[Rd] Interpretting R profiling output (was More efficient code?)
On Wed, 2005-07-06 at 19:54 +0100, Gavin Simpson wrote: > Dear List, > I fixed up the code in coinertiaI to only return the bits I needed from La.svd() within the permutations - thus producing a 10% speed up. I am still a little unclear about the results from Rprof() (below). Do the timings under self time for .Call and .Fortran include the time spent actually running the called compiled code or are they the overhead of setting up the calls to the compiled code? Many thanks, Gav > > summaryRprof(filename = "Rprof.out") > $by.self > self.time self.pct total.time total.pct > ".Call" 50.40 59.6 50.40 59.6 > "%*%"10.50 12.4 10.50 12.4 > ".Fortran"2.78 3.3 2.78 3.3 > "La.svd" 2.52 3.0 57.98 68.6 > "^" 2.48 2.9 2.48 2.9 > "t.default" 2.30 2.7 2.30 2.7 > "matrix" 1.92 2.3 1.98 2.3 > "as.double" 1.78 2.1 2.70 3.2 > "list"0.88 1.0 0.88 1.0 > "as.double.default" 0.86 1.0 0.86 1.0 > "rep.default" 0.74 0.9 0.86 1.0 > "sum" 0.72 0.9 2.58 3.1 > "!" 0.50 0.6 0.50 0.6 > "diag"0.44 0.5 1.46 1.7 > "qr.coef" 0.42 0.5 6.26 7.4 > "permtest"0.38 0.4 83.60 98.9 > "is.finite" 0.38 0.4 0.38 0.4 > "storage.mode<-" 0.36 0.4 3.26 3.9 > "as.integer" 0.34 0.4 0.40 0.5 > "t" 0.32 0.4 2.62 3.1 > "$" 0.32 0.4 0.32 0.4 > "paste" 0.28 0.3 0.54 0.6 > "teststat"0.24 0.3 83.10 98.3 > "residualMatrix" 0.22 0.3 10.32 12.2 > "qr" 0.20 0.2 1.24 1.5 > ... > > $by.total > total.time total.pct self.time self.pct > "predcoca.perm" 84.50 100.0 0.00 0.0 > "permtest"83.60 98.9 0.38 0.4 > "teststat"83.10 98.3 0.24 0.3 > "coinertiaI" 73.24 86.7 0.18 0.2 > "La.svd" 57.98 68.6 2.52 3.0 > ".Call" 50.40 59.6 50.40 59.6 > "%*%" 10.50 12.4 10.50 12.4 > "residualMatrix" 10.32 12.2 0.22 0.3 > "qr.coef" 6.26 7.4 0.42 0.5 > "storage.mode<-" 3.26 3.9 0.36 0.4 > ".Fortran" 2.78 3.3 2.78 3.3 > "as.double"2.70 3.2 1.78 2.1 > "t"2.62 3.1 0.32 0.4 > "eval" 2.62 3.1 0.14 0.2 > "sum" 2.58 3.1 0.72 0.9 > ... > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Interpretting R profiling output (was More efficient code?)
