[R] texi2dvi: option "clean" also deletes the generated pdf file

Marius Hofert m_hofert at web.de
Thu Aug 19 15:13:33 CEST 2010 

Dear all,

many thanks for your help. I totally missed that texi2dvi is also a system command (I don't use that explicitly to compile my .tex docs). So I checked my "system-texi2dvi". It's quite interesting, if I use the option "--mostly-clean", everthing is removed. However, if I use just "--clean", then the generated pdf file is not removed. So the solution is to call (in the shell):
texi2dvi --clean --pdf ./test/myLaTeXFile2.tex
I can call this from within system() [or even use pdflatex directly from within system()]. I guess I don't need R's texi2dvi anymore.

Many thanks

Marius

Ps: Here is the output of what Duncan suggested:

> debug(tools:::.shell_with_capture)
> require(tools)
> filepath <- paste(getwd(),"/test/myLaTeXFile2.tex",sep="")
> sink(file=filepath)
>           cat("\\documentclass{article}\n")
>           cat("\\usepackage[T1]{fontenc}\n")
>           cat("\\usepackage[english]{babel}\n")
>           cat("\\usepackage{blindtext}\n")
>           cat("\\begin{document}\n")
>           cat("\\blindtext[10]\n")
>           cat("\\end{document}\n")
> sink()
> texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
debugging in: .shell_with_capture(paste(shQuote(texi2dvi), "--help"))
debug: {
    outfile <- tempfile("xshell")
    errfile <- tempfile("xshell")
    on.exit(unlink(c(outfile, errfile)))
    status <- if (.Platform$OS.type == "windows") 
        shell(sprintf("%s > %s 2> %s", command, outfile, errfile), 
            input = input, shell = "cmd.exe")
    else system(sprintf("%s > %s 2> %s", command, outfile, errfile), 
        input = input)
    list(status = status, stdout = readLines(outfile, warn = FALSE), 
        stderr = readLines(errfile, warn = FALSE))
}
Browse[2]> 
debug: outfile <- tempfile("xshell")
Browse[2]> 
debug: errfile <- tempfile("xshell")
Browse[2]> 
debug: on.exit(unlink(c(outfile, errfile)))
Browse[2]> 
debug: status <- if (.Platform$OS.type == "windows") shell(sprintf("%s > %s 2> %s", 
    command, outfile, errfile), input = input, shell = "cmd.exe") else system(sprintf("%s > %s 2> %s", 
    command, outfile, errfile), input = input)
Browse[2]> 
debug: system(sprintf("%s > %s 2> %s", command, outfile, errfile), input = input)
Browse[2]> 
debug: list(status = status, stdout = readLines(outfile, warn = FALSE), 
    stderr = readLines(errfile, warn = FALSE))
Browse[2]> 
exiting from: .shell_with_capture(paste(shQuote(texi2dvi), "--help"))
debugging in: .shell_with_capture(paste(shQuote(texi2dvi), opt_pdf, opt_quiet, 
    opt_extra, shQuote(file)))
debug: {
    outfile <- tempfile("xshell")
    errfile <- tempfile("xshell")
    on.exit(unlink(c(outfile, errfile)))
    status <- if (.Platform$OS.type == "windows") 
        shell(sprintf("%s > %s 2> %s", command, outfile, errfile), 
            input = input, shell = "cmd.exe")
    else system(sprintf("%s > %s 2> %s", command, outfile, errfile), 
        input = input)
    list(status = status, stdout = readLines(outfile, warn = FALSE), 
        stderr = readLines(errfile, warn = FALSE))
}
Browse[2]> 
debug: outfile <- tempfile("xshell")
Browse[2]> 
debug: errfile <- tempfile("xshell")
Browse[2]> 
debug: on.exit(unlink(c(outfile, errfile)))
Browse[2]> 
debug: status <- if (.Platform$OS.type == "windows") shell(sprintf("%s > %s 2> %s", 
    command, outfile, errfile), input = input, shell = "cmd.exe") else system(sprintf("%s > %s 2> %s", 
    command, outfile, errfile), input = input)
Browse[2]> 
debug: system(sprintf("%s > %s 2> %s", command, outfile, errfile), input = input)
Browse[2]> 
debug: list(status = status, stdout = readLines(outfile, warn = FALSE), 
    stderr = readLines(errfile, warn = FALSE))
Browse[2]> 
exiting from: .shell_with_capture(paste(shQuote(texi2dvi), opt_pdf, opt_quiet, 
    opt_extra, shQuote(file)))


On 2010-08-19, at 15:02 , Tim Gruene wrote:

