New warning in `as.data.frame.DataFrame()`

[Bisaloo]

(Discovered while working on const-ae/lemur#30.)

Since r-devel/r-svn@9e4249f, as.data.frame.DataFrame() will return the following warning:

Warning message:
In as.data.frame.DataFrame(x[[i]], optional = TRUE, validRN = FALSE) :
arguments in '...' ignored

because of the new validRN argument passed down from the as.data.frame() generic.

I believe the base R diff linked above makes the issue quite visible but please let me know if you'd like that I create a reprex.

[hpages]

Thanks @Bisaloo for the report.

Here's what I get with the latest R-devel:

library(S4Vectors)
library(IRanges)
DF <- DataFrame(aa=11:15, bb=Rle(2, 5), cc=letters[1:5], dd=IRanges(1:5, 10))

as.data.frame(DF)
#   aa bb cc dd.start dd.end dd.width
# 1 11  2  a        1     10       10
# 2 12  2  b        2     10        9
# 3 13  2  c        3     10        8
# 4 14  2  d        4     10        7
# 5 15  2  e        5     10        6

as.data.frame.DataFrame(DF)
#   aa bb cc dd.start dd.end dd.width
# 1 11  2  a        1     10       10
# 2 12  2  b        2     10        9
# 3 13  2  c        3     10        8
# 4 14  2  d        4     10        7
# 5 15  2  e        5     10        6

No warning.

So yes, a reprex + sessionInfo() would be nice 😉

Thanks,
H.

sessionInfo():

R Under development (unstable) (2026-08-24 r90445)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.4 LTS

Matrix products: default
BLAS:   /home/hpages/R/R-4.7.r90445/lib/libRblas.so 
LAPACK: /home/hpages/R/R-4.7.r90445/lib/libRlapack.so;  LAPACK version 3.12.1

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/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] IRanges_2.47.2       S4Vectors_0.51.7     BiocGenerics_0.59.12
[4] generics_0.1.4       BiocManager_1.30.27 

loaded via a namespace (and not attached):
[1] compiler_4.7.0 tools_4.7.0   

[hpages]

Oh I see, we get the warning when calling the data.frame() constructor on a DataFrame object:

df <- data.frame(DF)
# Warning messages:
# 1: In as.data.frame.DataFrame(x[[i]], optional = TRUE, validRN = FALSE) :
#   arguments in '...' ignored
# 2: In .local(x, row.names, optional, ...) :
#   'optional' argument was ignored

Yes, the first warning (arguments in '...' ignored) is new in R 4.7.

As for the 2nd warning, we only get it here because of the 4th column (the IRanges column). But it seems that we had this warning for a while (at least since BioC 3.22). Anyways, this one is a separate story.

Unfortunately, this change in the internal implementation of the data.frame() constructor triggers the new warning with other types of objects, not just with DataFrame objects:

df <- data.frame(Hits())
# Warning message:
# In .local(x, row.names, optional, ...) : arguments in '...' ignored

df <- data.frame(Pairs(11:15, 21:25))
# Warning message:
# In .local(x, row.names, optional, ...) : arguments in '...' ignored

library(Seqinfo)
df <- data.frame(Seqinfo())
# Warning messages:
# 1: In as.data.frame.Seqinfo(x[[i]], optional = TRUE, validRN = FALSE) :
#   supplied 'optional' value was ignored
# 2: In as.data.frame.Seqinfo(x[[i]], optional = TRUE, validRN = FALSE) :
#   extra arguments were ignored

library(GenomicRanges)
df <- data.frame(GRanges())
# Warning message:
# In .local(x, row.names, optional, ...) : arguments in '...' ignored

We even get an error with IRanges, GPos, or DNAStringSet objects:

data.frame(IRanges())
# Error in .as.data.frame.IPosRanges(x, row.names = NULL, optional = FALSE,  : 
#   unused argument (validRN = FALSE)

data.frame(GPos())
# Error in .as.data.frame.GPos(x, row.names = NULL, optional = FALSE, ...) : 
#   unused argument (validRN = FALSE)

library(Biostrings)
data.frame(DNAStringSet())
# Error in .local(x, row.names, optional, ...) : 
#   unused argument (validRN = FALSE)

Various fixes in various packages coming soon...

[hpages]

Fixed in S4Vectors 0.51.8 (see commit e4668d7).

Other related fixes to come in IRanges, Seqinfo, GenomicRanges, and Biostrings...