Revisions of R-base
Ana Guerrero (anag+factory)
accepted
request 1171133
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Factory Maintainer (factory-maintainer)
(revision 92)
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Dominique Leuenberger (dimstar_suse)
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request 1155848
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Factory Maintainer (factory-maintainer)
(revision 91)
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Ana Guerrero (anag+factory)
accepted
request 1124841
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Factory Maintainer (factory-maintainer)
(revision 90)
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Dominique Leuenberger (dimstar_suse)
accepted
request 1094852
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Factory Maintainer (factory-maintainer)
(revision 89)
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Dominique Leuenberger (dimstar_suse)
accepted
request 1083568
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Factory Maintainer (factory-maintainer)
(revision 88)
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Dominique Leuenberger (dimstar_suse)
accepted
request 1073781
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Factory Maintainer (factory-maintainer)
(revision 87)
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Dominique Leuenberger (dimstar_suse)
accepted
request 1033874
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Detlef Steuer (dsteuer)
(revision 86)
- CHANGES IN R 4.2.2: NEW FEATURES: * tools::Rdiff(useDiff = TRUE) checks for the presence of an external diff command and switches to useDiff = FALSE if none is found. This allows R CMD Rdiff to always work. * On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT can be used to switch to only 'best-effort' SSL certificate revocation checks with the default "libcurl" download method. This reduces security, but may be needed for downloads to work with MITM proxies (PR#18379). * (macOS) The run-time check for libraries from XQuartz for X11 and Tcl/Tk no longer uses otool from the Apple Developer Tools (PR#18400). * The LaTeX style for producing the PDF manuals, Rd.sty, now loads the standard amsmath, amsfonts and amssymb packages for greater coverage of math commands in the Rd \eqn and \deqn macros. The \mathscr LaTeX command is also provided (via the mathrsfs package, if available, or the amsfonts bundle otherwise), fulfilling the wish of PR#18398. * (Windows) The default format of readClipboard() and writeClipboard() has been changed to 13 (CF_UNICODETEXT). INSTALLATION on a UNIX-ALIKE: * The PDF manuals (if built) can be compacted by the new target make compact-pdf (at the top level or in directory doc/manual). * There is now configure support for LLVM clang 15 on Linux, which defaults to position-independent (PIE) executables whereas gfortran does not. * Many small changes to ease compilation (and suppress warnings) with LLVM clang 15. BUG FIXES:
Dominique Leuenberger (dimstar_suse)
accepted
request 986019
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Factory Maintainer (factory-maintainer)
(revision 85)
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Dominique Leuenberger (dimstar_suse)
accepted
request 972315
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Detlef Steuer (dsteuer)
(revision 84)
- CHANGES IN R 4.2.0: SIGNIFICANT USER-VISIBLE CHANGES: * The formula method of aggregate() now matches the generic in naming its first argument x (resolving PR#18299 by Thomas Soeiro). This means that calling aggregate() with a formula as a named first argument requires name formula in earlier versions of R and name x now, so portable code should not name the argument (code in many packages did). * Calling && or || with either argument of length greater than one now gives a warning (which it is intended will become an error). * Calling if() or while() with a condition of length greater than one gives an error rather than a warning. Consequently, environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has any effect. * Windows users should consult the WINDOWS section below for some profound changes including * Support for 32-bit builds has been dropped. * UTF-8 locales are used where available. * The default locations for the R installation and personal library folder have been changed. Thanks to Tomas Kalibera for months of work on the Windows port for this release. NEW FEATURES: * matrix(x, n, m) now warns in more cases where length(x) differs from n * m, as suggested by Abby Spurdle and Wolfgang Huber in Feb 2021 on the R-devel mailing list. This warning can be turned into an error by setting environment variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran does so unless it is already set.
Dominique Leuenberger (dimstar_suse)
accepted
request 962175
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Detlef Steuer (dsteuer)
(revision 83)
- CHANGES IN R 4.1.3: 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. BUG FIXES: * 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. Reported with a patch in PR#18228 by Brodie Gaslam. * Subscripting an array x without dimnames by a length(dim(x))-column character matrix gave "random" non-sense, now an error; reported in PR#18244 by Mikael Jagan. * ...names() now matches names(list(...)) closely, fixing PR#18247. * all.equal(*, scale = s) now works as intended when length(s) > 1, partly thanks to Michael Chirico's PR#18272. * 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.
