From rfrancois at mango-solutions.com  Sun Apr  1 09:51:20 2007
From: rfrancois at mango-solutions.com (Romain Francois)
Date: Sun, 01 Apr 2007 08:51:20 +0100
Subject: [Rd] Probem with argument "append" in "Rprof"
In-Reply-To: <460EC5A6.8080401@mango-solutions.com>
References: <460EC5A6.8080401@mango-solutions.com>
Message-ID: <460F6478.3050308@mango-solutions.com>

.... 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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[Rd] Probem with argument "append" in "Rprof"
Romain Francois