[R] Adding an Sweave Vignette to a package

Tue Jan 22 15:01:58 CET 2008

Doran, Harold wrote:
> 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.

Hmm, hard to tell, although I think it might make sense to upgrade your 
version of R, given I am correct that you are running R-2.2.0 (from the 
output you gave above).

Uwe

> 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.
> 
> ______________________________________________
> 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.