Gavin Simpson wrote: > On Wed, 2005-07-06 at 19:54 +0100, Gavin Simpson wrote: > >>Dear List, >> > > > I fixed up the code in coinertiaI to only return the bits I needed from > La.svd() within the permutations - thus producing a 10% speed up. I am > still a little unclear about the results from Rprof() (below). > > Do the timings under self time for .Call and .Fortran include the time > spent actually running the called compiled code or are they the overhead > of setting up the calls to the compiled code? They include both. The profiler only sees R calls, it doesn't know what goes on within functions. .Call() is an R call which internally calls some C function, but the profiler just sees the call to .Call. Duncan Murdoch > > Many thanks, > > Gav > > >>summaryRprof(filename = "Rprof.out") >>$by.self >> self.time self.pct total.time total.pct >>".Call" 50.40 59.6 50.40 59.6 >>"%*%"10.50 12.4 10.50 12.4 >>".Fortran"2.78 3.3 2.78 3.3 >>"La.svd" 2.52 3.0 57.98 68.6 >>"^" 2.48 2.9 2.48 2.9 >>"t.default" 2.30 2.7 2.30 2.7 >>"matrix" 1.92 2.3 1.98 2.3 >>"as.double" 1.78 2.1 2.70 3.2 >>"list"0.88 1.0 0.88 1.0 >>"as.double.default" 0.86 1.0 0.86 1.0 >>"rep.default" 0.74 0.9 0.86 1.0 >>"sum" 0.72 0.9 2.58 3.1 >>"!" 0.50 0.6 0.50 0.6 >>"diag"0.44 0.5 1.46 1.7 >>"qr.coef" 0.42 0.5 6.26 7.4 >>"permtest"0.38 0.4 83.60 98.9 >>"is.finite" 0.38 0.4 0.38 0.4 >>"storage.mode<-" 0.36 0.4 3.26 3.9 >>"as.integer" 0.34 0.4 0.40 0.5 >>"t" 0.32 0.4 2.62 3.1 >>"$" 0.32 0.4 0.32 0.4 >>"paste" 0.28 0.3 0.54 0.6 >>"teststat"0.24 0.3 83.10 98.3 >>"residualMatrix" 0.22 0.3 10.32 12.2 >>"qr" 0.20 0.2 1.24 1.5 >>... >> >>$by.total >> total.time total.pct self.time self.pct >>"predcoca.perm" 84.50 100.0 0.00 0.0 >>"permtest"83.60 98.9 0.38 0.4 >>"teststat"83.10 98.3 0.24 0.3 >>"coinertiaI" 73.24 86.7 0.18 0.2 >>"La.svd" 57.98 68.6 2.52 3.0 >>".Call" 50.40 59.6 50.40 59.6 >>"%*%" 10.50 12.4 10.50 12.4 >>"residualMatrix" 10.32 12.2 0.22 0.3 >>"qr.coef" 6.26 7.4 0.42 0.5 >>"storage.mode<-" 3.26 3.9 0.36 0.4 >>".Fortran" 2.78 3.3 2.78 3.3 >>"as.double"2.70 3.2 1.78 2.1 >>"t"2.62 3.1 0.32 0.4 >>"eval" 2.62 3.1 0.14 0.2 >>"sum" 2.58 3.1 0.72 0.9 >>... >> __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] axTicks on a reverse ylog plot (PR#7973)
Here we go:
the quick fix is really easy, just sorting stuff in axTicks()
(.../src/library/graphics/R/axis.R, diff'ed against R-release) is
sufficient:
--- axis.R
+++ axis-fix.R
@@ -29,7 +29,8 @@
stop("invalid positive 'axp[3]'")
if(is.null(usr)) usr <- par("usr")[if(is.x) 1:2 else 3:4]
else if(!is.numeric(usr) || length(usr) != 2) stop("invalid
'usr'")
-ii <- round(log10(axp[1:2]))
+ii <- round(log10(sort(axp[1:2])))
+usr <- sort(usr)
x10 <- 10^((ii[1] - (iC >= 2)):ii[2])
r <- switch(iC, ## axp[3]
x10,## 1
BTW: In your R code below, you have to use (as documented)
grid(equilogs = FALSE)
We might want to consider to change axTicks anyway:
We could return values from the internal axis() calculations
and therefore replace axTicks calculations by stuff that is much more
reliable. Opinions?
The current equilogs default argument setting is inconvinient anyway,
because it does not fit with the current device setting for real axis
ticks (which can also be done in R, of course).
Uwe Ligges
[EMAIL PROTECTED] wrote:
> There is still issues with the reversed y-log scale plot:
>
> # Test case A: works as expected
> plot(10:100,log="y",ylim=c(100,11))
> grid()
> par("yaxp")
>
> # Test case B: grid does not have horizontal lines; par("yaxp") is
> different
> plot(1:100,log="y",ylim=c(100,10))
> grid()
> par("yaxp")
>
> In the second test case, axTicks for the horizontal lines (in grid())
> returns numeric(0) for spacing ... how do the tick marks get drawn in
> the first place??
