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HDoran@air.org

2005-Jul-08 13:36 UTC

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

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

Duncan Murdoch

2005-Jul-08 14:09 UTC

head link

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

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

Doran, Harold

2005-Jul-08 15:25 UTC

head link

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

Duncan and d-level

Your proposed solution works well and seems to resolve the issue. I
previously noted to you that it seemed to run slower, but this is not
true. I restarted R and it is equally as fast. Thank you for your
attention to this matter.

-Harold

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca] 
Sent: Friday, July 08, 2005 10:10 AM
To: Doran, Harold
Cc: r-devel at stat.math.ethz.ch
Subject: Re: [Rd] Sweave resource leak: leftover temp files (PR#7999)

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

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R devel - Jul 2005 - Sweave resource leak: leftover temp files (PR#7999)

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