> Dear Marius,
> 
> I see. I suppose it's a matter of your version of texi2dvi then - when I do the
> same in a freshly created directory (including the "test" directory), cutting
> and pasting your very code into R leaves me only with "myLaTeXFile2.pdf" and
> "test/myLaTeXFile2.tex"
> 
> This is texi2dvi --version
> texi2dvi (GNU Texinfo 4.11) 1.104
> 
> Tim
> 
> On Thu, Aug 19, 2010 at 01:55:06PM +0200, Marius Hofert wrote:
>> Dear Tim,
>> 
>> if I run ...
>> 
>> ## Example 2: texi2dvi also deletes the generated .pdf
>> require(tools)
>> filepath <- paste(getwd(),"/test/myLaTeXFile2.tex",sep="")
>> sink(file=filepath)
>>          cat("\\documentclass{article}\n")
>>          cat("\\usepackage[T1]{fontenc}\n")
>>          cat("\\usepackage[english]{babel}\n")
>>          cat("\\usepackage{blindtext}\n")
>>          cat("\\begin{document}\n")
>>          cat("\\blindtext[10]\n")
>>          cat("\\end{document}\n")
>> sink()
>> texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE) 
>> 
>> ... on a "fresh-and-clean" working directory (and also no files in the subdirectory ./test), I only get the file myLaTeXFile2.tex in ./test, so *everything* (including the .pdf) is deleted :-(
>> 
>> I work with R version 2.11.1 (2010-05-31) on a MacBook Pro running 10.6.4.
>> 
>> Cheers,
>> 
>> Marius
>> 
>> On 2010-08-19, at 13:38 , Tim Gruene wrote:
>> 
>>> Dear Marius,
>>> 
>>> yes, that's what I had meant.
>>> 
>>> I am sorry I had not actually tested my suggestion nor your problem (bad
>>> practice). Now I have and actually in case 2 you describe I only end up
>>> with test/myLaTeXFile2.tex and myLaTeXFile2.pdf.
>>> 
>>> If, however, I run texi2dvi at least once with option 'clean=F', the auxiliary files
>>> are generated and left in the path. Also upon a subsequent run with the option
>>> 'clean=T', they are not being deleted. 
>>> 
>>> Could this also be the case for you, i.e., that you once used the option
>>> 'clean=F' (or not set at all) and now are made believe 'clean=T' does not work
>>> because they are still there but actually left-overs from the old run?
>>> 
>>> I run "R version 2.7.1 (2008-06-23)" on Debian stable.
>>> 
>>> Kind regards, Tim
>>> 
>>> On Thu, Aug 19, 2010 at 12:41:57PM +0200, Marius Hofert wrote:
>>>> Dear Tim,
>>>> 
>>>> you mean
>>>> 
>>>> require(tools)
>>>> filepath <- paste(getwd(),"/test/myLaTeXFile2.tex",sep="")
>>>> sink(file=filepath)
>>>>         cat("\\documentclass{article}\n")
>>>>         cat("\\usepackage[T1]{fontenc}\n")
>>>>         cat("\\usepackage[english]{babel}\n")
>>>>         cat("\\usepackage{blindtext}\n")
>>>>         cat("\\begin{document}\n")
>>>>         cat("\\blindtext[10]\n")
>>>>         cat("\\end{document}\n")
>>>> sink()
>>>> texi2dvi(filepath,pdf=TRUE,quiet=TRUE,texi2dvi=getOption("texi2dvi --mostly-clean"))
>>>> 
>>>> ?
>>>> The problem is that this does not work. It produces the same output as my "Example 2" without the "clean"-option. So it leaves all files in the working directory. 
>>>> 
>>>> The reason why I am looking for a "clean-up" is that I have to compile several hundred LaTeX files in different directories...
>>>> 
>>>> Cheers,
>>>> 
>>>> Marius
>>>> 
>>>> 
>>>> On 2010-08-19, at 12:33 , Tim Gruene wrote:
>>>> 
>>>>> Dear Marius,
>>>>> 
>>>>> from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
>>>>> 'clean=F' and use 'texi2dvi = getOption("texi2dvi --mostly-clean")' instead.
>>>>> 
>>>>> Tim
>>>>> 
>>>>> On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
>>>>>> Dear expeRts,
>>>>>> 
>>>>>> below are two examples of using texi2dvi. The problem becomes clear from the 
>>>>>> second example: on cleaning, texi2dvi also deletes the generated .pdf file.
>>>>>> Is there a solution?
>>>>>> 
>>>>>> Cheers,
>>>>>> 
>>>>>> Marius
>>>>>> 
>>>>>> ## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
>>>>>> require(tools)
>>>>>> sink(file="myLaTeXFile1.tex")
>>>>>>        cat("\\documentclass{article}\n")
>>>>>>        cat("\\usepackage[T1]{fontenc}\n")
>>>>>>        cat("\\usepackage[english]{babel}\n")
>>>>>>        cat("\\usepackage{blindtext}\n")
>>>>>>        cat("\\begin{document}\n")
>>>>>>        cat("\\blindtext[10]\n")
>>>>>>        cat("\\end{document}\n")
>>>>>> sink()
>>>>>> texi2dvi("myLaTeXFile1.tex",pdf=TRUE,clean=TRUE,quiet=TRUE) 
>>>>>> 
>>>>>> ## Example 2: texi2dvi also deletes the generated .pdf
>>>>>> require(tools)
>>>>>> filepath <- paste(getwd(),"/test/myLaTeXFile2.tex",sep="")
>>>>>> sink(file=filepath)
>>>>>>        cat("\\documentclass{article}\n")
>>>>>>        cat("\\usepackage[T1]{fontenc}\n")
>>>>>>        cat("\\usepackage[english]{babel}\n")
>>>>>>        cat("\\usepackage{blindtext}\n")
>>>>>>        cat("\\begin{document}\n")
>>>>>>        cat("\\blindtext[10]\n")
>>>>>>        cat("\\end{document}\n")
>>>>>> sink()
>>>>>> texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
>>>>>> 
>>>>>> ______________________________________________
>>>>>> 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.
>>>>> 
>>>>> -- 
>>>>> --
>>>>> Tim Gruene
>>>>> Institut fuer anorganische Chemie
>>>>> Tammannstr. 4
>>>>> D-37077 Goettingen
>>>>> 
>>>>> GPG Key ID = A46BEE1A
>>>>> 
>>> 
>>> -- 
>>> --
>>> Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
>>> 
>>> GPG Key ID = A46BEE1A
>>> 
> 
> -- 
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
>

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