[Rd] Spurious warning in as.data.frame.factor()

[Hervé Pagès]

Hi,

The acrobatics that as.data.frame.factor() is going thru in order to 
recognize a direct call don't play nice if as.data.frame() is an S4 
generic:

     df <- as.data.frame(factor(11:12))

     suppressPackageStartupMessages(library(BiocGenerics))
     isGeneric("as.data.frame")
     # [1] TRUE

     df <- as.data.frame(factor(11:12))
     # Warning message:
     # In as.data.frame.factor(factor(11:12)) :
     #   Direct call of 'as.data.frame.factor()' is deprecated. Use 
'as.data.frame.vector()' or 'as.data.frame()' instead

This spurious warning showed up on the recent Bioconductor daily build 
reports after we've updated the build machines to the latest R devel. 
It's causing some confusion and breaks at least one unit test.

Thanks,

H.

 > sessionInfo()
R Under development (unstable) (2024-03-06 r86056)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB              LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] BiocGenerics_0.49.1

loaded via a namespace (and not attached):
[1] compiler_4.4.0

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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