similar to: 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

Hi all, Thanks to Prof. Ripley, Prof. Gentleman, and Simon Wood (did I miss anyone?). The problem seemed to have gone away. Everyone suggested using some malloc debugger (such as Electric Fence). All I did was following half of what BDR suggested below, i.e., changing all the S_alloc() calls to Calloc() and Free(). I didn't get to try efence, and the problem seems to have disappeared! As

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

Hi I have the feeling, that the argument stringsAsFactors has no impact in the function expand.grid: a <- c("PR", "NC", "A2", "BS") b <- c(1, 0.5, 0.25, 0.125, 0.0625, 0.03125) class(expand.grid(css, fscs, stringsAsFactors=FALSE)[[1]]) [1] "factor" class(expand.grid(css, fscs, stringsAsFactors=TRUE)[[1]]) [1] "factor" Also, when

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

Hi Community, I have a question about how to pass command line parameters to R script running in the batch mode. The problem is: there is a banch of data files which are to be processed by R script called from a web-server, i.e. in the batch mode. The web server generates data files and passes their names calling 'R CMD BATCH' one by one for every file. Now the question is how to

I have a few questions on formatting wireframe plots: 1. How can I remove (or at least "white-out") the border on the plot? (I.e., the 2-d box around the whole plotting area, not the 3-d cube). I'm willing to hack the code if necessary. 2. Is it possible to suppress plotting of all sides of the cube except for the axes? 3. Is there a reliable way to print expressions in

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

Full_Name: Dr. Hans A. Kestler Version: 1.8.1. OS: Linux, Win, Mac OSX Submission from: (NULL) (134.60.73.116) The code below produces after a different number of iterations i the following error: Error in optim(par = rep(0.5, length(edges)), loglik, method = "L-BFGS-B", : non-finite value supplied by optim This was reproducible on different machines (Mac G4 OSX, AMD Opteron

Hello, JIT compiler interferes with internal R completions: compiler::enableJIT(2) utils:::functionArgs("density", '') gives: utils:::functionArgs("density", '') Note: no visible global function definition for 'bw.nrd0' Note: no visible global function definition for 'bw.nrd' Note: no visible global function definition for 'bw.ucv'

Hi, I have problems when calling fft_factor and fft_work directly in my C-code. Martin Maechler already told me that I should not do this -- anyway, the code works fine if the length of the vector is a multiple of 2,3,5. If the length of the vector has different form I get, in some cases, a segmentation fault when work and iwork are freed (I use C's malloc to allocate memory for work and

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

I am writing a function to work with class I am defining. I have a question about using nargs() inside of parentheses function. nargs() shows the same for supplying 1 argument, or no arguments at all. Here is a small example: > "[.myclass"<-function(x,...) print(nargs()-1) > x<-c(1,2,3) > class(x)<-"myclass" > x[] [1] 1 > x[1] [1] 1 > x[1,2] [1] 2

I initially sent this to the biocore mailing list - but it was suggested that r-devel would also find it interesting. Many of us use a macro like #define CALL_DEF(fname, nargs) { #fname, (DL_FUNC)&fname, nargs} for use in function registration for use with .Call. For example, using the example from R Extension manual, if we want to register a C function myCall with three arguments, we

I have an S3 class called "tis" (Time Indexed Series) which may or may not have multiple columns. I have a function "[<-.tis" that I've reproduced below. My question is this: inside of "[<-.tis", how can I distinguish between calls of the form x[i] <- someValue and x[i,] <- someValue ? In either case, nargs() is 3, and looking at the values

I have an S3 class called "tis" (Time Indexed Series) which may or may not have multiple columns. I have a function "[<-.tis" that I've reproduced below. My question is this: inside of "[<-.tis", how can I distinguish between calls of the form x[i] <- someValue and x[i,] <- someValue ? In either case, nargs() is 3, and looking at the values

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

The survival package, like many others, has several helper functions that are not declared in the namespace, since their only use is to be called by other "main" functions of the package.? This works well since the functions in the survival namespace can see them --- without ::: arguments --- and others don't. Until a situation I ran into this week, for which I solicit comments

Hello everybody, I've run into some strange behavior with memory sanitizer that I can't explain and hope somebody with more knowledge of the implementation would be able to help me out or at least point me into the right direction. For background, I'm using memory sanitizer to check Julia (julialang.org), which uses (or at least will once I track down a few bugs) MCJIT for the code

I am running R 2.8.1 on SUSE Linux. I would like to be able to set R_PROFILE to two different possibilities. One when R is called by R CMD BATCH and another any other time. Is this possible? Mark Lyman, Statistician Engineering Systems & Integration, ATK