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

[Martin Morgan]

On 09/27/2012 01:05 PM, Tengfei Yin wrote:
>
>
> On Thu, Sep 27, 2012 at 2:42 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>> 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...

As you go down that road, you'll want to make sure that 
vignette(package="ggbio") and help.start() pages for ggbio list 
appropriate files -- the pdf, Rnw, and R files for your real vignette. 
Also, although the Bioconductor build system runs R CMD check 
--no-vignettes, it seems like you'd like to have the R code in the 
vignette run as part of the check. Hacking might be quite painful! Martin

>
> 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
>         <yintengfei at gmail.com <mailto: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.
>         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]]
>
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>
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>
>
>     --
>     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 at fhcrc.org <mailto:hpages at fhcrc.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
>
>
>


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