Re: [R] Adding an Sweave Vignette to a package

From: Doran, Harold <HDoran_at_air.org>
Date: Tue, 22 Jan 2008 08:48:54 -0500


Thanks, Uwe. Before I modify this path, I want to make sure of one thing. My path is set according to the specifications in the document prescribed by Duncan Murdoch (at link below). Indeed, my path includes the proper location of my MikTex and pdflatex.exe files. Here is my path from the command you gave below:

"c:\\Rtools\\bin;C:\\Perl\\bin\\;c:\\Rtools\\MinGW\\bin;c:\\texmf\\mikte
k\\bin;c:\\cygwin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System3
2\\Wbem;C:\\subversion\\Subversion\\bin;C:\\Program
Files\\R\\R-2.2.0\\bin; "

http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset

AFAIK, the path indeed is set according to the Murdoch prescription for building R packages, my pdflatex.exe lives in the directory pointed to in this path, yet R cannot see it when doing Rcmd build.

I can successfully build and use the package at this point (again as my other problem now solved). However, I am not sure what I should work on to resolve the issue of building the vignette.

There are so many steps in building a package, I may have missed something somewhere. So, if you see an error I appreciate any advice.

Harold

> -----Original Message-----
> From: Uwe Ligges [mailto:ligges_at_statistik.tu-dortmund.de]
> Sent: Tuesday, January 22, 2008 4:15 AM
> To: Doran, Harold
> Cc: James W. MacDonald; R Help
> Subject: Re: [R] Adding an Sweave Vignette to a package
>
> In R, type
> Sys.getenv("PATH")
> and you will probably find that the PATH does not include the
> path of the pdflatex executable of the mikTeX distribution.
>
> Uwe
>
>
> Doran, Harold wrote:
> > Jim
> >
> > First thanks for your patience. I use MikTex as well. I do
> have both
> > (texti2dvi and pdflatex) on my local machine. I copied and
> pasted the
> > code below and stepped through it. I think this break down with the
> > following error. Indeed, I think there is a path problem.
> >
> > However, I don't see a resolution in either Writing R Extensions or
> > the Leisch paper. So, I'm not quite sure what path to
> modify and/or how.
> >
> > Error in texi2dvi("TheVignette.tex", pdf = TRUE) :
> > unable to run pdflatex on 'TheVignette.tex'
> > In addition: Warning message:
> > In system(paste(shQuote(latex), "-interaction=nonstopmode",
> texfile)) :
> > "pdflatex" not found
> >
> >> -----Original Message-----
> >> From: James W. MacDonald [mailto:jmacdon_at_med.umich.edu]
> >> Sent: Monday, January 21, 2008 4:53 PM
> >> To: Doran, Harold
> >> Cc: R Help
> >> Subject: Re: [R] Adding an Sweave Vignette to a package
> >>
> >> What TeX variant are you using? If texi2dvi() can't find
> texi2dvi, it
> >> tries to fall back on pdflatex which has to be in the path.
> >>
> >> I have always had good luck with MikTeX, which does have texi2dvi.
> >>
> >> You could always try
> >>
> >> library(tools)
> >> Sweave("TheVignette.Rnw")
> >> debug(texi2dvi)
> >> texi2dvi("TheVignette.tex", pdf=TRUE)
> >>
> >> and step through to see where it fails, although on the surface it
> >> looks like a path problem.
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >>
> >> Doran, Harold wrote:
> >>> There is now and it looks like I got through the first
> >> phase. But, now
> >>> I get the error below.
> >>>
> >>> * DONE (MiscPsycho)
> >>> * creating vignettes ... ERROR
> >>> Loading required package: statmod
> >>> Below is what alpha *would be* if the item were removed
> >>>
> >>> Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
> >>> quiet)
> >>> :
> >>> unable to run pdflatex on 'MP.tex'
> >>> Calls: buildVignettes -> texi2dvi
> >>> In addition: Warning messages:
> >>> 1: In readLines(f[1]) : incomplete final line found on 'MP.Rnw'
> >>> 2: In system(paste(shQuote(latex), "-interaction=nonstopmode",
> >>> texfile))
> >>> :
> >>> "pdflatex" not found
> >>> Execution halted
> >>>
> >>> I do have pdflatex, it's what I use all of the time.
> >> However, how do I
> >>> point to it for this build process?
> >>>
> >>>> -----Original Message-----
> >>>> From: James W. MacDonald [mailto:jmacdon_at_med.umich.edu]
> >>>> Sent: Monday, January 21, 2008 4:09 PM
> >>>> To: Doran, Harold
> >>>> Cc: R Help
> >>>> Subject: Re: [R] Adding an Sweave Vignette to a package
> >>>>
> >>>> Hi Harold,
> >>>>
> >>>> Doran, Harold wrote:
> >>>>> I'm finalizing development of a package that will include a
> >>>> vignette.
> >>>>> Without the vignette, the package builds fine with no
> >>>> warnings and is
> >>>>> ready for distribution. Now, I am following the directions for
> >>>>> developing vignettes "Sweave, Part II: Package Vignettes"
> >>>> by Friedrich
> >>>>> Leisch.
> >>>>>
> >>>>> I am using a windows XP machine (other session info
> >> below). Here is
> >>>>> what I have done.
> >>>>>
> >>>>> 1) I add the 'inst/doc' directory to the package source tree.
> >>>>> 2) I have added the following information in the preamble
> >>>> of the .Rnw
> >>>>> file
> >>>>>
> >>>>> % \VignetteIndexEntry{An \texttt{R} Package for Miscellaneous
> >>>>> Psychometric Analyses} % \VignetteDepends{MiscPsycho,
> statmod} %
> >>>>> \VignetteKeyword{misc}
> >>>>>
> >>>>> 3) I then copy the file "MP.Rnw" to the 'inst/doc' directory.
> >>>>> 4) I then run Rcmd build g:\MiscPsycho
> >>>>>
> >>>>> The process begins as usual and it even tries to create the
> >>>> vignette.
> >>>>> However, it runs into an error at code chunk 1
> >> complaining that it
> >>>>> cannot find the function called simRasch(). This simRasch
> >>>> function is
> >>>>> one of the functions developed for this package and one
> that will
> >>>>> exist only when the package is built. The build process
> is halted.
> >>>>>
> >>>>> I'm not sure how to handle this. Any advice is appreciated.
> >>>> Is there a library(MiscPsycho) at the beginning of that
> code chunk?
> >>>>
> >>>> Best,
> >>>>
> >>>> Jim
> >>>>
> >>>>
> >>>>> Harold
> >>>>>
> >>>>>> sessionInfo()
> >>>>> R version 2.6.1 (2007-11-26)
> >>>>> i386-pc-mingw32
> >>>>>
> >>>>> locale:
> >>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> >>>>> States.1252;LC_MONETARY=English_United
> >>>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >>>>>
> >>>>> attached base packages:
> >>>>> [1] stats graphics grDevices utils datasets
> >> methods base
> >>>>>
> >>>>> other attached packages:
> >>>>> [1] statmod_1.3.3
> >>>>>
> >>>>> loaded via a namespace (and not attached):
> >>>>> [1] tools_2.6.1
> >>>>>
> >>>>> ______________________________________________
> >>>>> R-help_at_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.
> >>>> --
> >>>> James W. MacDonald, M.S.
> >>>> Biostatistician
> >>>> Affymetrix and cDNA Microarray Core University of
> Michigan Cancer
> >>>> Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
> >>>> 734-647-5623
> >>>>
> >> --
> >> James W. MacDonald, M.S.
> >> Biostatistician
> >> Affymetrix and cDNA Microarray Core
> >> University of Michigan Cancer Center
> >> 1500 E. Medical Center Drive
> >> 7410 CCGC
> >> Ann Arbor MI 48109
> >> 734-647-5623
> >>
> >
> > ______________________________________________
> > R-help_at_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.
>



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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. Received on Tue 22 Jan 2008 - 13:53:15 GMT

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