> -mt
>
> --please do not edit the information below--
>
> Version:
> platform = powerpc-apple-darwin8.1.0
> arch = powerpc
> os = darwin8.1.0
> system = powerpc, darwin8.1.0
> status = Patched
> major = 2
> minor = 1.1
> year = 2005
> month = 06
> day = 26
> language = R
>
> Locale:
> en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>
> Search Path:
> .GlobalEnv, package:methods, package:stats, package:graphics,
> package:grDevices, package:utils, package:datasets, Autoloads,
> package:base
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] Error message using Packages | Install | Cancel
If we click on the Cancel button after the Packages | Install menu items in Windows 2.1.1 (dated 2005-06-23) it gives an error message. There really should be no error here since we intended not to install anything -- that is why we pressed Cancel. This is what appears on the console: > utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, type = type) : no packages were specified __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Sweave resource leak: leftover temp files (PR#7998)
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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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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Re: [Rd] Sweave resource leak: leftover temp files
On 7/8/2005 9:36 AM, Doran, Harold 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
> }
There's a wordwrapping error there: the temps <- list.files(...) and
unlink(temps...) should be on separate lines.
I'd also put them immediately after the Sweave call, but they should be
fine where you have them. (The advantage of putting them immediately
after Sweave is that you don't need to think about the next line. If it
created a temp file and you wanted to keep it, you'd need the extra
lines first. But it doesn't, so it doesn't really matter.)
Duncan Murdoch
>
>
> 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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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, [EMAIL PROTECTED] 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:[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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Re: [Rd] Sweave resource leak: leftover temp files (PR#7999)
On 7/8/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > We're planning (or in the process of?) changing the bug reporting > system, so this is only a temporary inconvenience. > I think these points have been raised before but, just in case, some aspects of this, if its changing anyways, that would be nice to see would be: - integration with svn - expansion from bug tracking to issue, change and wishlist tracking Also it would be nice to have a consistent standard way to: - track issues, changes and wishlists in individual packages, not just in R __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] pairs() uses col argument for axes coloring
On 7/8/2005 8:52 AM, Olaf Mersmann wrote: > Hi Duncan, > > On 7/8/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote: >> Olaf Mersmann wrote: > *snip* >> > Looking at the source for pairs() suggests, that this is the case >> > because col is part of the ... argument list which is passed on to >> > localAxis (and from there to axis). Wouldn't it be more approptiate to >> > use the same color box() uses to draw the border around each >> > scatterplot? If yes, should I open a bug for this or how would such a >> > feature request be handled? >> >> The best way is to get the source to pairs() (from the SVN repository >> in https://svn.r-project.org/R/trunk/src/library/graphics/R/pairs.R not >> from looking at it in R), work out what changes are needed, and submit >> them as a patch. You can post the patch in the R-bugs list, or just >> send it to me. Thanks! > > I attached my patch to pairs.R to fix the problem. They way I 'solved' > the issue is by simply ignoring any col argument that is passed to > localAxis and from there to axis. At first I had thought about adding > col explicitly to the argument list of pairs() and then only passing > it on to the panel functions, but that would possibly break existing > code (for example the example panel.cor() in the pairs() man page). I like your fix. It makes pairs() act like plot() in its treatment of col and col.axis parameters. I do find the col.axis treatment a little weird (affecting the labels, but not the axis), but that's a different issue. I'll commit your patch to R-devel and R-patched. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Sweave resource leak: leftover temp files (PR#7999)
Gabor Grothendieck <[EMAIL PROTECTED]> writes: > On 7/8/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > > > We're planning (or in the process of?) changing the bug reporting > > system, so this is only a temporary inconvenience. > > > > I think these points have been raised before but, just in case, some > aspects of this, if its changing anyways, that would be nice to see > would be: > > - integration with svn > - expansion from bug tracking to issue, change and wishlist tracking > > Also it would be nice to have a consistent standard way to: > > - track issues, changes and wishlists in individual packages, not just in R Well, since I'm going on vacation as of *now*, it's not going to happen until August... Re. the last point, it does require that package maintainers play along. They have not been very good at closing issues in the Add-on section of the current bug repo, which is why we currently recommend users to approach the maintainer directly. As a general matter, nobody is going to do bug repository maintenance as a full-time job, so we need to go with a turnkey solution like Bugzilla. We're likely going to lose the mailing list integration as we know it -- we can probably send a copy of all bug reports to r-devel, but there's not going to be a nice way to save the followups automagically. Users will also likely be requested to obtain a password and login before submitting a bug. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message using Packages | Install | Cancel
