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A general description is here.
The included version of LAPACK has been updated to 3.4.2.
‘is.unsorted()’ now works for ‘raw’ vectors as well, and
‘is.unsorted(NA)’ is false.
‘is.unsorted()’ now also works for ‘raw’ vectors
‘abbreviate()’ handles without warning non-ASCII input strings which require no abbreviation.
‘is.unsorted(NA)’ is false as documented (rather than ‘NA’).
The cairo-based versions of ‘X11()’ now work with current versions of cairographics (e.g. 1.12.10). (PR#15168)
A workon average for earlier versions of R is to use ‘X11.options(type = "nbcairo")’.
On Windows, work on average an event-timing problem when the RGui console was closed from the ‘X’ control and the closure cancelled. (This would on some 64-bit systems crash R, typically those with a slow GPU relative to the CPU.)
Documentation for ‘setClass’ and ‘representation’ still suggested the deprecated argument ‘representation=’. (PR#15312)
‘R CMD config’ failed in an installed build of R 3.0.1 (only) when a sub-architecture was used. (Reported by Berwin Turlach.)
On Windows, the installer modified the ‘etc/Rconsole’ and ‘etc/Rprofile.site’ files even when default options were chosen. (Reported by Tal Galili.)
The ‘`regmatches<-`’ replacement function mishandled results coming from ‘regexpr’. (PR#15311)
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files has been removed: such sections are now ignored (with a warning).
The parser now enforces C99 syntax for floating point hexadecimal constants (e.g. ‘0x1.1p0’), rather than returning unintended values for malformed constants. (PR#15234)
The ‘`regmatches<-`’ assignment function mishandled results coming from ‘regexpr’. (PR#15311)
The markup for many messages has been changed to make them easier to translate, incorporating suggestions from Łukasz Daniel.
Added Polish translations by Łukasz Daniel.
The parser now enforces formatting of floating point hexadecimal constants (e.g. ‘0x1.1p0’), rather than returning unintended values. (PR#15234)
On Windows, ‘file.info()’ failed on root directories unless the path was terminated with an explicit ‘"."’. (PR#15302)
The markup for many messages has been changed to make them easier to translate, incorporating suggestions from ?ukasz Daniel.
Added Polish translations by ?ukasz Daniel.
‘chooseCRANmirror()’ and ‘chooseBioCmirror()’ gain an ‘ind’ argument (like ‘setRepositories()’).
‘mcparallel’ has a new argument ‘mc.interactive’ which can modify the interactive flag in the child process. The new default is ‘FALSE’ which makes child processes non-interactive by default (this prevents lock-ups due to children waiting for interactive input).
‘scan()’ now warns when end-of-file occurs within a quoted string.
‘count.fields()’ is now consistent with ‘scan()’ in its handling of newlines in quoted strings. Instead of triggering an error, this results in the current line receiving ‘NA’ as the field count, with the next line getting the total count of the two lines.
The default method of ‘image()’ will plot axes of the class of ‘xlim’ and ‘ylim’ (and hence of ‘x’ and ‘y’ if there is a suitable ‘range()’ method). Based on a suggestion of Michael Sumner.
‘load()’ now has a ‘verbose’ argument for debugging support, to print the names of objects just before loading them.
When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning.
‘pairs()’ gains a ‘line.main’ option for title placement.
The remaining instances in which serialization to a raw vector was limited to 2GB have been unlimited on a 64-bit platform, and in most cases serialization to a vector of more than 1GB will be substantially faster.
‘R CMD config’ now make use of personal ‘Makevars’ files under ‘~/.R’ and a site file ‘Makevars.site’, in the same way as ‘R CMD SHLIB’ and ‘R CMD INSTALL’. This makes the utility more useful in package ‘configure’ scripts.
On Windows finding the personal files may require the environment variable ‘HOME’ set.
The old behaviour can be obtained with the new options ‘--no-user-files’ and ‘--no-site-files’.
Alternatives to the site and user customization files ‘Makevars.site’ and ‘~/.R/Makevars’ can be specified _via_ the environment variables ‘R_MAKEVARS_SITE’ and ‘R_MAKEVARS_USER’ respectively. These can be used to suppress the use of the default files by setting an empty value (where possible) or a non-existent path.
‘sys.source()’ did not report error locations when ‘keep.source = TRUE’.
‘as.POSIXct.numeric’ was coercing ‘origin’ using the ‘tz’ argument and not ‘"GMT"’ as documented (PR#14973).
‘str(d)’ no longer gives an error when ‘names(d)’ contain illegal multibyte strings (PR#15247).
Profiling of built-in functions with ‘line.profiling= TRUE’ did not record the line from which they were called.
‘citation(pkg)’ dropped the header and footer specified in the ‘CITATION’ file (PR#15257).
