Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-13 Thread Pariksheet Nanda
Hi Hervé, On 10/13/21 12:43 PM, Hervé Pagès wrote: On 12/10/2021 15:43, Pariksheet Nanda wrote: The function in question is: replace_unstranded <- function (gr) { idx <- strand(gr) == "*" if (length(idx) == 0L)    ^ Not related to the "internal logical

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-13 Thread Hervé Pagès
Hi Pariksheet, On 12/10/2021 15:43, Pariksheet Nanda wrote: The function in question is: replace_unstranded <- function (gr) {     idx <- strand(gr) == "*"     if (length(idx) == 0L) ^ Not related to the "internal logical NA value has been modified" error but

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-13 Thread Martin Morgan
The problem with using gdb is you'd find yourself in the garbage collector, but perhaps quite removed from where the corruption occurred, e.g., gc() might / will likely be triggered after you've returned to the top-level evaluation loop, and the part of your code that did the corruption might

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-12 Thread Pariksheet Nanda
Thanks, Martin and Henrik! My previous confusing reply from a few minutes ago was due my university GMail hiding your replies in All Mail. I'll consider both your suggestions carefully and thank you again for the quick and thoughtful replies. Pairksheet On 10/12/21 8:03 PM, Henrik

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-12 Thread Pariksheet Nanda
Hi all, On 10/12/21 6:43 PM, Pariksheet Nanda wrote: Error in `...`: internal logical NA value has been modified In the R source code, this error is in src/main/memory.c so I was thinking one way of investigating might be to run `R --debugger gdb`, then running R to load the symbols and

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-12 Thread Henrik Bengtsson
In addition to checking with Valgrind, the ASan/UBsan and rchk platforms on R-Hub (https://builder.r-hub.io/) can probably also be useful; > rhub::check(platform = "linux-x86_64-rocker-gcc-san") > rhub::check(platform = "ubuntu-rchk") /Henrik On Tue, Oct 12, 2021 at 4:54 PM Martin Morgan

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-12 Thread Martin Morgan
It is from base R https://github.com/wch/r-source/blob/a984cc29b9b8d8821f8eb2a1081d9e0d1d4df56e/src/main/memory.c#L3214 and likely indicates memory corruption, not necessarily in the code that triggers the error (this is when the garbage collector is triggered...). Probably in *your* C code

[Bioc-devel] Strange "internal logical NA value has been modified" error

2021-10-12 Thread Pariksheet Nanda
Hi folks, I've been told to ask some of my more fun questions on this mailing list instead of Slack. I'm climbing the ladder of submitting my first Bioconductor package (https://gitlab.com/coregenomics/tsshmm) and feel like there are gremlins that keep adding rungs to the top of the ladder.