This blog is updated daily.
A general description is here.
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite,
nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's
PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
‘dotchart()’ gets new options ‘ann’, ‘xaxt’, ‘frame.plot’ and ‘log’.
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite, nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
‘dotchart(*, pch=., groups=.)’ now works better. Reported by Robert and confirmed by Nic Rochette in PR#16953.
‘R CMD check’ now optionally checks ‘configure’ and ‘cleanup’ scripts for non-Bourne-shell code (‘bashisms’).
‘power.t.test()’ works in more cases when returning values of n smaller than 2.
‘barplot()’ could get spacings wrong if there were exactly two bars PR#15522. Patch by Michael Chirico.
The formula interface to ‘t.test()’ and ‘wilcox.test()’ has been extended to handle one-sample and paired tests.
‘barplot()’ could get spacings wrong if there was exactly two bars PR#15522. Patch by Michael Chirico.
‘get_all_vars(f, d)’ now also works for cases, e.g. where ‘d’ contains a matrix. Reported by Simon Wood in 2009 and patch provided by Ben Bolker in PR#13624.
The formula interface to ‘t.test’ and ‘wilcox.test’ has been extended to handle one-sample and paired tests.
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user-level functions ‘.traceback()’ and ‘traceback()’, fulfilling the wish of PR#17580, reported incl. two patch proposals by Brodie Gaslam.
‘methods(class = class(glm(..)))’ now warns more usefully and only once.
‘format(object.size(.), digits=NULL)’ now works, fixing PR#17628 reported by Jonathan Carroll.
‘R_tryCatch’ no longer transfers control for all conditions. Reported and patch provided by Lionel Henry in PR#17617.
The backquote function ‘bquote()’ has a new argument ‘splice’ to enable splicing a computed list of values into an expression, like ‘,@’ in LISP's backquote.
The formula interface to ‘t.test’ has been extended to handle one-sample and paired tests.
‘R_tryCatch’ no longer transfers control for all conditions. Reported and patch provided by Linoel Henry in PR#17617.
The internal version number of R-devel has been set to 4.0.0, reflecting the intention that the next non-patch release should be 4.0.0.
‘R --help’ now mentions the option ‘--no-echo’ (renamed from ‘--slave’) and its previously undocumented short form ‘-s’.
‘options(warn=1e11)’ is an error now, instead of later leading to C stack overflow because of infinite recursion.
‘grepl(NA, *)’ now returns ‘logical’ as documented.
R now builds by default against a PCRE2 library for Perl-like regular expressions if available at build time on non-Windows platforms (otherwise PCRE1 is used as in older versions of R).
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The version of PCRE used can be obtained via ‘extSoftVersion()’, PCRE1 has versions < 10, PCRE2 versions >= 10.
Added an argument ‘add_datalist(*, small.size = 0)’ to allow the creation of a ‘data/datalist’ file even when the total size of the data sets is small.
The deprecated support for specifying C++98 in package installation has been removed.
Certain ‘Ops’ (notably comparison such as ‘==’) now also work for 0-length data frames, after reports by Hilmar Berger.
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite, nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
R now builds by default against PCRE2 library for Perl-like regular expressions if available at build time on non-Windows platforms (otherwise PCRE1 is used as in older versions of R).
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The version of PCRE used can be obtained via ‘extSoftVersion()’, PCRE1 has versions < 10, PCRE2 versions >= 10.
Either PCRE >= 8.32 (Nov 2012) or PCRE2 is required: the deprecated provision for 8.20-8.31 has been removed.
The minimum required version of ‘libcurl’ is now 7.28.0 (Oct 2012).
PCRE2 is used if available: this is strongly recommended as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables). ‘configure’ will warn if PCRE2 is not found and fall back to PCRE1. ‘configure’ options ‘--without-pcre1’ and ‘--without-pcre2’ can be used to exclude one or the other (but at least one of PCRE2 and PCRE1 is required).
R now builds by default against PCRE2 library for Perl-like regular expressions if available at build time on non-Windows platforms (otherwise PCRE1 is used as in older versions of R)
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The version of PCRE used can be obtained via ‘extSoftVersion()’, PCRE1 has versions < 10, PCRE2 versions >= 10.
Add an argument ‘add_datalist(*, small.size = 0)’ to allow the creation of a ‘data/datalist’ file even when the total size of the data sets is small.
PCRE2 is used if available: this is strongly recommended as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables).
‘postscript(.., title = *)’ now signals an error when the title string contains a character which produces corrupt PostScript, thanks to Daisuko Ogawa's PR#17607.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as ‘dir.exists()’, ‘file.exists()’, ‘file.access()’, ‘file.info()’, ‘list.files()’, ‘normalizePath()’ and ‘path.expand()’) treat this like any other non-existent file, often with a warning.
There is a new function ‘infoRDS()’ providing information about the serialization format of a serialized object.
A package with Fortran source code and perhaps C (but not C++) sources can request for its shared object/DLL to be linked by the Fortran compiler by including a line ‘USE_FC_TO_LINK=’ in ‘src/Makevars[.win]’.
The known reason for doing so is a package which uses Fortran (only) OpenMP on a platform where the Fortran OpenMP runtime is incompatible with the C one (e.g. ‘gfortran’ 9.x with ‘clang’).
Add an arguemnt ‘add_datalist(*, small.size = 0)’ to allow the creation of a ‘data/datalist’ file even when the total size of the data sets is small.
Header ‘R_ext/Print.h’ defines ‘R_USE_C99_IN_CXX’ and hence exposes ‘Rvprintf’ and ‘REprintf’ if used with a C++11 compiler.
allow ‘add_datalist(*, small.size=0)’ to create a ‘data/datalist’ file
also in case the data sets are small.
S3 method lookup now by default skips the elements of the search path between the global and base environments.
Support in ‘R CMD config’ for ‘F77’, ‘FCPIFCPLAGS’, ‘CPP’, ‘CXXCPP’ and ‘CXX98’ and similar is deprecated. (‘CPP’ is found from the system ‘make’ and may well not be set.)
Use ‘$CC -E’ and ‘$CXX -E’ instead of ‘CPP’ and ‘CXXCPP’.
‘pchisq(<LRG>, <LRG>, ncp=100)’ no longer takes practically forever in some cases. Hence ditto for corresponding ‘qchisq()’ calls.
Support for specifying C++98 in package installation has been removed.
Support in ‘R CMD config’ for ‘F77’, ‘FCPIFCPLAGS’, ‘CPP’, ‘CXXCPP’ and ‘CXX98’ and similar is deprecated. (‘CPP’ is found from the system ‘make’ and may well not be set.)
Support in ‘R CMD config’ for ‘F77’, ‘FCPIFCPLAGS’, ‘CXXCPP’ and ‘CXX98’ and similar is deprecated.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘R_ext/BLAS.h’ and ‘R_ext/Lapack.h’ but to avoid extensive breakage this is only exposed when ‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments used by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘R_ext/BLAS.h’ or ‘R_ext/Lapack.h’.
‘R CMD check’ has a new option to mitigate checks leaving files/directories in ‘/tmp’. See the ‘R Internals’ manual - this is part of ‘--as-cran’.
‘format(as.symbol("foo"))’ now works (returning ‘"foo"’).
allow ‘add_datalist(*, small.size=0)’ to create a ‘data/datalist’ file also in case the data sets are small.
There is a new help document accessed by ‘help("file path encoding")’ detailing how file paths with marked encodings are handled.
There is a new function ‘infoRDS()’ providing information about serialization format of a serialized object.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as ‘dir.exists()’, ‘file.exists()’, ‘file.access()’, ‘file.info()’, ‘list.files’, ‘normalizePath()’ and ‘path.expand()’) treat this like any other non-existent file, often with a warning.
(Windows) ‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing is possible when ‘winpty’ is installed.
‘iconv()’ has a new option ‘sub = "Unicode"’ to translate UTF-8 input invalid in the ‘to’ encoding using ‘<U+xxxx>’ escapes.
