revdeps hilldiv, wxgenR broken when melt redirect removed

[tdhock]

revdep check machine https://rcdata.nau.edu/genomic-ml/data.table-revdeps/analyze/2024-12-18/
says that #6651 broke

* checking examples ... ERROR
Running examples in 'hilldiv-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: div_profile_plot
> ### Title: Diversity profile plot
> ### Aliases: div_profile_plot
> ### Keywords: alpha beta gamma hill
> 
> ### ** Examples
> 
> data(bat.diet.otutable)
> data(bat.diet.hierarchy)
> #One sample example
> bat.diet.sample <- bat.diet.otutable[,1]
> profile.onesample <- div_profile(count=bat.diet.sample,qvalues=seq(from = 0, to = 5, by = (0.1)))
> div_profile_plot(profile.onesample)
> #Multiple samples
> profile.multiplesamples <- div_profile(bat.diet.otutable)
> div_profile_plot(profile.multiplesamples)
Error in melt.default(profile) : 
  The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(profile). In the next version, this warning will become an error.
Calls: div_profile_plot ... melt -> melt.default -> stopf -> raise_condition -> signal
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
div_profile 7.021  0.035   7.141
* checking PDF version of manual ... OK

and wxgenR:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building 'Vignette_BlacksburgVA.Rmd' using rmarkdown
--- finished re-building 'Vignette_BlacksburgVA.Rmd'

--- re-building 'Vignette_LowerSantaCruzRiverBasinAZ.Rmd' using rmarkdown

Quitting from lines 198-201 [unnamed-chunk-6] (Vignette_LowerSantaCruzRiverBasinAZ.Rmd)
Error: processing vignette 'Vignette_LowerSantaCruzRiverBasinAZ.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(.). In the next version, this warning will become an error.
--- failed re-building 'Vignette_LowerSantaCruzRiverBasinAZ.Rmd'

SUMMARY: processing the following file failed:
  'Vignette_LowerSantaCruzRiverBasinAZ.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK

I will notify them.

[tdhock]

I submitted a PR to hilldiv anttonalberdi/hilldiv#4 but I get the feeling they may not submit an update to CRAN any time soon (last CRAN release 5 years ago).

[tdhock]

I emailed [email protected] about wxgenR:
Hi David
I'm writing you because you are listed as the maintainer of the wxgenR package on CRAN.
There is a new issue when checking wxgenR using the new version of data.table that we plan to release in the next month or so: https://github.com/Rdatatable/data.table/issues/6670
I looked at the wxgenR code on CRAN, and I believe the fix should be changing melt(id = 1:6) to reshape2::melt(id = 1:6) on line 191 of Vignette_LowerSantaCruzRiverBasinAZ.Rmd
Can you please make that change, and submit an update of wxgenR to CRAN in the next week or so?
CRAN requires data.table to submit updates which do not break dependent packages like wxgenR.
Thanks
Toby

[tdhock]

David confirmed on email that he will fix wxgenR

[MichaelChirico]

Added WAI Working as intended to make it clearer in the Milestone logs which issues still require triage; this one doesn't need attention from data.table devs before release.

[TysonStanley]

Is this issue closed for purposes of 1.17.0?

[MichaelChirico]

yes the WAI label is intended to convey "nothing left for us to do before release"