search for: rprof

Displaying 20 results from an estimated 255 matches for "rprof".

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2007 Mar 31
1
Probem with argument "append" in "Rprof"
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...
2001 Oct 23
2
Possible bug, Rprof() and scan(pipe()) (PR#1140)
This looks like a bug? Unable to use scan(pipe()) while profiling. I have no idea whether this version of R violates the "do not use `Rprof' in an executable built for profiling" warning in ?Rprof. Thanks -Don > version _ platform powerpc-apple-darwin1.4 arch powerpc os darwin1.4 system powerpc, darwin1.4 status Patched major 1 minor 3.1 year 2001 month 10 day 15 language R >...
2009 Jun 12
1
Rprof loses all system() time
Rprof seems to ignore all time spent inside system() calls. E.g., this simple example actually takes about 10 seconds, but Rprof thinks the total time is only 0.12 seconds: > Rprof("sleep-system.out") ; system.time(system(command="sleep 10")) ; Rprof(NULL) user system elapsed...
2004 May 13
0
Rprof ignores top-level computation (PR#6883)
Full_Name: John Garvin Version: 1.9.0 OS: Linux Submission from: (NULL) (128.42.129.78) This may or may not technically be a bug, but it's certainly an annoyance. Rprof only takes into account computation that occurs inside functions. If a time-consuming operation occurs outside a function, it doesn't record the time it takes. Consider this program 'array.r': Rprof() foo <- array(1:1000000, dim=c(100,50,200)) bar <- c(1:1000, dim=c(1000000,3)) f...
2010 Jan 05
1
Naming functions for the purpose of profiling
Hi all, I have some long-running code that I'm trying to profile. I am seeing a lot of time spent inside the <Anonymous> function. Of course, this can in fact be any of several functions, but I am unable to see how I could use the information from Rprof.out to discern which function is taking the most time. An example line from my Rprof.out is: rbernoulli <Anonymous> runOneRound FUN lapply sfLapply doTryCatch tryCatchOne tryCatchList tryCatch try eval.with.vis eval.with.vis source In my case, the <Anonymous> functions seem to be an...
2004 Oct 19
0
Question on Rprof(); was: Re: sapply and loop
Yes. It should have something to do with read/write permissions, but it is not clear how it happens. I can write file to C drive using R. I usually write my results matrix to a txt file in C drive. For Rprof(), the boot.out file can be created, but only with one line sample.interval=20000 The situation is the same even if I specify the directory to the D drive,where I have the full read/write permissions. Anyway, I do success in my own laptops. Thanks. Yours, Zhen >From: Uwe Ligges <ligges...
2010 Sep 23
0
R CMD Rprof --help suggestion
Hi, >From reading ?Rprof, I checked R CMD Rprof --help and learned that there are options to specify the min % to print. This is currently (R-devel r52975) displayed with the --help option as --min%total minimum % to print for 'by total' --min%self minimum % to print for 'by self'...
2002 Jun 11
2
Puzzled by what Rprof is telling me
I am using Rprof() to help find ways to improve performance. I found a function whose total seconds and self seconds were large. I replaced it with something else. The something else had a small number of total seconds and self seconds. But the total time did not decrease. I don't understand how that could...
2011 Feb 11
1
Help optimizing EMD::extrema()
Hi folks, I'm attempting to use the EMD package to analyze some neuroimaging data (timeseries with 64 channels sampled across 1 million time points within each of 20 people). I found that processing a single channel of data using EMD::emd() took about 8 hours. Exploration using Rprof() suggested that most of the compute time was spent in EMD::extrema(). Looking at the code for EMD:extrema(), I managed to find one obvious speedup (switching from employing rbind() to c()) and I suspect that there may be a way to further speed things up by pre-allocating all the objects that are c...
2012 Dec 11
1
Rprof causing R to crash
I'm trying to use Rprof() to identify bottlenecks and speed up a particullary slow section of code which reads in a portion of a tif file and compares each of the values to values of predictors used for model fitting. I've written up an example that anyone can run. Generally temp would be a section of a tif read int...
2020 Feb 26
1
Profiling: attributing costs to place of invocation (instead of place of evaluation)?