Dominique Leuenberger (dimstar_suse)
accepted
request 930112
from
Factory Maintainer (factory-maintainer)
(revision 82)
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Richard Brown (RBrownSUSE)
accepted
request 912679
from
Factory Maintainer (factory-maintainer)
(revision 81)
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Dominique Leuenberger (dimstar_suse)
accepted
request 899423
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Factory Maintainer (factory-maintainer)
(revision 80)
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Dominique Leuenberger (dimstar_suse)
accepted
request 894139
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Detlef Steuer (dsteuer)
(revision 79)
- CHANGES IN R 4.1.0: FUTURE DIRECTIONS: * It is planned that the 4.1.x series will be the last to support 32-bit Windows, with production of binary packages for that series continuing until early 2023. SIGNIFICANT USER-VISIBLE CHANGES: * Data set esoph in package datasets now provides the correct numbers of controls; previously it had the numbers of cases added to these. (Reported by Alexander Fowler in PR#17964.) NEW FEATURES: * www.omegahat.net is no longer one of the repositories known by default to setRepositories(). (Nowadays it only provides source packages and is often unavailable.) * Function package_dependencies() (in package tools) can now use different dependency types for direct and recursive dependencies. * The checking of the size of tarball in R CMD check --as-cran <pkg> may be tweaked via the new environment variable _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_, as suggested in PR#17777 by Jan Gorecki. * Using c() to combine a factor with other factors now gives a factor, an ordered factor when combining ordered factors with identical levels. * apply() gains a simplify argument to allow disabling of simplification of results. * The format() method for class "ftable" gets a new option justify. (Suggested by Thomas Soeiro.) * New ...names() utility. (Proposed by Neal Fultz in PR#17705.) * type.convert() now warns when its as.is argument is not specified, as the help file always said it _should_. In that case, the default is changed to TRUE in line with its change in
Richard Brown (RBrownSUSE)
accepted
request 882498
from
Detlef Steuer (dsteuer)
(revision 78)
- CHANGES IN R 4.0.5: BUG FIXES: * The change to the internal table in R 4.0.4 for iswprint has been reverted: it contained some errors in printability of 'East Asian' characters. * For packages using LazyData, R CMD build ignored the --resave-data option and the BuildResaveData field of the DESCRIPTION file (in R versions 4.0.0 to 4.0.4).
Dominique Leuenberger (dimstar_suse)
accepted
request 872357
from
Detlef Steuer (dsteuer)
(revision 77)
- CHANGES IN R 4.0.4: NEW FEATURES: * File share/texmf/tex/latex/jss.cls has been updated to work with LaTeX versions since Oct 2020. * Unicode character width tables (as used by nchar(, type = "w")) have been updated to Unicode 12.1 by Brodie Gaslam (PR#17781), including many emoji. * The internal table for iswprint (used on Windows, macOS and AIX) has been updated to include many recent Unicode characters. INSTALLATION on a UNIX-ALIKE: * If an external BLAS is specified by --with-blas=foo or _via_ environment variable BLAS_LIBS is not found, this is now a configuration error. The previous behaviour was not clear from the documentation: it was to continue the search as if --with-blas=yes was specified. BUG FIXES: * all.equal(x,y) now "sees" the two different NAs in factors, thanks to Bill Dunlap and others in PR#17897. * (~ NULL)[1] and similar formula subsetting now works, thanks to a report and patch by Henrik Bengtsson in PR#17935. Additionally, subsetting leaving an empty formula now works too, thanks to suggestions by Suharto Anggono. * .traceback(n) keeps source references again, as before R 4.0.0, fixing a regression; introduced by the PR#17580, reported including two patch proposals by Brodie Gaslam. * unlist(plst, recursive=FALSE) no longer drops content for pairlists with list components, thanks to the report and patch by Suharto Anggono in PR#17950. * iconvlist() now also works on MUSL based (Linux) systems, from a report and patch suggestion by Wesley Chan in PR#17970.
