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.intervalexcept
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)
--
Mango Solutions
data analysis that delivers
Tel: +44(0) 1249 467 467
Fax: +44(0) 1249 467 468
Mob: +44(0) 7813 526 123
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[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.intervalexcept
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)
--
Mango Solutions
data analysis that delivers
Tel: +44(0) 1249 467 467
Fax: +44(0) 1249 467 468
Mob: +44(0) 7813 526 123
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