From murdoch at stats.uwo.ca  Fri Jul  8 16:09:52 2005
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Fri, 08 Jul 2005 10:09:52 -0400
Subject: [Rd] Sweave resource leak: leftover temp files (PR#7999)
In-Reply-To: <20050708133630.3F642103DA@slim.kubism.ku.dk>
References: <20050708133630.3F642103DA@slim.kubism.ku.dk>
Message-ID: <42CE8930.4060009@stats.uwo.ca>

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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] Sweave resource leak: leftover temp files (PR#7999)
Duncan Murdoch