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

[Rob C]

Comments in-line:

> Date: Sat, 9 Jul 2022 16:29:57 -0400
> From: Ben Bolker <bbolker using gmail.com>
> To: R Package Development <r-package-devel using r-project.org>
> Subject: [R-pkg-devel] help/advice on debugging
> Message-ID: <d2a61bd8-1b87-a2b2-8f24-14ba72b9e6f0 using mcmaster.ca>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
>    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.

Thanks for taking over an orphaned package.  Not an easy task!

>
>    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 think that dnapath is calling `gtools::permutations` from
`dnapath.R` around lines 339-343 [1], not `gtools::permute`.

Changes to  the file `combinations.R` in `gtools` where `permutations`
resides were made in June 2021 [2].

>
>     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>>.
>

I could not find an obvious place where the join above is happening in
the vignette, unfortunately, so I can't be of more help than just
pointing you in a different direction.

> 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

Rob Carnell

[1] https://github.com/cran/dnapath/blob/34089ec1f3c505692554dcaa49b55d0ce36a91e2/R/dna.R
[2] https://github.com/r-gregmisc/gtools/blob/62e599c3f634f0bc0f99f586e39200a850ef186c/R/combinations.R