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

[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. 
  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