[R-pkg-devel] help/advice on debugging

[Ben Bolker]

   For some stupid reason I agreed to take over maintenance of the 
now-orphaned `gtools` package ("how much trouble could that be, after 
all?"), which has 203 strong reverse dependencies.

   CRAN is reporting that exactly **one** of them, dnapath, is
failing reverse dependency checks ("changed to worse").

   I am having trouble replicating this (I'm running R-devel, can't 
install bioconductor packages on R-devel, working on doing everything in 
a Docker container, blah blah blah ...)

   In any case I am mystified as to how my new version of the package 
could be breaking something in the downstream package, since AFAICT the 
*only* functionality that `dnapath` is using from gtools is `permute()`, 
which is (1) a one-line wrapper for sample() and (2) hasn't changed in 
many years.

    I will try to figure out how much more time to invest in this rabbit 
hole before continuing the conversation with the CRAN maintainers, but 
in the meantime any insights or advice would be welcome.

   The problem is in vignette rebuilding, errors of this form in both of 
the package vignettes:

   Can't join on `x$entrezgene_id` x `y$entrezgene_id` because of
   incompatible types.
   ℹ `x$entrezgene_id` is of type <double>>.
   ℹ `y$entrezgene_id` is of type <character>>.

References:

https://win-builder.r-project.org/incoming_pretest/gtools_3.9.3_20220709_010826/reverseDependencies/summary.txt

https://github.com/r-gregmisc/gtools

  cheers
    Ben Bolker