Closed
Description
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has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated.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has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated.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.