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
Good day,
I see a checking failure for ClassifyR for Windows Server 2019 only. The error
is
Error: BiocParallel errors
4 remote errors, element index: 1, 4, 6, 8
6 unevaluated and other errors
first remote error: could not find function "colData"
Is there anything I can change in my code
Remember that Windows doesn�t have �forked� parallelism; all processes are
running in separate processes where the functions in use need to be made
explicitly available.
Likely you can emulate this error on non-windows by using �SnowParam()� instead
of MulticoreParam(), e.g.,
>
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
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
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
Hello,
Ah, I had a few different uses of MultiAssayExperiment::colData in a particular
function of the package, but one line had only colData without the scoping in
front. I wish that R error messages displayed R file names and line numbers
more often.
--
On 12/10/2021 14:24, Hervé Pagès wrote:
Probably the build/ folder that doesn't belong to a package source tree.
You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da)
but that was after the builds started so this will only be reflected on
Wednesday's build report.
I meant on
Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept 24:
https://cran.r-project.org/package=rjags
and for some reason they modified the code they use in their onLoad()
hook to find JAGS on Windows. They were using in rjags 4-10:
readRegistry("SOFTWARE\\JAGS",
Hi all,
My package just got accepted and was added to the nightly build on Friday.
The build report shows error in installation which it did not show earlier
during package submission ( pkg submission issue here surfaltr · Issue
#2256 · Bioconductor/Contributions (github.com))
This is the
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.
Probably the build/ folder that doesn't belong to a package source tree.
You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da)
but that was after the builds started so this will only be reflected on
Wednesday's build report.
Best,
H.
On 12/10/2021 06:50, Pooja Gangras
Thank you so much, Herve! It makes sense to me now. I imported R2jags in my
package, which depends on rjags.
Regards,
Zhi Yang
On Tue, Oct 12, 2021 at 1:14 PM Hervé Pagès
wrote:
> Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept 24:
>
>
Probably the build/ folder that doesn't belong to a package source tree.
You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da)
but that was after the builds started so this will only be reflected on
Wednesday's build report.
Best,
H.
On 12/10/2021 06:50, Pooja Gangras
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