From HDoran at air.org  Fri Jul  8 15:36:30 2005
From: HDoran at air.org (HDoran@air.org)
Date: Fri,  8 Jul 2005 15:36:30 +0200 (CEST)
Subject: [Rd] Sweave resource leak: leftover temp files (PR#7999)
Message-ID: <20050708133630.3F642103DA@slim.kubism.ku.dk>

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



[Rd] Sweave resource leak: leftover temp files (PR#7999)
HDoran@air.org