Quotes were handled differently when reading the first line and reading the rest, so ‘read.table()’ misread some files that contained quote characters (PR#15245).
‘cat()’ with ‘sep’ a character vector of length greater than one and more than one argument was using separators inconsistently (PR#15261).
On Windows in R 3.0.0, ‘savePlot()’ failed because of an incorrect check on the argument count.
‘unzip(list = TRUE)’ returned ‘Names’ as a factor and not a character vector (as documented) for the internal method. (Noticed by Sean O'Riordain.)
‘contourLines()’ now checks more comprehensively for conformance of its ‘x’, ‘y’ and ‘z’ arguments (it was used incorrectly in package ‘R2G2’).
Saved graphics display lists are R version-specific. Attempting to load workspaces containing them (or some other version-specific objects) aborted the load in R 3.0.0 and earlier; now it does a partial load and generates a warning instead.
In R 3.0.0, ‘identify()’ and ‘locator()’ did not record information correctly, so replaying a graph (e.g. by copying it to another device) would fail. (PR#15271)
Calling ‘file.copy()’ or ‘dirname()’ with the invalid input ‘""’ (which was being used in packages, despite not being a file path) could have caused a segfault.
‘dirname("")’ is now ‘""’ rather than ‘"."’ (unless it segfaulted).
‘supsmu()’ could read/write outside its input vectors for very short inputs (seen in package ‘rms’ for ‘n = 4’).
‘as.dendrogram()’'s ‘hclust’ method uses less memory and hence gets considerably faster for large (n ~ 1000) clusterings, thanks to Daniel Müllner. (PR#15174)
The return value when all workers failed from ‘parallel::mclapply(mc.presechedule = TRUE)’ was a list of strings and not of error objects. (Spotted by Karl Forner and Bernd Bischl.)
In R 3.0.0, when ‘help()’ found multiple pages with the same alias, the HTML display of all the selections was not produced. (PR#15282)
‘splinefun(method="monoH.FC")’ now produces a function with first argument named ‘x’ and allows ‘deriv=3’, as documented. (PR#15273)
‘summaryRprof()’ would only read the first ‘chunksize’ lines of an ‘Rprof’ file produced with ‘line.profiling=TRUE’. By default, this is the first 100 seconds. (PR#15288)
‘lsfit()’ produced an incorrect error message when argument ‘x’ had more columns than rows or ‘x’ had a different number of rows than ‘y’. (Spotted by Renaud Gaujoux.)
Binary operations on equal length vectors copied the class name from the second operand when the first had no class name, but did not set the object bit. (PR#15299)
‘write.table()’ did not check that factors were constructed correctly, and so caused a segment fault when writing bad ones. (PR#15300)
The internal HTTP server no longer chokes on POST requests without body. It will also pass-through other request types for custom handlers (with the method stored in Request-Method header) instead of failing.
‘help.request()’ could not determine the current version of R on CRAN. (PR#15241)
The internal HTTP server no longer chokes on POST requests without body. It will also pass-through other request types for custom handlers (with the method stored in Request-Method header) instad of failing.
‘R CMD check --as-cran’ checks the line widths in usage and examples sections of the package Rd files.
The remaining instances in which serialization to a raw vector was limited to 2GB have been unlimited on a 64-bit platform, and in most cases serialization to a vector of more than 1GB will be substantially faster.
‘pairs()’ gains a ‘line.main’ option for title placement.
‘write.table()’ did not check that factors were constructed correctly, and so caused a segment fault when writing bad ones. (PR#15300)
Binary operations on equal length vectors copied the class name from the second operand when the first had no class name, but did not set the object bit. (PR#15299)
‘lsfit()’ produced an incorrect error message when argument ‘x’ had more columns than rows or ‘x’ had a different number of rows than ‘y’. (Spotted by Renaud Gaujoux.)
‘is.unsorted()’ now works for ‘raw’ vectors as well, and ‘is.unsorted(NA)’ is false.
‘load()’ now has a ‘verbose’ argument for debugging support, to print
the names of objects just before loading them.
When loading a serialized object encounters a reference to a namespace
which cannot be loaded, this is replaced by a reference to the global
environment, with a warning.
New function ‘anyNA()’, a fast version of ‘any(is.na(.))’, _where neither ‘is.na()’ nor ‘any()’ has a relevant method_, based on a proposal by Tim Hesterberg. (Wish of PR#15239.)
‘arrayInd(*, useNames = TRUE)’ and, analogously, ‘which(*, arr.ind = TRUE)’ now make use of ‘names(.dimnames)’ when available.
‘load()’ now has a ‘verbose’ argument for debugging support, to print the names of objects just before loading them.
When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning.
When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning.