New function ‘list2DF()’ for creating data frames from lists of variables.
‘R CMD config’ no longer knows about the unused settings ‘F77’ and ‘FCPIFCPLAGS’, nor ‘CXX98’ and similar.
Support for specifying C++98 in package installation is deprecated.
‘installTrChar’ (which is nowadays is wrapped by ‘installChar’) is defined in ‘Rinternals.h’. (Neither are part of the API.)
‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing is possible when ‘winpty’ is installed.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as ‘dir.exists()’, ‘file.exists()’, ‘file.access()’, ‘file.info()’, ‘normalizePath()’ and ‘path.expand()’) treat this like any other non-existent file, with a warning.
‘file.path()’ has some support for file paths not in the session encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output is marked as UTF-8.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate using escapes as previously.
A C++ compiler default is set only if the C++11 standard is supported: it no longer falls back to C++98.
‘installChar’ is now remapped in ‘Rinternals.h’ to ‘installTrChar’, of which it has been a wrapper since R 3.6.0. Neither are part of the API, but packages using ‘installChar’ can replace it if they depend on ‘R >= 3.6.2’.
‘installTrChar’ which is nowadays a wrapper for ‘installChar’ is defined in ‘Rinternals.h’. (Neither are part of the API.)
‘conformMethod()’ now works correctly in cases containing a “‘&&’ logic” bug, reported by Henrik Bengtsson. It now creates methods with ‘"missing"’ entries in the signature. Consequently, ‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls with named arguments where needed.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to UTF-8 or the native encoding), rather than translate using escapes as previously.
‘assertError()’ and ‘assertWarning()’ (in package ‘tools’) can now check for _specific_ error or warning classes _via_ the new optional second argument ‘classes’ (which is not back compatible with previous use of an unnamed second argument).
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user-level functions ‘.traceback()’ and ‘traceback()’, fulfilling the wish of PR#17580, reported (incl. patch proposal) by Brodie Gaslam.
‘package.skeleton()’ now explicitly lists all exports in the ‘NAMESPACE’ file.
‘file.path()’ has some support for file paths not in the session encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output is UTF-8 and marked as such.
‘package.skeleton()’ now explicitly lists all exports.
New function ‘.S3method()’ to register S3 methods in R scripts.
‘DF2formula()’, the utility for the data frame method of ‘formula()’, now works without parsing and explicit evaluation, starting from Suharto Anggono's suggestion in PR#17555.
‘data.matrix()’ now converts character columns to factors and from this to integers.
‘format.default(*, scientific = FALSE)’ now corresponds to a practically most extreme ‘options(scipen = n)’ setting rather than arbitrary ‘n = 100’.
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user level functions ‘.traceback()’ and ‘traceback()’, fulfilling the wish of PR#17580, reported (incl. patch proposal) by Brodie Gaslam.
Auto-printing S4 objects no longer duplicates the object, for faster speed and reduced memory consumption. Reported by Aaron Lun.
‘as.numeric(<call>)’ now gives correct error message.
Printing ‘ls.str()’ no longer wrongly shows ‘"<missing>"’ in rare cases.
‘str(x)’ gets a new ‘deparse.lines’ option with a default to speed it up when ‘x’ is a large ‘call’ object.
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user level functions ‘.traceback()’ and ‘traceback()’, fulfilling the whish of PR#17580, reported (incl. patch proposal) by Brodie Gaslam.
‘options(str = .)’ is correctly initialized at package ‘utils’ load time, now. A consequence is that ‘str()’ in scripts now is more consistent to interactive use, e.g., when displaying function(**) argument lists.
‘dgamma(x, shape, log=TRUE)’ now longer overflows to ‘Inf’ for shape < 1 and very small ‘x’, fixing PR#17577, reported by Jonathan Rougier.
Buffer overflow in building error messages fixed. Reported by Benjamin Tremblay.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at
installation which is used by the prototypes in headers ‘BLAS.h’ and
‘Lapack.h’ but to avoid extensive breakage this is only exposed when
‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments use by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘BLAS.h’ or ‘Lapack.h’.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘BLAS.h’ and ‘Lapack.h’ but to avoid extensive breakage this is only exposed when ‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments used by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘BLAS.h’ or ‘Lapack.h’.
‘apply(diag(3), 2:3, mean)’ now gives a helpful error message.
‘conformMethod()’ also gives correct error messages in another case of
signature mismatches, reported by Suharto Anggono.
‘conformMethod()’ also gives correct error messages in another case of signature mismatches, reported by Suharto Anggono.
Detection of the C stack direction has been moved from run-time to
‘configure’: this is safer with LTO builds and allows the detection to
be overridden - see file ‘config.site’.
Detection of the C stack direction has been moved from run-time to ‘configure’: this is safer with LTO builds and allows the detection to be overridden - see file ‘config.site’.
The default detection of the shell variable ‘libNN’ is overridden for derivatives of Debian Linux, some of which have started to have a ‘/usr/lib64’ directory. (E.g. Ubuntu 19.04.) As before, it can be specified in ‘config.site’.
‘R CMD config’ knows the values of ‘AR’ and ‘RANLIB’, often set for LTO builds.
The use of a character vector with ‘.Fortran()’ is formally deprecated and gives a non-portability warning. (It has long been strongly discouraged in ‘Writing R Extensions’.)
On Windows, GUI package installation via ‘menuInstallPkgs()’ works again, thanks to Len Weil's and Duncan Murdoch's PR#17556.
‘R CMD check’ on ‘data()’ fixing PR#17558 thanks to Duncan Murdoch.
‘quasi(*, variance = list(..))’ now works more efficiently, and should work in all cases fixing PR#17560. Further, ‘quasi(var = mu(1-mu))’ and ‘quasi(var = "mu ^ 3")’ now work, and ‘quasi(variance = "log(mu)")’ now gives a correct error message.
Creation of lazy loading database during package installation is again robust to Rprofile changing the current working directory (PR#17559).
‘boxplot(y ~ f, horizontal=TRUE)’ now produces correct x- and y-labels.
‘rbind.data.frame()’ allows to keep ‘<NA>’ levels from factor columns (PR#17562) via new option ‘factor.exclude’.
Additionally, it works in one more case with matrix-columns which had been reported on 2017-01-16 by Krzysztof Banas.
Correct messaging in C++ pragma checks in ‘tools’ code for ‘R CMD check’, fixing PR#17566 thanks to Xavier Robin.
print()ing and auto-printing no longer differs for ‘function’s with a user defined ‘print.function’, thanks to Bill Dunlap's report.
On Windows, ‘writeClipboard(.., format = <n>)’ now does correctly pass ‘format’ to the underlying C code, thanks to a bug report (with patch) by Jenny Bryan.
‘as.data.frame()’ treats 1D arrays the same as vectors, PR#17570.
Improvements in ‘smoothEnds(x, *)’ working with ‘NA’s (towards ‘runmed()’ working in that case, in the next version of R).
‘vcov(glm(<quasi>), dispersion = *)’ works correctly again, fixing PR#17571 thanks to Pavel Krivitsky.
‘R CMD INSTALL’ of binary packages on Windows now works also with per-directory locking.
‘R CMD INSTALL’ and ‘install.packages()’ on Windows are now more robust against a locked file in an earlier installation of the package to be installed. The default value of option ‘install.lock’ on Windows has been changed to ‘TRUE’.
On Unix alikes (when ‘readline’ is active), only expand tilde (‘~’) file names starting with a tilde, instead of almost all tildes.
In R documentation (‘*.Rd’) files, ‘\item [..]’ is no longer treated specially when rendered in LaTeX and hence pdf, but rather shows the brackets in all cases.
‘runmed(x, *)’ gets new option ‘na.action’ determining _how_ to handle ‘NaN’ or ‘NA’ in ‘x’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, and no longer segfaults for ‘"Turlach"’, as reported by Hilmar Berger.
