similar to: transient memory allocation and external pointers

Hello, I have been developing a package for phylogenetic analysis which I plan to submit to CRAN soon. It passes R CMD check with no warnings on my linux and Mac OS X machines. I don't have much experience with Windows and have been using the win-builder service to see how the package compiles on Windows. (Thank you for this service, Uwe, it is a huge time saver for me!) I have tried

I have some compiled code that works under winXp but not under linux (kernel 2.6.10-5). I'm also using R 2.1.0 After debugging, I've discovered that in this code: #define NMAX 256 long **box; ... box = (long **)R_alloc(NMAX, sizeof(long *)); //<---HERE THE SIGSEGV for (i=0; i<NMAX; i++) box[i] = (long *) R_alloc(NMAX, sizeof(long)); inside the *first* call to the

I have some compiled code that works under winXp but not under linux (kernel 2.6.10-5). I'm also using R 2.1.0 After debugging, I've discovered that this code: #define NMAX 256 long **box; ... box = (long **)R_alloc(NMAX, sizeof(long *)); gives a null pointer, so subsequent line: for (i=0; i<NMAX; i++) box[i] = (long *) R_alloc(NMAX, sizeof(long)); gives a SIGSEGV signal.

Valgrind (without gctorture) reports memory misuse: % R --debugger=valgrind --debugger-args="--leak-check=full --num-callers=18" ... > x <- 1:200000 > y <- rep(letters[1:5], length(x) / 5L) > for (i in 1:1000) { + # x[y == 'a'] <- x[y == 'b'] + x <- `[<-`(x, y == 'a', x[y == 'b']) + cat(i, '') + } 1 2 3 4 5 6 7 8 9 10

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

Hi, I'm currently R porting SF Mersenne Twister algorithm of Matsumoto and Saito. To get the full power of their code, I want to use their fonction fill_array32 which need aligned memory. That is to say I need to use the C function memalign on windows, posix_memalign on linux and classic malloc on Mac OS. In 'writing R extenstion', they recommand to use R_alloc function to

Hi, I'm currently R porting SF Mersenne Twister algorithm of Matsumoto and Saito. To get the full power of their code, I want to use their fonction fill_array32 which need aligned memory. That is to say I need to use the C function memalign on windows, posix_memalign on linux and classic malloc on Mac OS. In 'writing R extenstion', they recommand to use R_alloc function to

WRE explains that R_alloc() can be used to allocate memory which automatically gets released by R at the end of a .C, .Call or .External, even in the case of an error or interruption. This is a really great feature to prevent memory leaks. I was wondering if there is a way to extend this mechanism to allow for automatically running UNPROTECT and custom finalizers at the end of a .Call as well.

Dear All, In a package, I want to use some C code where I am using a structure (as the basic element of a linked list) with flexible array members. Basically, this is a structure where the last component is an incomplete array type (e.g., Harbison & Steel, "C, a reference manual, 5th ed.", p. 159) such as: struct Sequence { struct Sequence *next; int len; unsigned int

Full_Name: Wolfgang Huber Version: R-devel_2005-03-10 OS: alphaev68-dec-osf4.0f Submission from: (NULL) (62.253.128.15) This report concerns allocation of large (>2^31 byte) chunks of memory with R_alloc. I suspect it is a bug/typo but please don't hate me if it's actually a feature: In R, I can happily create large matrices: > a= matrix(0, nrow=191481, ncol=3063) > dim(a) [1]

Hi, A recent discussion on the list about tryCatch and signals made me think about memory allocation and signals in C extension modules. What happens to the memory allocated by R_alloc and Calloc if the user pressed Ctr-C during the call? R-ext doesn't seem to discuss this. I'd guess that R_alloc is interrupt-safe while Calloc is not, but I am not sure. In any case a paragraph in R-ext

Hi, I am trying to implement an algorithm in C which will be called via the .Call() interface. While reading the 'Writing R Extension' manual, I stumbled upon the R_alloc() function for allocating storage for C objects. The manual says it should be used to allocate storage if an C object is needed/created while manipulating R objects within a function called via the .Call() interface.

Hi all, im triyng to implement a bayesian model with R and c++. I have a strange problem. I can't reproduce the error with a small script and then i post the original one. The problem is after the line for(MCMC_iter2=0;MCMC_iter2<thin;MCMC_iter2++) For the first 34 iterations all work fine, after, all the simulations of mu_acc_P return an "nan". If i delete the line

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

Had been looking into Luke Tierney's R_AllocatePtr() and was left with a question about exactly when does R reclaim heap memory. Implication of 'simpleref.nw' is that one can allocate C data on the R heap, and as long as pointer object is alive, the data and pointer will remain valid. But it calls allocString() which is implemented using R_alloc(). 'Writing R Extensions" says

Dear R-devel, While tracking down some hard-to-reproduce bugs in a package I maintain, I stumbled on a behavior change between R 2.15.0 and the current R-devel (or SVN trunk). In 2.15.0 and earlier, if you passed an 0-length vector of the right mode (e.g., double(0) or integer(0)) as one of the arguments in a .C() call with DUP=TRUE (the default), the C routine would be passed NULL (the C

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

Hi, Could someone please point to an example of passing strings from .C() calls back to R? I want to be able to do something like this: str <- .C("return_foo_string", str=character(1))$str void return_foo_string(char ** str) { *str = "foo"; } The above code has at least two memory allocation "concerns": 1) How to properly allocate "foo". I

Hi, I am trying to use dynamic memory allocation in the C code to be called by R through the .C interface. I have used R_alloc as explained in the Writing R Extensions and included the R.h header. The program compiles fine but fails when linking. Obviously it needs a library file where R_alloc is found. I have tried to link by adding R.dll to list of files at the end of the link command but

Full_Name: Dan Kelley Version: 2.2.1 OS: Mac OSX Submission from: (NULL) (129.173.23.36) I'm having difficulties getting R_alloc() to work on a 64-bit Mac running R 2.2.1 installed via a .dmg file obtained from the R site. Details are given below, in a level of detail that I hope is appropriate. My eye was particularly drawn to line #2 in the gdb 'where' output, but line #1 seems