[R] Adding an Sweave Vignette to a package

[Uwe Ligges]

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.