On 7/8/2005 8:56 AM, Gabor Grothendieck wrote: > If we click on the Cancel button after the Packages | Install menu items in > Windows 2.1.1 (dated 2005-06-23) it gives an error message. There > really should > be no error here since we intended not to install anything -- that is why > we pressed Cancel. This is what appears on the console: > >> utils:::menuInstallPkgs() > Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, > type = type) : > no packages were specified I'd consider a patch to fix this, but it doesn't look serious enough to make it onto my list of things to do myself. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [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:[EMAIL PROTECTED]
Sent: Friday, July 08, 2005 10:10 AM
To: Doran, Harold
Cc: r-devel@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, [EMAIL PROTECTED] 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:[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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Re: [Rd] Error message using Packages | Install | Cancel
On 7/8/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 7/8/2005 8:56 AM, Gabor Grothendieck wrote: > > If we click on the Cancel button after the Packages | Install menu items in > > Windows 2.1.1 (dated 2005-06-23) it gives an error message. There > > really should > > be no error here since we intended not to install anything -- that is why > > we pressed Cancel. This is what appears on the console: > > > >> utils:::menuInstallPkgs() > > Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, > > type = type) : > > no packages were specified > > I'd consider a patch to fix this, but it doesn't look serious enough to > make it onto my list of things to do myself. > > Duncan Murdoch > Sure. I will file a bug report so it does not get lost. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Packages | Install >Cancel gives error msg in Windows GUI (PR#8000)
Full_Name: G. Grothendieck Version: R version 2.1.1, 2005-06-23 OS: Windows XP Submission from: (NULL) (216.59.244.202) In the Windows GUI, choosing the Packages Menu, then Install and then clicking on Cancel gives an error message saying that nothing was specified to be installed: > utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, type = type) : no packages were specified however, its not erroneous -- we intended not to install anything. That is why we pressed Cancel. This was discussed on r-devel. See: https://www.stat.math.ethz.ch/pipermail/r-devel/2005-July/033923.html __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] pgamma(Inf, 1.1, 1.1) (PR#8001)
The call of pgamma(Inf, 1.1, 1.1) does not finish on my machines within 5 minutes... (both under Linux and Windows). Haven't looked in the sources yet. Thanks to Dietrich Trenkler for bringing this up in a private discussion. Uwe Ligges --please do not edit the information below-- Version: platform = i386-pc-mingw32 arch = i386 os = mingw32 system = i386, mingw32 status = major = 2 minor = 1.1 year = 2005 month = 06 day = 20 language = R Windows NT 4.0 (build 1381) Service Pack 6 Locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 Search Path: .GlobalEnv, package:methods, package:stats, package:graphics, package:grDevices, package:datasets, package:utils, package:fortunes, Autoloads, package:base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Packages | Install >Cancel gives error msg in Windows GUI (PR#8002)
On 7/8/2005 11:46 AM, [EMAIL PROTECTED] wrote: > Full_Name: G. Grothendieck > Version: R version 2.1.1, 2005-06-23 > OS: Windows XP > Submission from: (NULL) (216.59.244.202) > > > > In the Windows GUI, choosing the Packages Menu, then Install and then > clicking on Cancel gives an error message saying that nothing was specified > to be installed: > >> utils:::menuInstallPkgs() > Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, type = > type) : > no packages were specified > > however, its not erroneous -- we intended not to install anything. That > is why we pressed Cancel. > > This was discussed on r-devel. See: > > https://www.stat.math.ethz.ch/pipermail/r-devel/2005-July/033923.html My conclusion there was that this error message should not be appearing, but it's not worth my time to fix. I'll move this bug report to the wishlist. If someone wants to submit a patch to fix it, I'll look at it. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Suggestion: Help users sort data frames
I've noticed that a frequently asked question on R-help is how to sort a
data frame by multiple columns. Since this question is asked so often,
making this task easier for users seems a worthwhile goal.
