[Bioc-devel] Strange "internal logical NA value has been modified" error
Henrik Bengtsson
henr|k@bengt@@on @end|ng |rom gm@||@com
Wed Oct 13 02:03:49 CEST 2021
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 <mtmorgan.bioc using gmail.com> wrote:
>
> 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-bounces using r-project.org on behalf of pariksheet.nanda using 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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