‘conformMethod()’ now correctly works in cases containing a “‘&&’ logic” bug, reported by Henrik Bengtsson. It now creates methods with ‘"missing"’ entries in the signature. Consequently, ‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls with named arguments where needed.
‘runmed(x, *)’ gets new option ‘na.action’ determining how to handle
‘NaN’ or ‘NA’ in ‘x’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently
for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, also based on
‘smoothEnds(y)’ working with ‘NA’s, and no longer segfaults for
‘"Turlach"’, as reported by Hilmar Berger.
Improvements in ‘smoothEnds(x, *)’ working with ‘NA’s (towards ‘runmed()’ working in that case, in the next version of R).
‘runmed(x, *)’ gets new option ‘na.action’ determining how to handle ‘NaN’ or ‘NA’ in ‘x’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, also based on ‘smoothEnds(y)’ working with ‘NA’s, and no longer segfaults for ‘"Turlach"’, as reported by Hilmar Berger.
‘available.packages()’ and hence ‘install.packages()’ now pass their ‘...’ argument to ‘download.file()’, fulfilling the wish of PR#17532; subsequently, ‘available.packages()’ gets new argument ‘quiet’, solving PR#17573.
‘methods:::conformMethod()’ had ‘&&’ where ‘&’ was needed. (Spotted by
Henrik Bengtsson.)
‘methods:::conformMethod()’ had ‘&&’ where ‘&’ was needed. (Spotted by Henrik Bengtsson.)
On Unix alikes (when ‘readline’ is active), only expand tilde (‘~’) file names starting with a tilde, instead of almost all tildes.
In R documentation (‘*.Rd’) files, ‘\item [..]’ is no longer treated specially when rendered in LaTeX and hence pdf, but rather shows the brackets in all cases.
‘R CMD INSTALL’ of binary packages on Windows now works also with per-directory locking.
‘R CMD INSTALL’ and ‘install.packages()’ on Windows are now more robust against a locked file in an earlier installation of the package to be installed. The default value of option ‘install.lock’ on Windows has been changed to ‘TRUE’.
On Windows, ‘writeClipboard(.., format = <n>)’ now does correctly pass ‘format’ to the underlying C code, thanks to a bug report (with patch) by Jenny Bryan.
‘stopifnot()’ gets new argument ‘exprObject’ to allow an R object of class ‘expression’ (or other ‘language’) to work more consistently, thanks to suggestions by Suharto Anggono.
‘vcov(glm(<quasi>), dispersion = *)’ works correctly again, fixing PR#17571 thanks to Pavel Krivitsky.
‘runmed(x, *)’ when ‘x’ contains missing values now works for ‘algorithm="Stuetzle"’, also based on ‘smoothEnds(y)’ working with NA's, and no longer segfaults for the ‘"Turlach"’ algorithm; reported by Hilmar Berger.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘BLAS.h’ and ‘Lapack.h’ but to avoid extensive breakage this is only exposed when ‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments use by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘BLAS.h’ or ‘Lapack.h’.
‘R CMD config’ knows the values of ‘AR’ and ‘RANLIB’, often set for LTO builds.
The default detection of the shell variable ‘libNN’ is overridden for
derivatives of Debian Linux, some of which have started to have a
‘/usr/lib64’ directory. (E.g. Ubuntu 19.04.) As before, it can be
specified in ‘config.site’.
The default detection of the shell variable ‘libNN’ is overridden for derivatives of Debian Linux, some of which have started to have a ‘/usr/lib64’ directory. (E.g. Ubuntu 19.04.) As before, it can be specified in ‘config.site’.
There is a new variant option ‘--enable-lto=check’ for checking consistency of BLAS/LAPACK/LINPACK calls - see ‘Writing R Extensions’.
‘as.data.frame()’ treats 1D arrays the same as vectors, PR#17570.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the propotypes in headers ‘BLAS.h’ and ‘Lapack.h’ but to avoid extensive breakage this is only exposed when ‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments use by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘BLAS.h’ or ‘Lapack.h’.
Long vectors are now supported as the ‘seq’ argument of a ‘for()’ loop.
The default detection of the shell variable ‘libNN’ is overridden for derivatives of Debian Linux, some of which have started to have a ‘/usr/lib64’ directory. (E.g. Ubuntu 19.04.) As before, it can be specified in ‘config.site’.
There is a new variant option ‘--enable-lto=check’ for checking consistency of BLAS/LAPACK calls - see ‘Writing R Extensions’.
User-set ‘DEFS’ (e.g., in ‘config.site’) is now used for compiling packages (including base packages).
‘available.packages()’ and hence ‘install.packages()’ now pass their ‘...’ argument to ‘download.file()’, fulfilling the wish of PR#17532.
[On Windows only], ‘writeClipboard(.., format = <n>)’ now does correctly pass ‘format’ to the underlying C code, thanks to a bug report (with patch) by Jenny Bryan.
[On Windows only], ‘writeClipboard(.., format = <n>)’ now does correctly pass ‘format’ to the underlying C code, thanks to a bug report (with patch) by Jenny Brian.
‘rbind.data.frame()’ allows to keep ‘<NA>’ levels from factor columns (PR#17562) via new option ‘factor.exclude’.
Additionally, it works in one more case with matrix-columns which had been reported on 2017-01-16 by Krzysztof Banas.
Detection of the C stack direction has been moved from run-time to ‘configure’: this is safer with LTO builds and allows the detection to be overridden - see file ‘config.site’.
User-set ‘DEFS’ (e.g., in ‘config.site’ is now used for compiling packages (including base packages).
‘available.packages()’ and hence ‘install.packages()’ now pass their ‘...’ to ‘download.file()’, fulfilling the wish of PR#17532.
The use of a character vector with ‘.Fortran()’ is formally deprecated and gives a non-portability warning. (It has long been strongly discouraged in ‘Writing R Extensions’.)
print()ing and auto-printing no longer differs for ‘function’s with a user defined ‘print.function’, thanks to Bill Dunlap's report.
‘assertError()’ and ‘assertWarning()’ (in package ‘tools’) can now check for _specific_ error or warning classes _via_ the new optional second argument ‘classes’ (which is not back compatible with previous use of an unnamed second argument.)
‘approxfun()’ and ‘approx()’ gain a new argument ‘na.rm’ defaulting to true. If set to false, missing ‘y’ values now propagate into the interpolated values.
Long vectors are now supported in ‘for()’ loops.
‘rbind.data.frame()’ no longer drops ‘<NA>’ levels from factor columns by default, PR#17562.
The use of a character vector with ‘.Fortran()’ is depreacated and gives a non-portability warning.
‘rbind.data.frame()’ allows to keep ‘<NA>’ levels from factor columns (PR#17562) via new option ‘factor.exclude’.
Correct messaging in C++ pragma checks in ‘tools’ code for ‘R CMD check’, fixing PR#17566 thanks to Xavier Robin.
Long vectors are now supported in ‘for’ loops.
‘rbind.data.frame()’ no longer drops ‘<NA>’ levels from factor columns (PR#17562).
‘boxplot(y ~ f, horizontal=TRUE)’ now produces correct x- and y-labels.
‘approxfun()’ and ‘approx()’ gain option ‘na.rm = TRUE’. If set to false, missing y values now propagate into interpolated values.
‘quasi(*, variance = list(..))’ now works more efficiently, and should work in all cases fixing PR#17560. Further, ‘quasi(var = mu(1-mu))’ and ‘quasi(var = "mu ^ 3")’ now work, and ‘quasi(variance = "log(mu)")’ now gives a correct error message.
Creation of lazy loading database during package installation is again robust to Rprofile changing the current working directory (PR#17559).
‘quasi(*, variance = list(..))’ now works more efficiently, and should work in all cases fixing PR#17560.
‘Df2formula()’, the utility for the data frame method of ‘formula()’, now works without parsing and explicit evaluation, starting from Suharto Anggono's suggestion in PR#17555.
Long-standing issue where the X11 device could lose events shortly after startup has been addressed PR#16702.
‘R CMD check’ on ‘data()’ fixing PR#17558 thanks to Duncan Murdoch.