Dominique Leuenberger (dimstar_suse)
accepted
request 841472
from
Detlef Steuer (dsteuer)
(revision 76)
- CHANGES IN R 4.0.3: NEW FEATURES: * On platforms using configure option --with-internal-tzcode, additional values "internal" and (on macOS only) "macOS" are accepted for the environment variable TZDIR. (See ?TZDIR.) On macOS, "macOS" is used by default if the system timezone database is a newer version than that in the R installation. * When install.packages(type = "source") fails to find a package in a repository it mentions package versions which are excluded by their R version requirement and links to hints on why a package might not be found. * The default value for options("timeout") can be set from enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting to 60 (seconds) if that is not set or invalid. This may be needed when child R processes are doing downloads, for example during the installation of source packages which download jars or other forms of data. LINK-TIME OPTIMIZATION on a UNIX-ALIKE: * There is now support for parallelized Link-Time Optimization (LTO) with GCC and for 'thin' LTO with clang _via_ setting the LTO macro. * There is support for setting a different LTO flag for the Fortran compiler, including to empty when mixing clang and gfortran (as on macOS). See file config.site. * There is a new LTO_LD macro to set linker options for LTO compilation, for example to select an alternative linker or to parallelize thin LTO. DEPRECATED AND DEFUNCT: * The LINPACK argument to chol.default(), chol2inv(), solve.default() and svd() has been defunct since R 3.1.0. Using
Dominique Leuenberger (dimstar_suse)
accepted
request 817664
from
Factory Maintainer (factory-maintainer)
(revision 75)
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Dominique Leuenberger (dimstar_suse)
accepted
request 812058
from
Detlef Steuer (dsteuer)
(revision 74)
- CHANGES IN R 4.0.1: NEW FEATURES: * paste() and paste0() gain a new optional argument recycle0. When set to true, zero-length arguments are recycled leading to character(0) after the sep-concatenation, i.e., to the empty string "" if collapse is a string and to the zero-length value character(0) when collapse = NULL. A package whose code uses this should depend on R (>= 4.0.1). * The summary(<warnings>) method now maps the counts correctly to the warning messages. BUG FIXES: * aov(frml, ...) now also works where the formula deparses to more than 500 characters, thanks to a report and patch proposal by Jan Hauffa. * Fix a dozen places (code, examples) as Sys.setlocale() returns the new rather than the previous setting. * Fix for adding two complex grid units via sum(). Thanks to Gu Zuguang for the report and Thomas Lin Pedersen for the patch. * Fix parallel::mclapply(..., mc.preschedule=FALSE) to handle raw vector results correctly. PR#17779 * Computing the base value, i.e., 2, "everywhere", now uses FLT_RADIX, as the original machar code looped indefinitely on the ppc64 architecture for the longdouble case. * In R 4.0.0, sort.list(x) when is.object(x) was true, e.g., for x <- I(letters), was accidentally using method = "radix". Consequently, e.g., merge(<data.frame>) was much slower than previously; reported in PR#17794. * plot(y ~ x, ylab = quote(y[i])) now works, as e.g., for xlab; related to PR#10525. * parallel::detect.cores(all.tests = TRUE) tries a matching OS name
Dominique Leuenberger (dimstar_suse)
accepted
request 797070
from
Detlef Steuer (dsteuer)
(revision 73)
- CHANGES IN 4.0.0: SIGNIFICANT USER-VISIBLE CHANGES: * Packages need to be (re-)installed under this version (4.0.0) of R. * matrix objects now also inherit from class "array", so e.g., class(diag(1)) is c("matrix", "array"). This invalidates code incorrectly assuming that class(matrix_obj)) has length one. S3 methods for class "array" are now dispatched for matrix objects. * There is a new syntax for specifying _raw_ character constants similar to the one used in C++: r"(...)" with ... any character sequence not containing the sequence )". This makes it easier to write strings that contain backslashes or both single and double quotes. For more details see ?Quotes. * R now uses a stringsAsFactors = FALSE default, and hence by default no longer converts strings to factors in calls to data.frame() and read.table(). A large number of packages relied on the previous behaviour and so have needed/will need updating. * The plot() S3 generic function is now in package base rather than package graphics, as it is reasonable to have methods that do not use the graphics package. The generic is currently re-exported from the graphics namespace to allow packages importing it from there to continue working, but this may change in future. Packages which define S4 generics for plot() should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being looked for on the search path (as in a namespace, the base namespace has precedence over the search path). REFERENCE COUNTING:
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