Submitted by vmartin on
r4.2.1    R 4.3.0 is now the default version on migale's R and also on RStudio
  3.17 (BiocManager 1.30.20)
rstudio  2023.03.1+446

CHANGES IN R 4.3.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

  • Calling && or || with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form

        'length = 4' in coercion to 'logical(1)'

    Environment variable _R_CHECK_LENGTH_1_LOGIC2_ no longer has any effect.

NEW FEATURES

  • The included BLAS sources have been updated to those shipped with LAPACK version 3.10.1. (This caused some platform-dependent changes to package check output.) And then to the sources from LAPACK version 3.11.0 (with changes only to double complex subroutines).

  • The included LAPACK sources have been updated to include the four Fortran 90 routines rather than their Fortran 77 predecessors. This may give some different signs in SVDs or eigendecompositions.. (This completes the transition to LAPACK 3.10.x begun in R 4.2.0.)

  • The LAPACK sources have been updated to version 3.11.0. (No new subroutines have been added, so this almost entirely bug fixes: Those fixes do affect some computations with NaNs, including R's NA.)

  • The parser now signals classed errors, notably in case of the pipe operator |>. The error object and message now give line and column numbers, mostly as proposed and provided by Duncan Murdoch in PR#18328.

  • toeplitz() is now generalized for asymmetric cases, with a toeplitz2() variant.

  • xy.coords() and xyz.coords() and consequently, e.g., plot(x,y, log = "y") now signal a classed warning about negative values of y (where log(.) is NA). Such a warning can be specifically suppressed or caught otherwise.

  • Regular expression functions now check more thoroughly whether their inputs are valid strings (in their encoding, e.g. in UTF-8).

  • The performance of grep(), sub(), gsub() and strsplit() has been improved, particularly with perl = TRUE and fixed = TRUE. Use of useBytes = TRUE for performance reasons should no longer be needed and is discouraged: it may lead to incorrect results.

  • apropos() gains an argument dot_internals which is used by the completion (help(rcompgen)) engine to also see base internals such as .POSIXct().

  • Support in tools::Rdiff() for comparing uncompressed PDF files is further reduced – see its help page.

  • qqplot(x, y, ...) gains conf.level and conf.args arguments for computing and plotting a confidence band for the treatment function transforming the distribution of x into the distribution of y (Switzer, 1976, Biometrika). Contributed by Torsten Hothorn.

  • Performance of package_dependencies() has been improved for cases when the number of dependencies is large.

  • Strings newly created by gsub(), sub() and strsplit(), when any of the inputs is marked as "bytes", are also marked as "bytes". This reduces the risk of creating invalid strings and accidental substitution of bytes deemed invalid.

  • Support for readLines(encoding = "bytes") has been added to allow processing special text files byte-by-byte, without creating invalid strings.

  • iconv(from = "") now takes into account any declared encoding of the input elements and uses it in preference to the native encoding. This reduces the risk of accidental creation of invalid strings, particularly when different elements of the input have different encoding (including "bytes").

  • Package repositories in getOption("repos") are now initialized from the ‘repositories’ file when utils is loaded (if not already set, e.g., in ‘.Rprofile’). (From a report and patch proposal by Gabriel Becker in PR#18405.)

  • compactPDF() gets a verbose option.

  • type.convert() and hence read.table() get new option tryLogical = TRUE with back compatible default. When set to false, converts "F" or "T" columns to character.

  • Added new unit prefixes "R" and "Q" for abbreviating (unrealistically large) sizes beyond 1027 in standard = "SI", thanks to Henrik Bengtsson's PR#18435.

  • as.data.frame()'s default method now also works fine with atomic objects inheriting from classes such as "roman", "octmode" and "hexmode", such fulfilling the wish of PR#18421, by Benjamin Feakins.

  • The as.data.frame.vector() utility now errors for wrong-length row.names. It warned for almost six years, with “Will be an error!”.

  • sessionInfo() now also contains La_version() and reports codepage and timezone when relevant, in both print() and toLatex() methods which also get new option tzone for displaying timezone information when locale = FALSE.

  • New function R_compiled_by() reports the C and Fortran compilers used to build R, if known.

  • predict(<lm>, newdata = *) no longer unnecessarily creates an offset of all 0s.

  • solve() for complex inputs now uses argument tol and by default checks for ‘computational singularity’ (as it long has done for numeric inputs).