On Windows, GUI package installation via ‘menuInstallPkgs()’ works again, thanks to Len Weil's and Duncan Murdoch's PR#17556.
‘formula(x)’ with ‘length(x) > 1’ character vectors, is deprecated now. Such use has been rare, and has ‘worked’ as expected in some cases only. In other cases, wrong ‘x’ have silently been truncated, not detecting previous errors.
Placeholder.
‘assertError()’ and ‘assertWarning()’ (package ‘tools’) now can check for _specific_ error or warning classes via new optional 2nd argument ‘classes’ (which is not back compatible with previous use of unnamed 2nd arg.)
‘format(x)’ with ‘length(x) > 1’ character vectors, is deprecated now. Such use has been very rare, and has ‘worked’ as expected in some cases only, also in one CRAN package. (As long as it's not defunct, it at least works consistently as ‘format(paste(x, collapse = " "))’.)
The default method for generating from a discrete uniform distribution (used in ‘sample()’, for instance) has been changed. This addresses the fact, pointed out by Ottoboni and Stark, that the previous method made ‘sample()’ noticeably non-uniform on large populations. See PR#17494 for a discussion. The previous method can be requested using ‘RNGkind()’ or ‘RNGversion()’ if necessary for reproduction of old results. Thanks to Duncan Murdoch for contributing the patch and Gabe Becker for further assistance.
The output of ‘RNGkind()’ has been changed to also return the ‘kind’ used by ‘sample()’.
‘R_GetCurrentEnv()’ allows C code to retrieve the current environment.
‘match(x, tab)’ now works for long _character_ vectors ‘x’, thanks to PR#17552 by Andreas Kersting.
The S4 generic signature of ‘rowSums()’, ‘rowMeans()’, ‘colSums()’ and
‘colMeans()’ is restricted to ‘"x"’.
Add ‘update_PACKAGES()’ for incrementally updating a package repository index, instead of rebuilding the index from scratch. Thanks to Gabe Becker in PR#17544 for the patch, based on part of his ‘switchr’ package.
The S4 generic signature of ‘rowSums()’, ‘rowMeans()’, ‘colSums()’ and ‘colMeans()’ is restricted to ‘"x"’.
Make macro ‘F77_VISIBILITY’ has been removed and replaced by ‘F_VISIBILITY’.
Make macros ‘F77’, ‘FCPIFCPLAGS’ and ‘SHLIB_OPENMP_FCFLAGS’ have been removed and replaced by ‘FC’, ‘FPICFLAGS’ and ‘SHLIB_OPENMP_FFLAGS’ respectively. (Most ‘make’ programs will set ‘F77’ to the value of ‘FC’, which is set for package compilation. But portable code should not rely on this.)
‘R CMD config’ no longer knows about the unused settings ‘F77’ and ‘FCPIFCPLAGS’.
New ‘str2lang()’ and ‘str2expression()’ as streamlined versions of ‘parse(text=., keep.source=FALSE)’ allow to abstract typical call constructions, e.g., in ‘formula’ manipulations. (Somewhat experimental)
The S4 generic signature of ‘rowSums()’, ‘rowMeans()’, ‘colSums()’ and ‘colMeans()’ is restricted to ‘"x"’.
‘R CMD config’ no longer knows about the unused ‘F77’ and ‘FCPIFCPLAGS’.
New ‘hcl.colors()’ function to provide wide range of HCL-based colour palettes with much better perceptual properties than the existing RGB/HSV-based palettes like ‘rainbow()’.
Also a new ‘hcl.pals()’ function to list available palette names for ‘hcl.colors()’.
Contributed by Achim Zeileis.
The default colours for ‘image()’ and ‘filled.contour()’ are now based on ‘hcl.colors()’.
The palette-generating functions ‘rainbow()’, ‘gray.colors()’, etc. get a new ‘rev’ argument to facilitate reversing the order of colors.
Support for ‘make install-strip’ has been enhanced.
The make macro ‘F_VISIBILITY’ is now preferred for both fixed-form and free-form Fortran, for use in ‘src/Makevars’ and similar.
‘R CMD INSTALL’ gains a new option ‘--strip’ which (where supported) strips installed shared object(s): this can also be achieved by setting the environment variable ‘_R_SHLIB_STRIP_’ to a true value.
The new option ‘--strip-lib’ attempts stripping of static and shared libraries installed under ‘lib’.
These are most useful on platforms using GNU ‘binutils’ (such as Linux) and compiling with ‘-g’ flags.
There is more support for installing UTF-8-encoded packages in a strict Latin-1 locale (and probably for other Latin locales): non-ASCII comments in R code (and ‘NAMESPACE’ files) are worked around better.
Make macro ‘F77_VISIBILITY’ have been removed and replaced by ‘F_VISIBILITY’.
Make macros ‘F77’, ‘FCPIFCPLAGS’ and ‘SHLIB_OPENMP_FCFLAGS’ have been removed and replaced by ‘FC’, ‘FPICFLAGS’ and ‘SHLIB_OPENMP_FFLAGS’ respectively. [‘F77’ has been reverted until Apr 15.]
‘as.matrix.data.frame()’ now produces better strings from logicals, thanks to PR#17548 from Gabe Becker.
‘R CMD build’ now removes ‘src/*.mod’ files on all platforms.
When reading console input from ‘stdin’ with re-encoding (‘R --encoding=enc < input’) the code on a Unix-alike now ensures that each converted input line is terminated with a newline even if re-encoding fails.
The interpretation of source code with extension ‘.f’ is changing. Previously this denoted FORTRAN 77 code, but current compilers no longer have a FORTRAN 77 mode and interpret it as ‘fixed-form’ Fortran 90 (or later where supported) code. Extensions ‘.f90’ and ‘.f95’ continue to indicate ‘free-form’ Fortran code.
Legal FORTRAN 77 code is also legal fixed-form Fortran 9x; however this change legitimizes the use of later features, in particular to replace features marked ‘obsolescent’ in Fortran 90 and ‘deleted’ in Fortran 2018 which ‘gfortran’ 8.x and later warn about.
‘R_unif_index’ is now considered to be part of the C API.
Class unions are unloaded when their namespace is unloaded (PR#17531, adapted from a patch by Brodie Gaslam).
Placeholder.
Serialization format version 3 becomes the default for serialization and saving of the workspace (‘save()’, ‘serialize()’, ‘saveRDS()’, ‘compiler::cmpfile()’). Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0. Serialization format version 2 is still supported and can be selected by ‘version = 2’ in the save/serialization functions. The default can be changed back for the whole R session by setting environment variables ‘R_DEFAULT_SAVE_VERSION’ and ‘R_DEFAULT_SERIALIZE_VERSION’ to ‘2’. For maximal back-compatibility, files ‘vignette.rds’ and ‘partial.rdb’ generated by ‘R CMD build’ are in serialization format version 2, and resave by default produces files in serialization format version 2 (unless the original is already in format version 3).
The default method for generating from a discrete uniform distribution (used in ‘sample()’, for instance) has been changed. This addresses the fact, pointed out by Ottoboni and Stark, that the previous method made ‘sample()’ noticeably non-uniform on large populations. See PR#17494 for a discussion. The previous method can be requested using ‘RNGkind()’ or ‘RNGversion()’ if necessary for reproduction of old results. Thanks to Duncan Murdoch for contributing the patch and Gabe Becker for further assistance.
‘Sys.setFileTime()’ has been vectorized so arguments ‘path’ and ‘time’ of length greater than one are now supported.
‘axis()’ gets new option ‘gap.axis = NA’ for specifying a multiplication factor for the minimal “gap” (distance) between axis labels drawn. Its default is ‘1’ for labels _parallel_ to the axis, and ‘0.25’ for perpendicular ones.
Perpendicular labels no longer overlap, fixing bug PR#17384.
The default method of ‘plot()’ gains new arguments ‘xgap.axis = NA’ and ‘ygap.axis = NA’ to be passed to the x- and y- ‘axis(.., gap.axis=*)’ calls.
