R for Windows 4.1.3

What's new in this version:

New features:
- The default version of Bioconductor has been changed to 3.14. (This is used by setRepositories and the menus in GUIs.)

Utilities:
- R CMD check --as-cran has a workaround for a bug in versions of file up to at least 5.41 which mis-identify DBF files last changed in 2022 as executables.

C-Level facilities:
- The legacy S-compatibility macros SINGLE_* in ‘R_ext/Constants.h’ (included by ‘R.h’) are deprecated and will be removed in R 4.2.0.

Fixed:
- Initialization of self-starting nls() models with initialization functions following the pre-R-4.1.0 API (without the ... argument) works again for now, with a deprecation warning.
- Fixed quoting of ~autodetect~ in Java setting defaults to avoid inadvertent user lookup due to leading ~, reported in PR#18231 by Harold Gutch.
- substr(., start, stop) <- v now treats negative stop values correctly
- Subscripting an array x without dimnames by a length(dim(x))-column character matrix gave "random" non-sense, now an error
- ...names() now matches names(list(...)) closely
- all.equal(*, scale = s) now works as intended when length(s) > 1
- print(x) for long vectors x now also works for named atomic vectors or lists and prints the correct number when reaching the getOption("max.print") limit; partly thanks to a report and proposal by Hugh Parsonage to the R-devel list
- all.equal(<selfStart>, *) no longer signals a deprecation warning
- reformulate(*, response=r) gives a helpful error message now when length(r) > 1
- Modifying globalCallingHandlers inside withCallingHandlers() now works or fails correctly
- hist(<Date>, breaks = "days") and hist(<POSIXt>, breaks = "secs") no longer fail for inputs of length 1
- qbeta(.001, .9, .009) and similar cases now converge correctly
- window(x, start, end) no longer wrongly signals “'start' cannot be after 'end'”
- data() now checks that its (rarely used) list argument is a character vector – a couple of packages passed other types and gave incorrect results
- which() now checks its arr.ind argument is TRUE rather coercing to logical and taking the first element – which gave incorrect results in package code
- model.weights() and model.offset() more carefully extract their model components, thanks to Ben Bolker and Tim Taylor's R-devel post
- list.files(recursive = TRUE) now shows all broken symlinks (previously, some of them may have been omitted, PR#18296)