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.b...@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-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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