‘removeSource()’ now works not only for functions but also for some language objects.
‘as.call()’, ‘rep.int()’, ‘rep_len()’ and ‘nchar()’ dispatch internally.
‘is(object, class2)’ looks for ‘class2’ in the calling namespace after looking in the namespace of ‘class(object)’.
‘extendrange(.., f)’ with a length-2 ‘f’ now extends separately to the left and the right.
‘lengths()’ dispatches internally to S4 methods.
‘download.file()’ on Windows now uses ‘URLdecode()’ to determine the file extension, and uses binary transfer (‘mode = "wb"’) also for file extension ‘.rds’.
The help page for ‘download.file()’ now contains the same information on all platforms.
Setting ‘C’ locale for collation _via_ environment variables ‘LC_ALL’ and ‘LC_COLLATE’ and _via_ a call to ‘Sys.setlocale()’ now takes precedence over environment variable ‘R_ICU_LOCALE’.
There is a new function, ‘nullfile()’, to give the file name of the null system device (e.g., ‘/dev/null’) on the current platform.
There are two new options, ‘keep.parse.data’ and ‘keep.parse.data.pkgs’, which control whether parse data are included into sources when ‘keep.source’ or ‘keep.source.pkgs’ is ‘TRUE’. By default, ‘keep.parse.data.pkgs’ is now ‘FALSE’, which changes previous behavior and significantly reduces space and time overhead when sources are kept when installing packages.
In ‘rapply(x, ..)’, ‘x’ can also be “list-like” and of length >= 2^{31}.
‘trimws()’ gets new optional ‘whitespace’ argument, allowing more extensive definitions of “space”, such as including Unicode spaces (as wished in PR#17431).
‘weighted.mean()’ no longer coerces the weights to a double/numeric vector, since ‘sum()’ now handles integer overflow. This makes ‘weighted.mean()’ more polymorphic and endomorphic, but be aware that the results are no longer guaranteed to be a vector of type ‘double’.
When loading namespaces, S3 method registrations which overwrite previous registrations are now noted by default (using ‘packageStartupMessage()’).
‘compiler::cmpfile()’ gains a ‘version’ argument, for use when the output file should be saved in serialization format 2.
The axis labeling in the default method of ‘pairs()’ may now be toggled by new options ‘horOdd’ and ‘verOdd’.
(Not Windows nor macOS.) Package ‘tcltk’ now supports an environment variable ‘R_DONT_USE_TK’ which if set disables Tk initialization. This is intended for use to circumvent errors in loading the package, e.g. with recent Linux running under an address sanitizer.
The ‘numeric’ method of ‘all.equal()’ gets optional arguments ‘countEQ’ and ‘formatFUN’. If ‘countEQ’ is true, the mean error is more sensible when many entries are *eq*ual.
‘outer(x,y, FUN = "*")’ is more efficient using ‘tcrossprod(u,v)’ instead of ‘u %*% t(v)’.
‘vcov(<mlm>)’ is more efficient via new optional arguments in ‘summary.mlm()’.
The default method of ‘summary()’ gets an option to choose the _kind_ of ‘quantile()’s to use; wish of PR#17438.
Fitting multiple linear models _via_ ‘lm()’ does work with _matrix_ offsets, as suggested in PR#17407.
The new functions ‘mem.maxVSize()’ and ‘mem.maxMSize()’ allow the maximal size of the vector heap and the maximal number of nodes allowed in the current ‘R’ process to be queried and set.
‘news()’ gains support for ‘NEWS.md’ files.
An effort has been started to have our reference manuals, i.e., all help pages. show platform-independent information (rather than Windows or Unix-alike specifics visible only on that platform). Consequently, the Windows version of ‘X11()’ / ‘x11()’ got identical formal arguments to the Unix one.
‘sessionInfo()$running’ has been factored out in a new variable ‘osVersion’.
‘slice.index()’ now also works for multi-dimensional margins.
‘untar()’ used with an external ‘tar’ command assumes this supports decompression including ‘xz’ and automagically detecting the compression type. This has been true of all mainstream implementations since 2009 (for GNU ‘tar’, since version 1.22): older implementations are still supported _via_ the new argument ‘support_old_tars’ whose default is controlled by environment variable ‘R_SUPPORT_OLD_TARS’. (It looks like NetBSD and OpenBSD have ‘older’ ‘tar’ commands for this purpose.)
The new function ‘asplit()’ allow splitting an array or matrix by its margins.
New functions ‘errorCondition()’ and ‘warningCondition()’ provide a convenient way to create structured error and warning objects.
‘.Deprecated()’ now signals a warning of class ‘"deprecatedWarning"’, and ‘.Defunct()’ now signals an error of class ‘"defunctError"’.
Many ‘package not found’ errors are now signaled as errors of class ‘"packageNotFoundError"’.
As an experimental feature, when ‘loadNamespace()’ fails because the requested package is not available the error is initially signaled with a ‘retry_loadNamespace’ restart available. This allows a calling handler to try to install the package and continue.
‘S3method()’ directives in ‘NAMESPACE’ can now also be used to perform _delayed_ S3 method registration.
Experimentally, setting environment variable ‘_R_CHECK_LENGTH_1_LOGIC2_’ will lead to warnings (or errors if the variable is set to a ‘true’ value) when ‘&&’ or ‘||’ encounter and use arguments of length more than one.
Added ‘"lines"’ and ‘"chars"’ coordinate systems to ‘grconvertX()’ and ‘grconvertY()’.
‘getOption()’ is more efficient notably for the rare case when called with two arguments, from several contributors in PR#17394.
In ‘.col(dim)’ and ‘.row(dim)’, ‘dim’ now may also be an integer-valued ‘"double"’.
‘sQuote()’ and ‘dQuote()’ get an explicit ‘q’ argument with obvious default instead of using ‘getOption("fancyQuotes")’ implicitly and unconditionally.
‘unzip()’ can list archives with comments and with spaces in file names even using an external ‘unzip’ command.
Command line completion has a new setting ‘rc.settings(dots = FALSE)’ to remove ‘...’ from the list of possible function arguments.
‘library()’ no longer checks packages with compiled code match ‘R.version$platform’. ‘loadNamespace()’ never has, and increasingly the ‘canonical name’ does not reflect the important characteristics of compiled code.
The primitive functions ‘drop()’ and ‘unclass()’ now avoid duplicating their data for atomic vectors that are large enough, by returning ‘ALTREP’ wrapper objects with adjusted attributes. R-level assignments to change attributes will also use wrapper objects to avoid duplicating data for larger atomic vectors. R functions like ‘structure()’ and ‘unname()’ will therefore not duplicate data in these settings. Generic vectors as produced by ‘list()’ are not yet covered by this optimization but may be in due course.
In ‘formals()’, ‘envir’ becomes an optional argument instead of being hardwired.
Instead of signalling an error for an invalid S4 object ‘x’, ‘str(x)’ now gives a warning and subsequently still shows most parts of ‘x’, e.g., when slots are missing.
‘gamma(x)’ and ‘lgamma(x)’ no longer warn when correctly returning ‘Inf’ or underflowing to zero. This helps maximum likelihood and similar computations.
‘convertColor()’ is now vectorized, so a lot faster for converting many colours at once. The new argument ‘vectorized’ to ‘colorConverter()’ ensures that non-vectorized colour converters still work. (Thanks to Brodie Gaslam.)
‘download.file()’ and ‘url()’ get new argument ‘headers’ for custom HTTP headers, e.g., allowing to perform basic http authentication, thanks to a patch contributed by Gábor Csárdi.
File-based connection functions ‘file()’, ‘gzfile()’, ‘bzfile()’ and ‘xzfile()’ now signal an error when used on a directory.
For ‘approx()’, ‘splinefun()’ _etc_, a new setting ‘ties = c("ordered", <fun>)’ allows skipping the sorting and still treat ties.
‘format(x)’ gives a more user friendly error message in the case where no method is defined. A minimal method is provided in ‘format.default(x)’ when ‘isS4(x)’ is true.
