 2012 at 4:48 PM, Hervé Pagès wrote: > Tengfei, > > > On 09/27/2012 01:05 PM, Tengfei Yin wrote: > >> >> >> 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. >> > > Note that the above Makefile is exactly (except for the package name > itself) the file used in the knitr package (which vignettes are of > course generated with knitr). > > All the details here: > > http://yihui.name/knitr/demo/**vignette/ > > The above document also covers the issue of "vignettes having to > go through Sweave first anyway", and, as you figured it out, it > seems that the workaround is required only if the syntax of your > vignette is not compatible with Sweave. And yes the workaround > involves putting a fake vignette first and do other kind of dark > voodoo. > > BTW I'm assuming you have a good reason to not use a Sweave-compatible > syntax, otherwise maybe you could reconsider, as that would make > things much easier (and you already get some nice improvements to > the rendering of your vignette, when using knitr in Sweave-compatible > mode). > Exactly, I am going to give up to do the dark voodoo...even though I came up with a solution, but not elegant at all looks like R CMD INSTALL run sweave again on my real Rnw to stangle the R file, so in my make file I have to copy a sweavable version of my real Rnw file in the right place, then in this case, the pdf and R code are consistency, but Rnw file are not really, it's just sweavable. At first I hope I can write a Rnw file with knitr without considering the compatibility with Sweave, but I guess that's too tricky, you are right, I already get most I need from knitr, and I can just tweak it to be compatible with sweave, and use above Makefile to get what I need without spending too much time hacking at those stuff. Thanks a lot. Tengfei > Cheers, > H. > > > > >> 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 >> >> >> >> > -- > 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]]