Re: [R] makefile for sweave

Wolfgang Raffelsberger Thu, 26 Nov 2009 07:52:22 -0800

Dear all,

I can't get texi2dvi working right. Basically I'd like to convert a .lexto .pdf without having to fiddle with the issue Sweave.sty not being inmy current directory (as this was sugested in other posts on this list).


When I'm in the R-Gui I can get the help via
?texi2dvi
(So I conclude its installed.)

However, when I try to use it to concert a .tex to .pdf I get trouble ...

For example :
A)
The file "test02.r" contains :
Sweave("Sweave_test01.rnw")
library(tools)
texi2dvi("Sweave_test01.tex", pdf =T)

Now, when I run on the linux command line :
R --vanilla -q < test02.r

I get :
> Sweave("Sweave_test01.rnw")
Writing to file Sweave_test01.tex
Processing code chunks ...
1 : term hide (label=chunk_ini)
2 : term verbatim eps pdf (label=Fig01)
3 : term tex (label=packageVersionInfo)
Loading required package: xtable

You can now run LaTeX on 'Sweave_test01.tex'
> library(tools)
> texi2dvi("Sweave_test01.tex", pdf =T)
Error in texi2dvi("Sweave_test01.tex", pdf = T) :
 Running 'texi2dvi' on 'Sweave_test01.tex' failed.
Messages:
sh: texi2dvi: command not found
Execution halted


B)

In a previous message on this list I found the following command line(s)suggested, but I my case it won't work


star5_R_test_> R CMD texi2dvi --help
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found

similarly, when execute (as sugested) I get the same error message

star5_R_test_> R CMD texi2dvi -p Sweave_test01.tex
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found

I don't understand how can a command can be present (= installed) andstill not being found as the error messages suggest ?


For completeness :
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu

locale:
[1] C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] xtable_1.5-6         mouse4302probe_2.5.0 AnnotationDbi_1.8.1

[4] mouse4302cdf_2.5.0 MASS_7.3-3 fdrtool_1.2.5[7] limma_3.2.1 affyPLM_1.22.0 preprocessCore_1.8.0[10] gcrma_2.18.0 affy_1.24.2 Biobase_2.6.0

loaded via a namespace (and not attached):

[1] Biostrings_2.14.3 DBI_0.2-4 IRanges_1.4.4 RSQLite_0.7-3[5] affyio_1.14.0 splines_2.10.0 tools_2.10.0




Thank's in advance,
Wolfgang


Charles C. Berry a écrit :

On Tue, 8 Sep 2009, Welma Pereira wrote:

Hello, I have the following makefile. The problem is that thebibliographydoesn t work. Any help would be appreciated! I really don t don twhat to

do..:-(



# The sources of the report (tex, Rnw and other files (e.g. bib, idx))
TEX_CMPS = Report problem
RNW_CMPS = prop1 prop2 ExeExps
OTHER =  Report.bib

# The name of the report to produce
all: Report.pdf

code: $(RNW_CMPS:=.R)

clean:
   rm -f  *.log *.dvi *~

# On what does the report depends?
Report.pdf: $(TEX_CMPS:=.tex) $(RNW_CMPS:=.tex) ${OTHER} makefile
   TEXINPUTS=${TPUTS} pdflatex $<
   TEXINPUTS=${TPUTS} pdflatex $<


IIRC

    R CMD texi2dvi -p <target.tex>

takes care of finding sweave.sty and running latex thru all theiterations needed to build cross-references and a usable pdf.


Try

    R CMD texi2dvi --help

at the shell prompt.

HTH,

Chuck


   rm *.log
#    mv *.aux  $(dir $<)

# How to build the tex files from the Rnw (Sweave) files
%.tex: %.Rnw
   echo "library(utils); options(width=60);  Sweave('$<')" | ${R_PRG}
--no-save --vanilla
   mv $(notdir $*.tex)  $(dir $<)


# How to build the R code files from the Rnw (Sweave) files
%.R: %.Rnw
   echo "library(utils); Stangle('$<')" | ${R_PRG} --no-save --vanilla

%.bib:
   TEXINPUTS=${TPUTS} pdflatex $<
   bibtex $<

%.aux:
   TEXINPUTS=${TPUTS} pdflatex $<
   bibtex $<

%.idx:
   TEXINPUTS=${TPUTS} pdflatex $<
   makeindex $<

cheers!

    [[alternative HTML version deleted]]

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Charles C. Berry                            (858) 534-2098

Dept of Family/PreventiveMedicine

E mailto:cbe...@tajo.ucsd.edu                UC San Diego

http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego92093-0901


______________________________________________


. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives

IGBMC,1 rue Laurent Fries, 67404 Illkirch Strasbourg, France

Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr

______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] makefile for sweave

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