At a minimum, the following changes to the documentation would surely be
helpful and reduce email postings to R-help:
1. In the "See Also" section of the help page for 'sort' it currently says:
"order for sorting on or reordering multiple variables".
Appending the phrase "(including data frames)" could be helpful.
2. Include a simple example on sorting a data frame in the 'sort' help.
In an ideal world this example should belong in the help for 'order', but
people are going to be reading the 'sort' page first. Here's one example:
# Sort a data frame by multiple columns
d = data.frame(b=factor(c("Hi","Med","Hi","Low"),levels=c("Low","Med","Hi"),
ordered=TRUE),
x=c("A","D","A","C"),y=c(8,3,9,9),z=c(1,1,1,2))
d[order(d$b,d$z,d$y),]
3. It looks like the help page for 'order' only shows sorting of matrices
(and row-wise sorting at that!). Since column-wise sorting is may be more
common, the example above might beneficially be included in the 'order'
help page as well.
A minor bug-report here: The help for 'order' includes this example:
## For character vectors we can make use of rank:
cy <- as.character(y)
rbind(x,y,z)[, order(x, -rank(y), z)]
I'm not sure what the intention was, but 'cy' is not used, so something
seems to be amis.
Alternatively, I wrote a formula-based function for sorting data frames
via calls like: sort.data.frame(~ -x +y +z, dat)
The function can be found here:
http://tolstoy.newcastle.edu.au/R/help/04/09/4300.html
When emails to R-help ask how to sort data frames, responses often
reference this function so it seems to have been very helpful for people.
I showed the function to Thomas Lumley and he said it looked nice but that
using a minus sign for reverse sorting is a bit anti-R flavored since a
minus sign usually means to omit terms from a formula.
Sincerely,
Kevin Wright
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Re: [Rd] Suggestion: Help users sort data frames
This functionality does seem needed in base R to me too but
in the interim you could create a package to make it available on
CRAN or if that seems excessive for just one function you could
contact the author of one of the multi-author packages and see if
they would include it in their package.
On 7/8/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
> I've noticed that a frequently asked question on R-help is how to sort a
> data frame by multiple columns. Since this question is asked so often,
> making this task easier for users seems a worthwhile goal.
>
> At a minimum, the following changes to the documentation would surely be
> helpful and reduce email postings to R-help:
>
> 1. In the "See Also" section of the help page for 'sort' it currently says:
> "order for sorting on or reordering multiple variables".
> Appending the phrase "(including data frames)" could be helpful.
>
> 2. Include a simple example on sorting a data frame in the 'sort' help.
> In an ideal world this example should belong in the help for 'order', but
> people are going to be reading the 'sort' page first. Here's one example:
>
> # Sort a data frame by multiple columns
> d = data.frame(b=factor(c("Hi","Med","Hi","Low"),levels=c("Low","Med","Hi"),
> ordered=TRUE),
> x=c("A","D","A","C"),y=c(8,3,9,9),z=c(1,1,1,2))
> d[order(d$b,d$z,d$y),]
>
> 3. It looks like the help page for 'order' only shows sorting of matrices
> (and row-wise sorting at that!). Since column-wise sorting is may be more
> common, the example above might beneficially be included in the 'order'
> help page as well.
>
> A minor bug-report here: The help for 'order' includes this example:
> ## For character vectors we can make use of rank:
> cy <- as.character(y)
> rbind(x,y,z)[, order(x, -rank(y), z)]
> I'm not sure what the intention was, but 'cy' is not used, so something
> seems to be amis.
>
>
>
> Alternatively, I wrote a formula-based function for sorting data frames
> via calls like: sort.data.frame(~ -x +y +z, dat)
> The function can be found here:
> http://tolstoy.newcastle.edu.au/R/help/04/09/4300.html
> When emails to R-help ask how to sort data frames, responses often
> reference this function so it seems to have been very helpful for people.
> I showed the function to Thomas Lumley and he said it looked nice but that
> using a minus sign for reverse sorting is a bit anti-R flavored since a
> minus sign usually means to omit terms from a formula.
>
>
> Sincerely,
>
> Kevin Wright
>
> __
> R-devel@r-project.org mailing list
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>
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