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 :) since it's the least tested. Probably writing out
of bounds.
This could be quite tricky to debug. I'd try to get something close to a
minimal reproducible example.
I'd try to take devtools out of the picture, maybe running the test/testhat.R
script from the command line using Rscript, or worst case creating a shell
package that adds minimal code and can be checked with R CMD build
--no-build-vignettes / R CMD check.
You could try inserting gc() before / after the unit test; it might make it
clear that the unit test isn't the problem. You could also try gctorture(TRUE);
this will make your code run extremely painfully slowly, which puts a big
premium on having a minimal reproducible example; you could put this near the
code chunks that are causing problems.
You might have success running under valgrind, something like R -d valgrind -f
minimal_script.R.
Hope those suggestions help!
Martin
On 10/12/21, 6:43 PM, "Bioc-devel on behalf of Pariksheet Nanda"
<bioc-devel-boun...@r-project.org on behalf of pariksheet.na...@uconn.edu> wrote:
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.
The latest head scratcher from running devtools::check() is a unit
test for a trivial 2 line function failing with this gem of an error:
> test_check("tsshmm")
══ Failed tests
════════════════════════════════════════════════════════════════
── Error (test-tss.R:11:5): replace_unstranded splits unstranded into +
and - ──
Error in `tryCatchOne(expr, names, parentenv, handlers[[1L]])`: internal
logical NA value has been modified
Backtrace:
█
1. ├─testthat::expect_equal(...) test-tss.R:11:4
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg =
"expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─GenomicRanges::GRanges(c("chr:100:+", "chr:100:-"))
5. └─methods::as(seqnames, "GRanges")
6. └─GenomicRanges:::asMethod(object)
7. └─GenomicRanges::GRanges(ans_seqnames, ans_ranges, ans_strand)
8. └─GenomicRanges:::new_GRanges(...)
9. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len)
10. └─S4Vectors::make_zero_col_DFrame(x_len)
11. └─S4Vectors::new2("DFrame", nrows = nrow, check =
FALSE)
12. └─methods::new(...)
13. ├─methods::initialize(value, ...)
14. └─methods::initialize(value, ...)
15. └─methods::validObject(.Object)
16. └─base::try(...)
17. └─base::tryCatch(...)
18. └─base:::tryCatchList(expr, classes,
parentenv, handlers)
19. └─base:::tryCatchOne(expr, names,
parentenv, handlers[[1L]])
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
The full continuous integration log is here:
https://gitlab.com/coregenomics/tsshmm/-/jobs/1673603868
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
return(gr)
sort(c(
gr[! idx],
`strand<-`(gr[idx], value = "+"),
`strand<-`(gr[idx], value = "-")))
}
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/R/hmm.R#L170-178
... and the unit test is:
test_that("replace_unstranded splits unstranded into + and -", {
expect_equal(replace_unstranded(GRanges("chr:100")),
GRanges(c("chr:100:+", "chr:100:-")))
expect_equal(replace_unstranded(GRanges(c("chr:100", "chr:200:+"))),
sort(GRanges(c("chr:100:+", "chr:100:-", "chr:200:+"))))
})
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/tests/testthat/test-tss.R#L11-L12
What's interesting is this is *not* reproducible by running
devtools::test() but only devtools::check() so as far as I know there
isn't a way to interactively debug this while devtools::check() is going
on?
Every few days I've seen on that "internal ... value has been modified"
which prevents me from running nearly any R commands. Originally I
would restart R, but then I found I could clear that error by running
gc(). No idea what causes it. Maybe some S4 magic?
Yes, I have downloaded the mailing lists for bioc-devel, r-devel,
r-help, and r-package-devel and see no mention of "value has been
modified" [1].
Any help appreciated.
Pariksheet
[1] Mailing lists downloader:
#!/bin/bash -x
for url in
https://stat.ethz.ch/pipermail/{bioc-devel,r-{devel,help,package-devel}}/
do
dir=$(basename $url)
wget \
--timestamping \
--no-remove-listing \
--recursive \
--level 1 \
--no-directories \
--no-host-directories \
--cut-dirs 2 \
--directory-prefix "$dir" \
--accept '*.txt.gz' \
--relative \
--no-parent \
$url
done
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