From hp@ge@@on@g|thub @end|ng |rom gm@||@com  Tue Mar 12 20:33:17 2024
From: hp@ge@@on@g|thub @end|ng |rom gm@||@com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 12 Mar 2024 12:33:17 -0700
Subject: [Rd] Spurious warning in as.data.frame.factor()
Message-ID: <ace9e76c-bad0-4eb3-b3f8-c9cccd6e9a9d@gmail.com>

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

-- 
Herv? Pag?s

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

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