Hi Consider the following example: f <- function(expr) g(expr) g <- function(expr) { ? h(expr) } h <- function(expr) { ? expr # evaluation happens here ? i(expr) } i <- function(expr) { ? expr # already evaluated, no costs here ? invisible() } rprof <- tempfile() Rprof(rprof) f(replicate(1e2, sample.int(1e4))) Rprof(NULL) cat(readLines(rprof), sep = "\n") #> sample.interval=20000 #> "sample.int" "FUN" "lapply" "sapply" "replicate" "h" "g" "f" #&g...
2005 Jul 21
3
Rprof fails in combination with RMySQL
Dear R community, I tried to optimized my R code by using Rprof. In my R code I'm using MySQL database connections intensively. After a bunch of queries R fails with the following error message: Error in .Call("RS_MySQL_newConnection", drvId, con.params, groups, PACKAGE = .MySQLPkgName) : RS-DBI driver: (could not connect mylogin@mydatab...
2002 Jul 19
1
Rprof and setMethod conflict?
I noticed this oddity about R profiling and setMethod. First, I "test out" Rprof. > require(methods) Loading required package: methods [1] TRUE > > Rprof("test.out") > data.frame("a") X.a. 1 a > Rprof(NULL) So far, so good. Next, I define myClass. > setClass("myClass", representation(mySlot = "numeric")) [1] &q...
2005 Feb 16
0
Profiling R code and C code (Rprof and gprof)
Hi, I have searched R mail list archive and couldn't find my answers. The R extension describes how to make use of Rprof to profile R code. gprof can be also used for the same purpose for the C codes when the C codes are written independently and provided with a main() function. I'm currently writing R codes meshed with C Codes, and use .Call as the interface between the two parts. Rprof reports details of e...
2002 Aug 26
1
Rprof and setMethod conflict (PR#1949)
Full_Name: Kevin C. Bartz Version: 1.5.1 OS: Solaris 2.6 Submission from: (NULL) (192.223.226.5) A while ago, I noticed this oddity about R profiling and setMethod. First, I "test out" Rprof. > require(methods) Loading required package: methods [1] TRUE > > Rprof("test.out") > data.frame("a") X.a. 1 a > Rprof(NULL) So far, so good. Next, I define myClass. > setClass("myClass", representation(mySlot = "numeric")) [1] &q...
2003 Mar 26
0
Rprof/UseMethod
I'm having difficulty with Rprof. I have a documentation example test.qss that runs fine without profiling, but under Rprof, > Rprof() > source("test.qss") Error in standardGeneric("model.matrix") : UseMethod used in an inappropriate fashion Luke wrote about a similar circumstance last summer:...
2004 Oct 16
7
sapply and loop
Dear all, I am doing 200 times simulation. For each time, I generate a matrix and define some function on this matrix to get a 6 dimension vector as my results. As the loop should be slow, I generate 200 matrice first, and save them into a list named ma, then I define zz<-sapply(ma, myfunction) To my surprise, It almost costs me the same time to get my results if I directly use a loop
2004 Oct 16
7
sapply and loop
Dear all, I am doing 200 times simulation. For each time, I generate a matrix and define some function on this matrix to get a 6 dimension vector as my results. As the loop should be slow, I generate 200 matrice first, and save them into a list named ma, then I define zz<-sapply(ma, myfunction) To my surprise, It almost costs me the same time to get my results if I directly use a loop
2010 Nov 19
1
memory profiling
I'm trying to configure Version 2.12.0 or R to do memory profiling. I've reconfigured the code: % ./compile --enable-memory-profiling=YES and verified that it's configured correctly by examining the output. I then rebuild R: % make Then I fire up R and run a script, using Rprof with the memory-profiling switch set to TRUE: Rprof("output", memory.profiling=TRUE); # a bunch of R code Rprof(NULL); When I examine the output, however, using either R CMD Rprof from the shell, or summaryRprof from within R, the output I see is identical to the output I got when I ran...
2003 Jul 15
1
Rprof
I find it difficult to find Rprof using the usual search tools... could I suggest that it be cross-referenced to profile Rprofile Profile to make this easier? url: www.econ.uiuc.edu/~roger/my.html Roger Koenker email rkoenker@uiuc.edu Department of Economics vox: 217-333-4558 University of Illinois fax: 217-244-6678 C...