‘which(x)’ now also works when ‘x’ is a long vector, thanks to Suharto Anggono's PR#17201. *NB*: this may return a double result, breaking the previous guarantee of an integer result.
‘seq.default()’ is more careful to return an ‘integer’ (as opposed to ‘double’) result when its arguments are large and/or classed objects; see comment #9 of Suharto Anggono's PR#17497.
The ‘plot()’ method for ‘lm’ and ‘glm’ fits, ‘plot.lm()’, gains a new option ‘iter.smooth’ with a default of ‘0’ for binomial fits, no longer down-weighting when smoothing the residuals.
‘zip()’ passes its list of files _via_ standard input to the external command when too long for the command line (on some platforms).
‘data()’ gains an ‘overwrite’ argument.
‘t.test()’ now also returns the standard error (in list component ‘stderr’).
‘model.matrix(*, contrasts.arg = CC)’ now warns about invalid ‘contrasts.arg’s.
Performance of ‘substr()’ and ‘substring()’ has been improved.
‘stopifnot()’ has been simplified thanks to Suharto Anggono's proposals to become considerably faster for cheap expressions.
The default ‘user agent’ has been changed when accessing ‘http://’ and ‘https://’ sites using ‘libcurl’. (A site was found which caused ‘libcurl’ to infinite-loop with the previous default.)
‘sessionInfo()’ now also contains ‘RNGkind()’ and prints it when it differs from the default; based on a proposal and patch by Gabe Becker in PR#17535. Also, ‘RNGversion(getRversion())’ works directly.
‘library()’ and ‘require()’ now allow more control over handling search path conflicts when packages are attached. The policy is controlled by the new ‘conflicts.policy’ option.
‘barplot()’ gets a formula method, thanks to a patch proposal by Arni Magnusson in PR#17521.
‘pmax()’ and ‘pmin(x)’ now also work for long vectors, thanks to Suharto Anggono's PR#17533.
‘bxp()’ now warns when omitting duplicated arguments.
New ‘hcl.colors()’ function to provide wide range of HCL-based colour palettes with much better perceptual properties than existing RGB/HSV-based palettes like ‘rainbow()’.
Also new ‘hcl.pals()’ function to list available palette names for ‘hcl.colors()’.
Contributed by Achim Zeileis.
Default colours for ‘image()’ and ‘filled.contour()’ are now based on ‘hcl.colors()’.
Palette-generating functions ‘rainbow()’, ‘gray.colors()’, etc. get new ‘rev’ argument to facilitate reversing the order of colors.
The options selected for the C++ compiler default to the C++11 standard if supported, otherwise to the C++98 standard.
Visibility macros such as ‘C_VISIBILITY’ can now be user-set (including to empty), e.g. in ‘config.site’.
Macro ‘FCLIBS’, which has sometimes been needed on Solaris, has been renamed to ‘FCLIBS_XTRA’.
Macro ‘F77’ is always set to the value of ‘FC’, so the latter should be set to user-select the Fortran compiler for both fixed-form and free-form Fortran. In particular, ‘gfortran’ is now the first choice for ‘F77’, not ‘f95’.
Macros ‘FFLAGS’ and ‘FCFLAGS’ remain distinct to allow for a compiler which needs a flag to select free- or fixed-form Fortran (most use the source-file extension to choose: ‘.f’ is fixed-form and ‘.f90’ and ‘.f95’ are free-form).
If only one of them is set, its value is used for both.
The special-casing of ‘CFLAGS’, ‘CXXFLAGS’ and ‘FFLAGS’ for Intel compilers on Linux has been removed: we do not have recent experience but the generic defaults now chosen are the same as those previously special-cased for ‘x86_64’.
If necessary, override the defaults on the ‘configure’ command line or in file ‘config.site’.
Long-untested ‘configure’ support for HP-UX and very old versions of Linux has been removed.
‘configure --with-blas’ (without specifying a value) includes OpenBLAS in its search (before ATLAS and a generic BLAS). This follows recent versions of the ‘ax_blas’ autoconf macro.
The ‘configure’ macro ‘MAKEINFO’ has been updated to ‘TEXI2ANY’.
Support for ‘make install’ has been enhanced.
Source package installation is by default ‘staged’: the package is installed into a temporary location under the final library directory and moved into place once the installation is complete. The benefit is that partially-installed packages are hidden from other R sessions.
The overall default is set by environment variable ‘R_INSTALL_STAGED’. ‘R CMD INSTALL’ has new options ‘--staged-install’ and ‘--no-staged-install’, and packages can use the ‘StagedInstall’ field in their ‘DESCRIPTION’ file to opt out. (That opt-out is a temporary measure which may be withdrawn in future.)
Staged installation requires either ‘--pkglock’ or ‘--lock’, one of which is used by default.
The interpretation of source code with extension ‘.f’ is changing. Previously this denoted FORTRAN 77 code, but current compilers no longer have a FORTRAN 77 mode and interpret it as ‘fixed-form’ Fortran 90 (or later where supported) code. Extensions ‘.f90’ and ‘.f95’ continue to indicate ‘free-form’ Fortran code.
Legal FORTRAN 77 code is also legal fixed-form Fortran 9x; however this change legitimizes the use of later features, in particular to replace features marked ‘obsolescent’ in Fortran 95 which ‘gfortran’ 8.x warns about.
Packages containing files in the ‘src’ directory with extensions ‘.f90’ or ‘.f95’ are now linked using the C or C++ compiler rather than the Fortran 9x compiler. This is consistent with fixed-form Fortran code and allows mixing of C++ and free-form Fortran on most platforms.
Consequentially, a package which includes free-form Fortran 9x code which uses OpenMP should include ‘SHLIB_OPENMP_CFLAGS’ (or the ‘CXXFLAGS’ version if they also include C++ code) in ‘PKG_LIBS’ rather than ‘SHLIB_OPENMP_FCFLAGS’ - fortunately on almost all current platforms they are the same flag.
Macro ‘PKG_FFLAGS’ will be used for the compilation of both fixed-form and free-form Fortran code unless ‘PKG_FCFLAGS’ is also set (in ‘src/Makevars’ or ‘src/Makevars.win’).
The make macro ‘F_VISIBILITY’ is now preferred for both fixed-form and free-form Fortran.
‘R CMD INSTALL’ gains a new option ‘--strip’ which strips installed shared object(s): this can also be achieved by setting the environment variable ‘_R_SHLIB_STRIP_’ to a true value.
The new option ‘--strip-lib’ attempts stripping of static and shared libraries installed under ‘lib’.
These are most useful on platforms using GNU ‘binutils’ (such as Linux) and compiling with ‘-g’ flags.
There is more support for installing UTF-8-encoded packages in a strict Latin-1 locale (and probably for other Latin locales): non-ASCII comments in R code are worked around better.
‘R CMD check’ now optionally checks makefiles for correct and portable use of the ‘SHLIB_OPENMP_*FLAGS’ macros.
‘R CMD check’ now evaluates ‘\Sexpr{}’ expressions (including those in macros) before checking the contents of ‘Rd’ files and so detects issues both in evaluating the expressions and in the expanded contents.
‘R CMD check’ now lists missing packages separated by commas and with regular quotes such as to be useful as argument in calling ‘install.packages(c(..))’; from a suggestion by Marcel Ramos.
‘tools::Rd2latex()’ now uses UTF-8 as its default output encoding.
‘R CMD check’ now checks line endings of files with extension ‘.hpp’ and those under ‘inst/include’. The check now includes that a non-empty file is terminated with a newline.
‘R CMD build’ will correct line endings in such files.
‘R CMD check’ now tries re-building all vignettes rather than stopping at the first error: whilst doing so it adds ‘bookmarks’ to the log. By default (see the ‘R Internals’ manual) it re-builds each vignette in a separate process.
It now checks for duplicated vignette titles (also known as ‘index entries’): they are used as hyperlinks on CRAN package pages and so do need to be unique.
