similar to: R 1.6.1: help with debugging error in RunGenCollect(), R_gc_internal

This is a followup to the R-help thread, "Error: STRING_ELT() can only be applied to a 'character vector', not a 'builtin'". Thanks to Prof. Brian Ripley for suggesting the use of gctorture and valgrind. I am getting segmentation faults that appear to come from a memory leak. I now have a reproducible example (below). It requires the "g.data" package

The following code crashes after about 300 iterations on my?x86_64-w64-mingw32?machine on R 3.5.2 --vanilla.?? Others have duplicated this (see?https://github.com/tidyverse/magrittr/issues/190?if necessary), but I don't know how machine/OS-dependent it may be.?? If it doesn't crash for you, please try increasing the length of the x vector. Substituting the commented-out line for the one

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

On an azure centos VM, I can reproduce this bug which reports either: *** caught segfault *** address 0x70000006a, cause 'memory not mapped' (crash) Or incompatible types (from builtin to integer) in subassignment type fix (no crash) Like Gabriel, I could not reproduce the bug on a mac laptop. Both R versions 3.5.1. Travers On Wed, Feb 27, 2019 at 9:08 AM William Dunlap via R-devel

Dear listers, a few days ago I asked a question about a problem I had with a C function programmed by myself to be called from R. Thanks to your help, I have been able to look a bit further into it, so now I can be a bit more specific when telling what happens. The fact is that, when my C function finishes its execution (after calling it via the ".C" interface), R seems ok but

The following code results in a seg fault. > sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-21 r42013) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics

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 =

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

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,

R does a great job with the fine details regarding plots. e.g in the following: library(lattice) y <- -4:4/10 xyplot(y~1, las=1) the y axis is labelled with numbers -0.4, -0.2, 0.0, 0.2, 0.4 with the numbers aligned on the decimal point. How do I get the same behaviour in the colorkey of a levelplot? e.g. levelplot(matrix(y,3,3)) the numbers in the colorkey seem left-aligned, and

A recent paper on visualisation (in Neuron, a leading neuroscience journal) surveyed how well previous articles in this journal labelled their graphs (e.g. axis labelling and describing their error bars). Of particular interest is that (only) 40% of plots labelled what their colorkey was showing (variable and units). The paper is at http://dx.doi.org/10.1016/j.neuron.2012.05.001 R is not yet

Full_Name: Stephen Eglen Version: 1.2.3 OS: Linux Submission from: (NULL) (128.252.204.186) The help file for image() currently says: The way in which `zlim' is divided into colours will be changed for the next major release (1.1.0) to divide the range into equal-length intervals. According to NEWS, this was indeed changed in 1.1.0, so perhaps it can now be removed from the

Full_Name: Stephen Eglen Version: 1.2.3 OS: Linux (Redhat 6.1) Submission from: (NULL) (128.252.204.186) Hi, two small typos in `?write.table' (R 1.2.3) In the doc of the append parameter: append: logical. If true, the output is appended to targshe file. that should be "... to the file". and in the Details section, a full-stop is missing after names: Normally there is no

The current R release candidate has a lack of protect bug (of very long standing) with respect to the R_print.na_string and R_print.na_string_noquote fields of the static R_print structure declared in Print.h. This shows up very occassionally as incorrect output from the following lines in reg-tests-2.R: x <- c("a", NA, "b") factor(x) factor(x, exclude="")

Full_Name: Stephen Eglen Version: 1.4 OS: Redhat Linux 7.1 Submission from: (NULL) (128.252.204.36) I think the brackets in the levels of cut() are slightly incorrect when include.lowest is TRUE. For example: > table(cut( c(1,4), include.lowest=T, right=F, breaks=c(1,2,3,4))) [1,2) [2,3) [3,4) 1 0 1 I think the last range in this case should be [3,4]. A similar problem

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:

Full_Name: stephen eglen Version: 1.0.0 OS: Unix (OSF/1) Submission from: (NULL) (129.215.238.26) Hi, in the documentation `Writing R Extensions', the section 3.6.1 (handling the effects of garbage collection) has the following typo: Protecting a SEXP pointer protexts ... Should that be `protects'? -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-

hi, Just a very simple question: is there an R equivalent to the matlab command find(X) which returns the indices of vector X that store non-zero elements? e.g. > find( [1 0 0 1 0]) ans = 1 4 so, in R, how do I do: ans <- rfind( c(1,0,0,1,0)) so that ans is the vector c(1,4) thanks, stephen -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help

> 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]