Re: [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:[EMAIL PROTECTED]
Sent: Friday, July 08, 2005 9:28 AM
To: Duncan Murdoch
Cc: Doran, Harold; [EMAIL PROTECTED]; 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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[Rd] Bug with Cor(..., method='spearman") and by() (PR#9921)
I posted this on R help, and a few others responded indicating they too
were able to replicate the error as a function of missing data. I
believe this should not be the case and hence and reporting it here.
### Code provided on R-Help by Ivar Herfindal
# Simulate data
testdata <- cbind.data.frame(gr=3Drep(letters[1:4], each=3D5), =
aa=3Drnorm(20),
bb=3Drnorm(20))
# Introduce some missingness
testdata[1:5, 2] <- NA
# This works fine
by(testdata[,c("aa", "bb")], testdata$gr, cor, use=3D"complete",
method=3D"pearson")
# This induces error
by(testdata[,c("aa", "bb")], testdata$gr, cor, use=3D"complete",
method=3D"spearman")
Error in FUN(data[x, ], ...) : 'x' is empty
## Alternatively, we can try this
# This works fine
by(testdata[,c('aa', 'bb')], testdata$gr, cor, use=3D'complete',
method=3D'pearson')
## This induces the same error
by(testdata[,c('aa', 'bb')], testdata$gr, cor, use=3D'complete',
method=3D'spearman')
Error in FUN(data[x, ], ...) : 'x' is empty
I am using Windows XP with session info below
Harold Doran
> sessionInfo()
R version 2.5.0 (2007-04-23)=20
i386-pc-mingw32=20
locale:
LC_COLLATE=3DEnglish_United States.1252;LC_CTYPE=3DEnglish_United
States.1252;LC_MONETARY=3DEnglish_United
States.1252;LC_NUMERIC=3DC;LC_TIME=3DEnglish_United States.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets"
"methods" "base"=20
other attached packages:
mlmRevlme4 Matrix lattice=20
"0.995-1" "0.99875-2" "0.99875-3""0.15-4"=20
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