.... And now I realize I gave the patches in the wrong order, let me try
again
Cheers,
Romain
Romain Francois wrote:
> [forgot to attach the second patch in the first mail, sorry.]
>
> Hello,
>
> Appending information to the profiler's output seems to generate
> problems. Here is a small example of code :
>
> <code r>
> require(boot)
> Rprof( memory.profiling = TRUE)
> Rprof(NULL)
> for(i in 1:2){
> Rprof( memory.profiling = TRUE, append = TRUE)
> example(boot)
> Rprof(NULL)
> }
> </code>
>
> The problem is that the file Rprof.out contains more than once the
> header information:
>
> $ grep "sample.interval=" Rprof.out
> memory profiling: sample.interval=20000
> memory profiling: sample.interval=20000
> memory profiling: sample.interval=20000
>
> and `summaryRprof` or `R CMD Rprof` are not dealing with it
>
>
>> idx <- grep( "sample", rownames( smp <- summaryRprof()[[1]] ) );
>>
> smp[idx, ]
> self.time self.pct total.time total.pct
> sample.interval=20000 0 0 0.04 0.1
>
> `sample.interval=20000` is incorrectly considered as a function.
>
>
> This is not too much of a big deal, but then if I ask for memory
> profiling information as well, I get nothing:
>
>
>> summaryRprof( mem = "stats")
>>
> Error in tapply(1:1L, list(index = c("sample.interval=20000:profiling:", :
> arguments must have same length
>
>> summaryRprof( mem = "tseries")
>>
> Error in data.frame(..., check.names = FALSE) :
> arguments imply differing number of rows: 1, 1490
>
>> summaryRprof( mem = "both")
>>
> Error in apply(sapply(strsplit(memstuff, ":"), as.numeric), 1, diff) :
> dim(X) must have a positive length
>
> $ R CMD Rprof Rprof.out
>
> Each sample represents seconds.
> Total run time: 0 seconds.
>
> Total seconds: time spent in function and callees.
> Self seconds: time spent in function alone.
>
> % total % self
> total seconds self seconds name
> Illegal division by zero at /usr/local/lib/R/bin/Rprof line 91, <> line
> 1491.
>
> A quick fix could be to ignore all the lines containing sample.interval=
> except the first one, but then if someone wants to actually change the
> interval argument in Rprof, it would not be correct. I attach a patch
> against R-devel/src/library/utils/R/summRprof.R to do that anyway, but I
> will look at a better solution.
>
> I am not fluent enough in Perl to do the same in the Rprof script, it
> looks like it does not handle the memory profiling information anyway. I
> am about to learn Perl, so I guess it could be a useful way to do it. I
> also attach a patch against R-devel/src/scripts/Rprof that would at
> least get rid of the memory profiling information (if any). This is not
> as good as dealing with it, but ... this is the first time I ever touch
> a Perl script.
>
>
> Cheers,
>
> Romain
>
>
>
>
>> version
>>
>
> _
> platform
> i686-pc-linux-gnu
> arch
> i686
> os
> linux-gnu
> system i686,
> linux-gnu
> status Under development
> (unstable)
> major
> 2
> minor 6.0
> year
> 2007
> month
> 03
> day
> 30
> svn rev
> 40983
> language
> R
> version.string R version 2.6.0 Under development (unstable) (2007-03-30
> r40983)
>
--
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--- /tmp/R-devel/src/library/utils/R/summRprof.R 2006-10-05 07:54:38.000000000 +0100
+++ summRprof.R 2007-03-31 21:10:31.000000000 +0100
@@ -32,8 +32,10 @@
repeat({
chunk<-readLines(filename,n=chunksize)
+ chunk <- chunk[ -grep("sample\\.interval=", chunk) ]
if (length(chunk)==0)
break
+
if (memory.profiling){
memprefix<-attr(regexpr(":[0-9]+:[0-9]+:[0-9]+:[0-9]+:",chunk),"match.length")
if (memory=="both"){
@@ -119,6 +121,7 @@
repeat({
chunk<-readLines(filename,n=chunksize)
+ chunk <- chunk[ -grep("sample\\.interval=", chunk) ]
if (length(chunk)==0)
break
memprefix<-attr(regexpr(":[0-9]+:[0-9]+:[0-9]+:[0-9]+:",chunk),
--- /tmp/R-devel/src/scripts/Rprof 2007-03-31 19:58:29.000000000 +0100
+++ Rprof 2007-03-31 21:23:16.000000000 +0100
@@ -57,11 +57,12 @@
%totalcounts = ();
while (<>) {
- if (/^sample\.interval=/) {
- s/sample\.interval=//;
+ if (/.*sample\.interval=/) {
+ s/.*sample\.interval=//;
$sample = $_ / 1e6;
} else {
chomp;
+ s/[^\"]*\"/"/;
@line = split(/ /);
%names = ();
$leaf = @line[0];
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