[Rd] Sweave resource leak: leftover temp files (PR#7999)
Duncan Murdoch
murdoch at stats.uwo.ca
Fri Jul 8 16:09:52 CEST 2005
One additional note: followups should only go to R-bugs if they have
the bug number on them (like this message does). Otherwise you end up
generating a separate bug report (PR#7999 was created in your reply to
my submission of PR#7998). Usually it's best just to cc R-devel, unless
you really have additional information to add to the bug report.
We're planning (or in the process of?) changing the bug reporting
system, so this is only a temporary inconvenience.
Duncan Murdoch
On 7/8/2005 9:36 AM, HDoran at air.org wrote:
> This is great. Thank you for your help, but let me make sure I fully
> understand. Here is the looping file I use to subset the data frame,
> create a tex file, and Sweave it. This results in N number of tex files
> where N is equal to the number of rows in the data frame.
>
> list <- unique(wide$stuid)
> master = "master.tex"
> for (i in list){
> tmp1 <- subset(wide, stuid==i)
> tmp2 <- paste(i, "tex", sep=".")
> Sweave("fam_template.Rnw", output=tmp2)
> file.append("fam_master.tex", tmp2)
> }
>
> If I follow correctly, I would need to place these commands inside the
> loop as follows:
>
> list <- unique(wide$stuid)
> master = "master.tex"
> for (i in list){
> tmp1 <- subset(wide, stuid==i)
> tmp2 <- paste(i, "tex", sep=".")
> keep <- list.files(tempdir(), full=TRUE) # keep previous temp
> files
> Sweave("fam_template.Rnw", output=tmp2)
> file.append("fam_master.tex", tmp2)
> temps <- list.files(tempdir(), full=TRUE) unlink(temps[!(temps %in%
> keep)]) # delete the newly created ones
> }
>
>
> Thank you for taking the time to look at this.
>
> Harold
>
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
> Sent: Friday, July 08, 2005 9:28 AM
> To: Duncan Murdoch
> Cc: Doran, Harold; r-bugs at r-project.org; Uwe Ligges; Sean O'Riordain
> Subject: Sweave resource leak: leftover temp files
>
> Harold, I've taken a closer look at your example and I'd call this an
> Sweave bug. It creates tempfiles each time you run it, and doesn't
> delete them at the end. For example:
>
> > list.files(tempdir())
> character(0)
> > testfile <- system.file("Sweave", "Sweave-test-1.Rnw", package =
> "utils") > Sweave(testfile, out="junk.tex") Writing to file junk.tex
> Processing code chunks ...
> 1 : print term verbatim
> 2 : term hide
> 3 : echo print term verbatim
> 4 : term verbatim
> 5 : echo term verbatim
> 6 : echo term verbatim eps pdf
> 7 : echo term verbatim eps pdf
>
> You can now run LaTeX on 'junk.tex'
> > list.files(tempdir())
> [1] "Rf10523" "Rf13872" "Rf17129" "Rf2055" "Rf2203" "Rf2403"
> "Rf27095"
> [8] "Rf2892" "Rf31415" "Rf5290" "Rf6251" "Rf6482" "Rf7055"
> "Rf724"
> > Sweave(testfile, out="C:/temp/junk.tex") Writing to file
> C:/temp/junk.tex Processing code chunks ...
> 1 : print term verbatim
> 2 : term hide
> 3 : echo print term verbatim
> 4 : term verbatim
> 5 : echo term verbatim
> 6 : echo term verbatim eps pdf
> 7 : echo term verbatim eps pdf
>
> You can now run LaTeX on 'C:/temp/junk.tex'
> > list.files(tempdir())
> [1] "Rf10523" "Rf12679" "Rf1311" "Rf13484" "Rf13872" "Rf17129"
> "Rf17288"
> [8] "Rf2055" "Rf21774" "Rf2203" "Rf23417" "Rf2403" "Rf27095"
> "Rf2892"
> [15] "Rf29444" "Rf31128" "Rf31415" "Rf32520" "Rf3338" "Rf5290"
> "Rf5551"
> [22] "Rf6251" "Rf6482" "Rf7055" "Rf724" "Rf7543" "Rf758"
> "Rf7673"
> > unlink(list.files(tempdir(),full=T))
> > list.files(tempdir())
> character(0)
>
> Harold: a workaround for this would be to wrap your Sweave call in
> something like this:
>
> keep <- list.files(tempdir(), full=TRUE) # keep previous temp files
>
> ... Call Sweave here ...
>
> temps <- list.files(tempdir(), full=TRUE) unlink(temps[!(temps %in%
> keep)]) # delete the newly created ones
>
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