‘R CMD check’ has more comprehensive checks on the ‘data’ directory and the functioning of ‘data()’ in a package.
‘R CMD check’ now checks ‘autoconf’-generated ‘configure’ files have their corresponding source files, including optionally attempting to regenerate them on platforms with ‘autoreconf’.
‘R CMD build’ has a new option ‘--compression’ to select the compression used for the tarball.
New pointer protection C functions ‘R_PreserveInMSet’ and ‘R_ReleaseFromMSet’ have been introduced to replace ‘UNPROTECT_PTR’, which is not safe to mix with ‘UNPROTECT’ (and with ‘PROTECT_WITH_INDEX’). Intended for use in parsers only.
‘NAMEDMAX’ has been raised to 7 to allow further protection of intermediate results from (usually ill-advised) assignments in arguments to ‘BUILTIN’ functions. Properly written package code should not be affected.
Argument ‘compressed’ of ‘untar()’ is deprecated - it is only used for external ‘tar’ commands which increasingly for extraction auto-detect compression and ignore their ‘zjJ’ flags.
‘var(f)’ and hence ‘sd(f)’ now give an error for ‘factor’ arguments; they gave a deprecation warning since R 3.2.3, PR#16564.
Package ‘tools’' ‘vignetteDepends()’ has been deprecated (it called a function deprecated since Feb 2016), being partly replaced by newly exported ‘vignetteInfo()’.
The ‘f77_f2c’ script has been removed: it no longer sufficed to compile the ‘.f’ files in R.
The deprecated legacy support of ‘make’ macros such as ‘CXX1X’ has been removed: use the ‘CXX11’ forms instead.
Make macro ‘F77_VISIBILITY’ is deprecated in favour of ‘F_VISIBILITY’.
Make macros ‘F77’, ‘FCPIFCPLAGS’ and ‘SHLIB_OPENMP_FCFLAGS’ are deprecated in favour of ‘FC’, ‘FPICFLAGS’ and ‘SHLIB_OPENMP_FFLAGS’ respectively.
‘$.data.frame’ had become an expensive version of the default method, so has been removed. (Thanks to Radford Neal for picking this up and to Duncan Murdoch for providing a patch.)
‘replayPlot(r)’ now also works in the same R session when ‘r’ has been “reproduced” from serialization, typically after saving to and reading from an RDS file.
‘substr()’ and ‘substring()’ now signal an error when the input is invalid UTF-8.
‘file.copy()’ now works also when its argument ‘to’ is of length greater than one.
‘mantelhaen.test()’ no longer suffers from integer overflow in largish cases, thanks to Ben Bolker's PR#17383.
Calling ‘setGeneric("foo")’ in a package no longer fails when the enclosing environment of the implicit generic ‘foo()’ is ‘.GlobalEnv’.
‘untar(file("<some>.tar.gz"), *)’ now gives a better error message, suggesting to use ‘gzfile()’ instead.
Method dispatch uses more relevant environments when looking up class definitions.
The documentation for ‘identify()’ incorrectly claimed that the indices of identified points were returned in the order that the points were selected. ‘identify()’ now has a new argument ‘order’ to allow the return value to include the order in which points were identified; the documentation has been updated. Reported by Richard Rowe and Samuel Granjeaud.
‘order(...., decreasing=c(TRUE, FALSE))’ could fail in some cases. Reported from StackOverflow via Karl Nordström.
User macros in Rd files now accept empty and multi-line arguments.
Changes in ‘print.*()’, thanks to Lionel Henry's patches in PR#17398:
• Printing lists, pairlists or attributes containing calls with S3 class no longer evaluate those.
• Printing S4 objects within lists and pairlists dispatches with ‘show()’ rather than ‘print()’, as with auto-printing.
• The indexing tags (names or ‘[[<n>]]’) of recursive data structures are now printed correctly in complex cases.
• Arguments supplied to ‘print()’ are now properly forwarded to methods when printing lists, pairlists or attributes containing S3 objects.
• The print parameters are now preserved when printing S3 objects or deparsing symbols and calls. Previously, printing lists containing S3 objects or expressions would reset these parameters.
• Printing lists, pairlists or attributes containing functions now uses ‘srcref’ attributes if present.
Calling ‘install.packages()’ with a length zero ‘pkgs’ argument now is a no-op (PR#17422).
‘unlist(x)’ now returns a correct ‘factor’ when ‘x’ is a nested list with factor leaves, fixing PR#12572 and PR#17419.
The documentation ‘help(family)’ gives more details about the ‘aic’ component, thanks to Ben Bolker's prompting.
The documentation for ‘attributes’ and ‘`attributes<-`’ now gives ‘x’ as name of the first and main argument which the implementation has been requiring, fixing PR#17434. For consistency, the first argument name is also changed from ‘obj’ to ‘x’ for ‘`mostattributes<-`’.
‘strwidth()’ now uses ‘par("font")’ as default font face (PR#17352).
‘plot(<table>, log="x")’ no longer warns about ‘log’.
The ‘print()’ method for ‘"htest"’ objects now formats the test statistic and parameter directly and hence no longer rounds to units _before_ the decimal point. Consequently, printing of ‘t.test()’ results with a small number of digits now shows non-large ‘df’'s to the full precision (PR#17444).
‘kruskal.test()’ and ‘fligner.test()’ no longer erroneously insist on numeric ‘g’ group arguments (PR#16719).
Printing a news db via the browser now does a much better job (PR#17433).
‘print.aov()’ missed column names in the multivariate case due to misspelling (reported by Chris Andrews).
‘axis()’ now creates valid ‘at’ locations also for small subnormal number ranges in log scale plots.
‘format.POSIXlt()’ now also recycles the ‘zone’ and ‘gmtoff’ list components to full length when needed, and its internal C code detects ‘have_zone’ in more cases. In some cases, this changes its output to become compatible with ‘format.POSIXct()’.
On Windows, ‘detectCores()’ in package ‘parallel’ now detects processors in all processor groups, not just the group R is running in (impacts particularly systems with more than 64 logical processors). Reported by Arunkumar Srinivasan.
On Windows, ‘socketSelect()’ would hang with more than 64 sockets, and hence ‘parallel::clusterApplyLB()’ would hang with more than 64 workers. Reported by Arunkumar Srinivasan.
‘as(1L, "double")’ now does coerce (PR#17457).
‘lm.influence()’, ‘influence.measures()’, ‘rstudent()’ etc now work (more) correctly for multivariate models (‘"mlm"’), thanks to (anonymous) stackoverflow remarks.
‘sample.int(2.9, *, replace=TRUE)’ again behaves as documented and as in R < 3.0.0, namely identically to ‘sample.int(2, ..)’.
Fixes to ‘convertColor()’ for chromatic adaptation; thanks to Brodie Gaslam PR#17473.
Using ‘\Sexpr[stage=install]{..}’ to create an ‘Rd’ section no longer gives a warning in ‘R CMD check’; problem originally posted by Gábor Csárdi, then reported as PR#17479 with a partial patch by Duncan Murdoch.
Parse data now include a special node for equal assignment.
‘split.default()’ no longer relies on ‘[[<-()’, so it behaves as expected when splitting an object by a factor with the empty string as one of its levels. Thanks to Brad Friedman for the report.
Line numbers in messages about ‘.Rd’ files are now more reliable, thanks to a patch from Duncan Murdoch.
In the ‘numeric’ method for ‘all.equal()’, a numeric ‘scale’ argument is now checked to be positive and allowed to be of length > 1. (The latter worked originally and with a warning in recent years).
Deferred string conversions now record the ‘OutDec’ option setting when not equal to the default. Reported by Michael Sannella.
When ‘y’ is numeric and ‘f’ a ‘factor’, ‘plot(y ~ f)’ nicely uses "y" and "f" as y- and x-labels. The more direct ‘boxplot(y ~ f)’ now does too. The new argument ‘ann = FALSE’ may be used to suppress these.
