similar to: Moderating consequences of garbage collection when in C

Hello. I'm still working on my OCaml-R binding and I get a segfault in the GetNewPage() function of memory.c. For the record, the OCaml-R binding seems to work fine with OCaml bytecode. The segfault here is the main issue I have with OCaml native code. OCaml-R can be found on the following links. Source code: http://yziquel.homelinux.org/gitweb/?p=ocaml-r.git;a=summary

dovecot v2.2.16 I've found a few bugs in Trash plugin. 1. If Quota set only messages limit (without storage limit) then Trash plugin does not expunge any message because Quota plugin sets too_large_r=TRUE. It's because quota_default_test_alloc function does not check if bytes_limit is set. /* if size is bigger than any limit, then it is bigger than the

Full_Name: Roger Bivand Version: 1.3.0 OS: GNU/Linux RH6.2, 7.0, Debian 2.2 Submission from: (NULL) (158.37.100.64) I'm working on interfacing ANN: A Library for Approximate Nearest Neighbor Searching (http://www.cs.umd.edu/~mount/ANN/) to R, following up a prototype package I tried in May 2000. ANN is written in C++; my C++ is very weak. Last year I didn't experience any problems with

This problem is with R 1.7.0 (as released) on Linux and Solaris. Details below are from Linux, Mandrake 9.1. The problem also happened with R 1.6.2 and on Mandrake 9.0. Vignettes often (for me) provokes problems with the misleading error message: * creating vignettes ... ERROR Error in sub(pattern, replacement, x, ignore.case, extended) : invalid argument Error in buildVignettes(dir =

Hello, I get a segfault when running glmmboot in my own package glmmML. Has happened many time before, but this time I get no hint of where in my C functions the error might be. I give the output below. Can this be an R bug? I suspect it has to do with repeated calls to 'vmmin' like this: for (...){ vmax = vmaxget(); vmmin(*p, b, &Fmin, bfun,

I've trapped this segfault with gdb, but I'm not sure what it means or what to do next. Paul _____ $ R -d gdb GNU gdb 4.17 Copyright 1998 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is

Hi, [System info: R 1.6.1 compiled from source (no args to configure) on Redhat 7.1 Linux i/386] I have some spatial statistics programs that recently (since R 1.6.1) have generated SIGSEGV. These R programs use the splancs library as well as some C code of my own for Voronoi analysis. The program has a big loop to fit various model parameters against a spatial distribution of biological

Hello, I'm evaluating this expression expression({ for(x in 1:5){ .Call('rh_status','x') }}) a million times from a program with R embedded in it. I have attached reproducible code that crashes with Program received signal SIGSEGV, Segmentation fault. 0x00002b499ca40a6e in R_gc_internal (size_needed=0) at memory.c:1309 1309 FORWARD_NODE(R_PPStack[i]); Current language:

Hi All, This is a very important issue. It would be very sad to leave most users unaware of a free speedup of this size. These options don't appear in the R --help output. They really should be added there. Additionally, if the garbage collector is working very hard, might it emit a note about better setting for these variables? It's not really my place to comment on design philosophy,

> fil2s <- read.table("../Data/fil2_s.txt", header = FALSE, sep = "\t") Program received signal SIGSEGV, Segmentation fault. 0x000000000041c2e1 in RunGenCollect (size_needed=8192000) at memory.c:1514 1514 PROCESS_NODES(); (gdb) > sessionInfo() R version 2.13.1 Patched (2011-08-25 r56798) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1]

>>>>> Peter Haverty <haverty.peter at gene.com> >>>>> on Mon, 19 Jan 2015 08:50:08 -0800 writes: > Hi All, This is a very important issue. It would be very > sad to leave most users unaware of a free speedup of this > size. These options don't appear in the R --help > output. They really should be added there. Indeed,

On Thu, Jan 15, 2015 at 3:55 PM, Michael Lawrence <lawrence.michael at gene.com> wrote: > Just wanted to start a discussion on whether R could ship with more > appropriate GC parameters. I've been doing a number of similar measurements, and have come to the same conclusion. R is currently very conservative about memory usage, and this leads to unnecessarily poor performance on

I've managed to trap the following segfault with xxgdb and gctorture() set. The segfault seems to move around if gctorture() is not set, but has now occurred twice in the same spot with it set. xxgdb gives the message Program received signal SIGSEGV, Segmentation fault. 0x71244 in RunGenCollect (size_needed=2) at memory.c:1027 and the source listing points to FORWARD_CHILDREN(s); in the

(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:

Hi Everyone, At the end of this email is a transcript of a problem I have found in RODBC version 2.3-1. It appears that the bug fix in odbcClose for the memory leak has meant that the garbage collector is falling over when it tries to free up the extPtr attribute of the RODBC connection pointer. Any advice on how to fix this? Thanks for your help, Tom

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

>>>>> "VW" == Viechtbauer Wolfgang (STAT) <Wolfgang.Viechtbauer at STAT.unimaas.nl> >>>>> on Fri, 26 Sep 2008 18:00:19 +0200 writes: VW> Hi all, I'm trying to fit a marginal (longitudinal) VW> model with an exponential serial correlation function to VW> the Orange tree data set. However, R crashes frequently VW>

Hello, I tried to use HostKeyAgent with sshd 6.7 under Linux. That worked for Linux clients. However, when I tried to connect from OpenSSH 6.2 under Mac OS X, the server disconnects: debug2: bits set: 1026/2048 debug1: SSH2_MSG_KEX_DH_GEX_INIT sent debug1: expecting SSH2_MSG_KEX_DH_GEX_REPLY Connection closed by 84.22.97.209 When I disabled HostKeyAgent and switched HostKey back to the private

I have Linux machine with Samba 3.5.11 working great. I was using passdb backend = tdbsam So when I tried to setup a second Linux machine I failed..since UID/GID's were different when I copied fiels from server 1 to server 2. Would you recommend me to use IDMAP_RID with Winbind? BTW, I don't have domain trusts (which is required to be "off" when using rid). It's a