similar to: [R] help debugging segfaults

Dear R-devel, Last week I got several responses to my question about debugging segfaults in my code (original post below). After I changed the S_alloc() calls to Calloc()/Free(), the symptom was gone, but I was told to keep looking. So I did: o Switched to Calloc/Free. Electric Fence did not find any problem. o Put assert(index < bound); assert(index >=0); everywhere in the C routine

(Sorry for the cross-post--- I wasn't sure which list is more appropriate...) Hi everyone, I've run into segfaults when using my randomForest package on large dataset (e.g., 100 x 15200) and large number of trees (e.g., ntree=7000 and mtry=3000). I'm wondering if anyone can give me some hints on where to look for the problem. The randomForest package mainly consists of two things:

(Sorry for the cross-post--- I wasn't sure which list is more appropriate...) Hi everyone, I've run into segfaults when using my randomForest package on large dataset (e.g., 100 x 15200) and large number of trees (e.g., ntree=7000 and mtry=3000). I'm wondering if anyone can give me some hints on where to look for the problem. The randomForest package mainly consists of two things:

I am trying to get our database interface (PADI) working with R. The code does some memory allocation and for Splus there is an ifdef which controls whether malloc or S_alloc is called. I did nm R.binary | grep alloc to see if this was supported and I find there are some choices: [2490] | 446036| 272|FUNC |GLOB |0 |7 |R_alloc [806] | 693956| 312|FUNC |LOCL |0 |7

Dear expeRts, The order in which the variables vary in expand.grid() is often unintuitive. I would like to suggest a 'method' slot for expand.grid() which requires only very little changes (100% backward compatible) and which allows one to control this order. Please find attached diffs against R-devel. Cheers, Marius ### ./src/library/base/R/expand.grid.R

(I dithered a bit about whether this belongs on r-help (as part of it is a general R question) or r-devel (as it's a question relating to putting stuff on CRAN) but decided it might be of general enough interest to go on the former ) I am currently preparing an R library to estimate approximate posterior distributions for parameters in Generalised Linear Mixed Models by Gibbs Sampling

I am trying to write a C function to create a vector of integers that can be used by the R calling function. I do not know the size of the vector in the R calling function. (Well, actually, I have an upper limit on the size, but that is so large that R cannot allocate it. What I'm doing in the function is to do a sieving procedure, and the result will be small enough to fit into my

Commit-ID: 9b625887a59c03c244b43550b576529f209dde11 Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=9b625887a59c03c244b43550b576529f209dde11 Author: H. Peter Anvin <hpa at linux.intel.com> AuthorDate: Tue, 5 Jan 2016 16:43:50 -0800 Committer: H. Peter Anvin <hpa at linux.intel.com> CommitDate: Tue, 5 Jan 2016 16:43:50 -0800 [klibc] i386: remove special

Does anyone know what exactly S_alloc() does? (Yes, it's porting time again ...) Thanks, -k =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- r-devel mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To:

Commit-ID: cf8147c43a60d9eb6a6713d16f30364a698a6936 Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=cf8147c43a60d9eb6a6713d16f30364a698a6936 Author: H. Peter Anvin <hpa at linux.intel.com> AuthorDate: Tue, 5 Jan 2016 18:31:40 -0800 Committer: H. Peter Anvin <hpa at linux.intel.com> CommitDate: Tue, 5 Jan 2016 18:35:16 -0800 [klibc] Add accept4(), handle

I want to write a little stand-alone C program that calls R_alloc, but I get a segmentation fault: int main(int argc, char** argv){ double* d = (double *)R_alloc(2, sizeof(double)); // <- segmentation fault! return 0; } gdb reveals that sizeof(double) evaluated to 0: > R_alloc (nelem=2, eltsize=0) at memory.c:1649 so it results in the segfault later. This is how I compile my

[sending this to R-devel, since it may be of general interest and could possibly lead to better instructions in the "R-exts" manual] Is this another case where only .Call() or .External() [or a fudge factor] solve my problem? Following situation: I use dyn.loaded C code to compute a recursive tree structure from my data. Beforehand I don't know how big the tree will

Dear R-devel, Can anyone give me some hints on how to go about debugging a strange segfault in my randomForest package? Here's the scoop: A user reported segfault when running predict() in the randomForest package. I asked for the data and code. The combination runs fine under WinXPPro, but does give segfault on one of our Linux boxes running R (1.7.0 through R-devel_2004-01-08) on

Running on an Alpha machine which reports (uname -a) OSF1 bsdx01.bs.ehu.es V4.0 878 alpha and using the binary distribution put together by Albrecht Gebhardt (in http://cran.at.r-project.org/bin/osf/osf4.0/tar/alpha_ev5/) I obtain core dumps whenever I try to use package rpart. I have R REMOVE'd the rpart package, downloaded the source rpart_1.0-7.tar from CRAN and

Dear R-devel, Apologies for bothering y'all with this seemingly perennial question. A user reported problem with my most recent version of randomForest (4.4-1), and I was able to reproduce it with his data with R-2.0.0 patched (2004-10-24) on WinXP Pro. The problem is that it crashes R on Windows. However, it does not happen on Linux (tried SUSE ES8 on our Opterons and Quantian on my

Dear R-devel This one seems a bit arcane for R-help. I very often use R to call routines written in Delphi (son of Pascal), doing "persistent" memory allocation within Delphi. That is, I start R and load the Delphi DLL; then I use .C to call a Delphi routine which allocates a piece of memory X and returns to R a pointer to X; then I do some more stuff in R; then I call another Delphi

Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/00000172.htm It does seem interesting that the C execution is that much slower from R than from a native C program. Could any of the more technically knowledgeable people explain why this is so? The author also have some thought-provoking opinions on R being no-good and that you should write

[I guess R-devel is more appropriate for this question:] Will CRAN maintainers accept binary packages (in addition to source) from the package maintainers? As an example, I develop and test randomForest on both Linux and WinNT, so I can always make the binary. This could make life a bit easier for BDR and DM. Are there any potential problems? Regards, Andy > -----Original Message-----

Is it possible to have a slightly more elaborate description, such as: BackwardCompatibleTo: x.x-x and if the new version is _not_ backward compatible, this would be the current version number? Just my $0.02... Andy -----Original Message----- From: Torsten Hothorn [mailto:Torsten.Hothorn@rzmail.uni-erlangen.de] Sent: Monday, October 28, 2002 7:25 AM To: ripley@stats.ox.ac.uk Cc:

Hello! I was wondering if it's possible to see the actual code of checkTmvArgs function that is part of the code for rtmvnorm (which is below - I just typed "rtmvnorm" on the prompt). I get an error: Error in checkTmvArgs(mean, sigma, lower, upper) : sigma must be a symmetric matrix At the same time I am pretty sure that the matrix I am passing as sigma is a var-covar matrix