Subassignment to no/empty rows of a data frame is more consistent and typically a no-op in all cases instead of sometimes an error; part of Emil Bode's PR#17483.
Calls like ‘formatC(*, zero.print = "< 0.001")’ no longer give an error and are further improved via new optional argument ‘replace.zero’. Reported by David Hugh-Jones.
‘methods::formalArgs("<fn>")’ now finds the same function as ‘formals("<fn>")’, fixing Emil Bode's PR#17499.
The ‘methods’ package better handles duplicated class names across packages.
The default method of ‘seq()’ now avoids integer overflow, thanks to the report and "cumsum" patch of Suharto Anggono's PR#17497.
‘sub()’ no longer loses encodings for non-ASCII replacements (PR#17509).
Fix for rotated raster image on X11 device. (Partial fix for PR#17148; thanks to Mikko Korpela).
‘formula(model.frame(frml, ..))’ now returns ‘frml’ in all cases, thanks to Bill Dunlap. The previous behavior is available as ‘DF2formula(<model.frame>)’.
‘ar.ols()’ also returns scalar ‘var.pred’ in univariate case (PR#17517).
‘normalizePath()’ now treats ‘NA’ path as non-existent and normalizes it to ‘NA’. ‘file.access()’ treats ‘NA’ file name as non-existent. ‘file.edit()’ and connection functions such as ‘file()’ now treat ‘NA’ file names as errors.
The internal ‘regularize.values()’ auxiliary of ‘approx()’, ‘splinefun()’ etc now warns again when there are ties and the caller did not specify ‘ties’. Further, it no longer duplicates ‘x’ and ‘y’ unnecessarily when ‘x’ is already sorted (PR#17515).
‘strtoi("", base)’ now gives ‘NA’ on all platforms, following its documentation. Reported by Michael Chirico.
In the definition of an S4 class, prototype elements are checked against the slots of the class, with giving a prototype for an undefined slot now being an error. (Reported by Bill Dunlap.)
From ‘setClassUnion()’, if environment variable ‘_R_METHODS_SHOW_CHECKSUBCLASSES’ is set to true, the internal ‘.checkSubclasses()’ utility prints debugging info to see where it is used.
‘max.col(m)’ with an ‘m’ of zero columns now returns integer ‘NA’ (instead of ‘1’).
‘axTicks()’ no longer returns small “almost zero” numbers (in exponential format) instead of zero, fixing Ilario Gelmetti's PR#17534.
‘isSymmetric(matrix(0, dimnames=list("A","b")))’ is ‘FALSE’ again, as always documented.
The ‘cairo_pdf’ graphics device (and other Cairo-based devices) now clip correctly to the right and bottom border.
There was an off-by-one-pixel bug, reported by Lee Kelvin.
‘as.roman(3) <= 2:4’ and all other comparisons now work, as do group ‘"Summary"’ function calls such as ‘max(as.roman(sample(20)))’ and ‘as.roman(NA)’. (Partly reported by Bill Dunlap in PR#17542.)
‘reformulate("x", response = "sin(y)")’ no longer produces extra back quotes, PR#17359, and gains new optional argument ‘env’.
When Reading console input from ‘stdin’ with re-encoding (‘R --encoding=enc < input’) the code on a Unix-alike now ensures that each converted input line is terminated with a newline even if re-encoding fails.
Class unions are unloaded when their namespace is unloaded (PR#17531, adapted from a patch by Brodie Gasla).
‘selectMethod()’ is robust to ANY-truncation of method signatures (thanks to Herve Pages for the report).
There is more support for installing UTF-8-encoded packages in a strict Latin-1 locale (and probably for other Latin locales): non-ASCII comments in R code are worked around better.
‘reformulate("x", response = "sin(y)")’ no longer produces extra back quotes, PR#17359, and gains new optional argument ‘env’.
When Reading console input from ‘stdin’ with re-encoding (‘R --encoding=enc < input’) the code on a Unix-alike now ensures that each converted input line is terminated with a newline even if re-encoding fails.
‘bxp()’ now warns when omitting duplicated arguments.
New ‘hcl.colors()’ function to provide wide range of HCL-based colour palettes with much better perceptual properties than existing RGB/HSV-based palettes like ‘rainbow()’.
Also new ‘hcl.pals()’ function to list available palette names for ‘hcl.colors()’.
Contributed by Achim Zeileis.
Default colours for ‘image()’ and ‘filled.contour()’ are now based on ‘hcl.colors()’.
Palette-generating functions ‘rainbow()’, ‘gray.colors()’, etc. get new ‘rev’ argument to facilitate reversing the order of colors.
Support for ‘make install’ has been enhanced.
‘R CMD INSTALL’ gains a new flag ‘--strip’ which strips installed shared object(s): this can also be achieved by setting the environment variable ‘_R_SHLIB_STRIP_’ to a true value.
This is most useful on platforms using GNU ‘binutils’ (such as Linux) and compiling with ‘-g’ flags: it has negligible effect on macOS.
‘pmax()’ and ‘pmin(x)’ now also work for long vectors, thanks to Suharto Anggono's PR#17533.
‘as.roman(3) <= 2:4’ and all other comparisons now work, as do group ‘"Summary"’ function calls such as ‘max(as.roman(sample(20)))’ and ‘as.roman(NA)’. (Partly reported by Bill Dunlap in PR#17542.)
‘R CMD build’ has a new option ‘--compression’ to select the compression used for the tarball.
‘R CMD check’ now checks ‘autoconf’-generated ‘configure’ files have their corresponding source files, including optionally attempting to regenerate them on platforms with ‘autoreconf’.
‘barplot()’ gets a formula method, thanks to a patch proposal by Arni Magnusson in PR#17521.
‘sum(x)’ and ‘sum(x1, x2, .., x<N>)’ with many or long logical or integer vectors no longer overflows (and returns ‘NA’ with a warning), but returns ‘double’ numbers in such cases.
On Unix-like platforms which support the ‘getline’ C library function, ‘system(*, intern = TRUE)’ no longer truncates (output) lines longer than 8192 characters, thanks to Karl Millar. (PR#16544)
New string utilities ‘startsWith(x, prefix)’ and ‘endsWith(x, suffix)’. Also provide speedups for some ‘grepl("^...", *)’ uses (related to proposals in PR#16490).
‘format.POSIXlt()’ behaved incorrectly in R 3.2.4. E.g. the output of ‘format(as.POSIXlt(paste0(1940:2000, "-01-01"), tz = "CET"), usetz = TRUE)’ ended in two ‘"CEST"’ time formats.
‘as.roman(3) <= 2:4’ and all other comparisons now work, as do group ‘"Summary"’ function calls such as ‘max(as.roman(sample(20)))’ and ‘as.roman(NA)’. (Parly reported by Bill Dunlap in PR#17542.)
‘library()’ and ‘require()’ now allow more control over handling search path conflicts when packages are attached. The policy is controlled by the new ‘conflicts.policy’ option.
‘sessionInfo()’ now also contains ‘RNGkind()’ and prints it when it differs from the default; based on a proposal and patch by Gabe Becker in PR#17535. Also, ‘RNGversion(getRversion())’ works directly.
Source package installation is by default ‘staged’: the package is installed into a temporary location under the final library directory and moved into place once the installation is complete. The benefit is that partially-installed packages are hidden from other R sessions.
The overall default is set by environment variable ‘R_INSTALL_STAGED’. ‘R CMD INSTALL’ has new options ‘--staged-install’ and ‘--no-staged-install’, and packages can use the ‘StagedInstall’ field in their ‘DESCRIPTION’ file to opt out. (That opt-out is a temporary measure which may be withdrawn in future.)
Staged installation requires either ‘--pkglock’ or ‘--lock’, one of which is used by default.
The ‘cairo_pdf’ graphics device (and other Cairo-based devices) now clip correctly to the right and bottom border.
There was an off-by-one-pixel bug, reported by Lee Kelvin.
‘isSymmetric(matrix(0, dimnames=list("A","b")))’ is ‘FALSE’ again, as always documented.