  • predict(<rank-deficient lm>, newdata=*) now obeys a new argument rankdeficient, with new default "warnif", warning only if there are non-estimable cases in newdata. Other options include rankdeficient = "NA", predicting NA for non-estimable newdata cases. This addresses PR#15072 by Russ Lenth and is based on his original proposal and discussions in PR#16158 also by David Firth and Elin Waring. Still somewhat experimental.

  • Rgui console implementation now works better with the NVDA screen reader when the full blinking cursor is selected. The underlying improvements in cursor handling may help also other screen readers on Windows.

  • The drop-field control in GraphApp can now be left with the TAB key and all controls can be navigated in the reverse order using the Shift+TAB key, improving accessibility of the Rgui configuration editor.

  • qnorm(<very large negative>, log.p=TRUE) is now fully accurate (instead of to “only” minimally five digits).

  • demo(error.catching) now also shows off withWarnings() and tryCatchWEMs().

  • As an experimental feature the placeholder _ can now also be used in the rhs of a forward pipe |> expression as the first argument in an extraction call, such as _$coef. More generally, it can be used as the head of a chain of extractions, such as _$coef[[2]].

  • Spaces in the environment variable used to choose the R session's temporary directory (TMPDIR, TMP and TEMP are tried in turn) are now fatal. (On Windows the ‘short path’ version of the path is tried and used if that does not contain a space.)

  • all.equal.numeric() gets a new optional switch giveErr to return the numeric error as attribute. Relatedly, stopifnot(all.equal<some>(a, b, ..)) is as “smart” now, as stopifnot(all.equal(....)) has been already, thus allowing customized all.equal<Some>() wrappers.

  • R on Windows is now able to work with path names longer than 260 characters when these are enabled in the system (requires at least Windows 10 version 1607). Packages should be updated to work with long paths as well, instead of assuming PATH_MAX to be the maximum length. Custom front-ends and applications embedding R need to update their manifests if they wish to allow this feature. See https://blog.r-project.org/2023/03/07/path-length-limit-on-windows for more information.

  • ‘Object not found’ and ‘Missing argument’ errors now give a more accurate error context. Patch provided by Lionel Henry in PR#18241.

  • The @ operator is now an S3 generic. Based on contributions by Tomasz Kalinowski in PR#18482.

  • New generic chooseOpsMethod() provides a mechanism for objects to resolve cases where two suitable methods are found for an Ops Group Generic. This supports experimenting with alternative object systems. Based on contributions by Tomasz Kalinowski in PR#18484.

  • inherits(x, what) now accepts values other than a simple character vector for argument what. A new generic, nameOfClass(), is called to resolve the class name from what. This supports experimenting with alternative object systems. Based on contributions by Tomasz Kalinowski in PR#18485.

  • Detection of BLAS/LAPACK in use (sessionInfo()) with FlexiBLAS now reports the current backend.

  • The "data.frame" method for subset() now warns about extraneous arguments, typically catching the use of ‘⁠=⁠’ instead of ‘⁠==⁠’ in the subset expression.

  • Calling a:b when numeric a or b is longer than one may now be made into an error by setting environment variable _R_CHECK_LENGTH_COLON_ to a true value, along the proposal in PR#18419 by Henrik Bengtsson.

  • density(x, weights = *) now warns if automatic bandwidth selection happens without using weights; new optional warnWbw may suppress the warning. Prompted by Christoph Dalitz' PR#18490 and its discussants.

  • rm(list = *) is faster and more readable thanks to Kevin Ushey's PR#18492.

  • The plot.lm() function no longer produces a normal Q-Q plot for GLMs. Instead it plots a half-normal Q-Q plot of the absolute value of the standardized deviance residuals.

  • The print() method for class "summary.glm" no longer shows summary statistics for the deviance residuals by default. Its optional argument show.residuals can be used to show them if required.

  • The tapply() function now accepts a data frame as its X argument, and allows INDEX to be a formula in that case. by.data.frame() similarly allows INDICES to be a formula.

  • The performance of df[j] <- value (including for missing j) and write.table(df) has been improved for data frames df with a large number of columns. (Thanks to Gabriel Becker's PR#18500, PR#18503 and discussants, prompted by a report from Toby Dylan Hocking on the R-devel mailing list.)

  • The matrix multiply operator %*% is now an S3 generic, belonging to new group generic matrixOps. From Tomasz Kalinowski's contribution in PR#18483.

  • New function array2DF() to convert arrays to data frames, particularly useful for the list arrays created by tapply().

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