similar to: R_alloc segfaults

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]

The current version of S_alloc in src/main/memory.c is char *S_alloc(long nelem, int eltsize) { unsigned int i, size; char *p = R_alloc(nelem, eltsize); for(i=0 ; i<size; i++) p[i] = 0; return p; } which segfaults because `size' is not initialized. I am not what the right fix is, adding size = nelem * eltsize; before the loop seems to work. As an aside ... I think the seed*

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

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. I'm having difficulties getting R_alloc() to work. The test platform is 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 sensible so I may just be displaying my ignorance by

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

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

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

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.

[Reposted from llvm-bugs mailing list. Also has an updated, hopefully better, patch associated with it.] Hi, The following program causes the LLVM GCC4 front end to ICE: struct A { virtual ~A(); }; template <typename Ty> struct B : public A { ~B () { delete [] val; } private: Ty* val; }; template <typename Ty> struct C : public A { C (); ~C (); }; template

The bulk is on my forums - the final post for today is: Results to date: A. It looks like I am going to need a newer compiler for C - xlc/xlC V11 apparently does not understand this code: "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) Syntax error. I will have to check if R-devel has different code before asking for assistence. +2139 #ifdef

I am calling 'vmmin' several times from a C function (which is called via .C). It works very well, except for memory consumption. The cause is that vmmin allocates memory via R_alloc, and this memory is not freed as vmmin exits. Instead all the allocated memory is freed on return of the .C call. In one application, I have 2000 functions of 500 variables each to minimize. In each call to

Dear list I have two (trivial) memory-questions related to a call with .C: If I allocate memory with R_alloc in a C-program (called with .C), will that memory "be taken from" the "available memory pool" (of a maximum of 4gb?) which R can allocate? (This is the impression I get from "Writing R extensions".) If instead I use malloc; will that memory then be taken

On 04-Jan-16 23:24, Michael Felt wrote: > The bulk is on my forums - the final post for today is: > > Results to date: > > A. It looks like I am going to need a newer compiler for C - xlc/xlC > V11 apparently does not understand this code: > > "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) > Syntax error. > > I will have to check

Hi, I would like to call R's lbfgsb function from my C/C++ code by including R_ext/Applic.h and linking against libR. Currently, I am allocating memory for x (and the other input arrays for lbfgsb) in my C/C++ code via malloc/new. However, this gives a segmentation fault when executing the program. I tried to allocate x via PROTECT(x = NEW_NUMERIC(n)); x_p = NUMERIC_POINTER(x);. This compiles

Hi, I am having problems when trying to apply factor analysis in a covariance matrix, > factanal(covmat=strip1cmcd, factors=5, control=list(lower=0.0264)) Error in optim(start, FAfn, FAgr, method = "L-BFGS-B", lower = lower, : non-finite value supplied by optim In addition: Warning message: NaNs produced in: sqrt(diag(cv)) I have searched for possible solutions in

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

Dear R users, I am currently trying to create my first personnal function and use it with the apply function. The purpose of this function is to create a vector summarizing the number of levels in a given selection of data.frame columns. I tried to transpose the indexation method used by the nlevels function but it doesn't seem to work. I did not find anything uesful in the archives so

Full_Name: Geordon Marchak Version: R-1.3.1 OS: Solaris 2.6 Submission from: (NULL) (199.67.239.91) Got the following error when compiling on Solaris 2.6 with the standard GNU gcc package (from the Sun site). BTW - linux compiles no problem (and fast too :-) # make `Makedeps' is up to date. gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -g -O2 -c

Full_Name: Chris Pelton Version: R-1.5.0 OS: Solaris & Submission from: (NULL) (169.237.121.210) I am unable to compile R-1.5.0, and am getting the following errors with make. I searched through the buglist and didn't see anything similar, although I wouldn't doubt if I was just using the wrong version of something. gcc version 3.0.3 gcc -I. -I../../src/include