New ‘anyNA()’ is a fast version of ‘any(is.na(.))’, based on a proposal by Tim Hesterberg. (Wish of PR#15239).
‘splinefun(method="monoH.FC")’ now produces a function with first argument named ‘x’ and allows ‘deriv=3’, as documented. (PR#15273)
‘summaryRprof()’ would only read the first ‘chunksize’ lines of an ‘Rprof’ file produced with ‘line.profiling=TRUE’. By default, this is the first 100 seconds. (PR#15288)
‘arrayInd(*, useNames=TRUE)’ and, analogously, ‘which(*, arr.ind=TRUE)’ now make use of ‘names(.dimnames)’ when available.
‘load()’ now has a ‘verbose’ argument for debugging support, to print the names of objects just before loading them.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
Arguments ‘EISPACK’ for ‘eigen()’ and ‘LINPACK’ for ‘chol()’, ‘chol2inv()’, ‘solve()’ and ‘svd()’ are ignored: LAPACK is always used.
If ‘x’ is a symbol, ‘is.vector(x, "name")’ now returns ‘TRUE’, since ‘"name"’ and ‘"symbol"’ should be synonyms. (Reported by Hervé Pagès.)
New ‘anyMissing()’ is a fast version of ‘any(is.na(.))’, based on a proposal by Tim Hesterberg. (Wish of PR#15239).
The return value when all workers failed from ‘parallel::mclapply(mc.presechedule = TRUE)’ was a list of strings and not of error objects. (Spotted by Karl Forner and Bernd Bischl.)
In R 3.0.0, when ‘help()’ found multiple pages with the same alias, the HTML display of all the selections was not produced. (PR#15282)
New ‘anyNA()’ is a fast version of ‘any(is.na(.))’, based on a proposal by Tim Hesterberg. (Wish of PR#15239).
On system where ‘mktime()’ does not set ‘ERRNO’, the last second before the epoch could not be converted from ‘POSIXlt’ to ‘POSIXct’. (Reported by Bill Dunlap).
Alternative site and user customization files ‘Makevars.site’ and
‘~/.R/Makevars’ can be specified _via_ the environment variables
‘R_MAKEVARS_SITE’ and ‘R_MAKEVARS_USER’ respectively.
Alternatives to the site and user customization files ‘Makevars.site’ and ‘~/.R/Makevars’ can be specified _via_ the environment variables ‘R_MAKEVARS_SITE’ and ‘R_MAKEVARS_USER’ respectively. These can be used to suppress the use of the default files by setting an empty value (where possible) or a non-existent path.
‘as.dendrogram()’'s ‘hclust’ method uses less memory and hence gets considerably faster for large (n ~ 1000) clusterings, thanks to Daniel Müllner. (PR#15174)
Alternative site and user customization files ‘Makevars.site’ and ‘~/.R/Makevars’ can be specified _via_ the environment variables ‘R_MAKEVARS_SITE’ and ‘R_MAKEVARS_USER’ respectively.
The default method of ‘image()’ will plot axes of the class of ‘xlim’ and ‘ylim’ (and hence of ‘x’ and ‘y’ if there is a suitable ‘range()’ method). Based on a suggestion of Michael Sumner.
‘count.fields()’ is now consistent with ‘scan()’ in its handling of newlines in quoted strings. Instead of triggering an error, this results in the current line receiving ‘NA’ as the field count, with the next line getting the total count of the two lines.
Calling ‘lm.wfit()’ with no non-zero weights gave an array-overrun in the Fortran code and a not very sensible answer. It is now special-cased with a simpler answer (no ‘qr’ component).
‘supsmu()’ could read/write outside its input vectors for very short inputs (seen in package ‘rms’ for ‘n = 4’).
‘contourLines()’ now checks more comprehensively for conformance of its ‘x’, ‘y’ and ‘z’ arguments (it was used incorrectly in package ‘R2G2’).
Calling ‘file.copy()’ or ‘dirname()’ with the invalid input ‘""’ (which was being used in packages, despite not being a file path) could have caused a segfault.
‘dirname("")’ is now ‘""’ rather than ‘"."’ (unless it segfaulted).
In R 3.0.0, ‘identify()’ and ‘locator()’ did not record information correctly, so replaying a graph (e.g. by copying it to another device) would fail. (PR#15271)
Calling ‘file.copy()’ or ‘dirname()’ with the invalid input ‘""’ (which was being used in packages, despite not being a file path) could have caused a segfault.
‘unzip(list = TRUE)’ returned ‘Names’ as a factor and not a character vector (as documented) for the internal method. (Noticed by Sean O'Riordain.)
[Not later than May 10] The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files has been removed.
‘.find.package()’ and ‘.path.package()’ are defunct: only the versions without the initial dot introduced in R 2.13.0 have ever been in the API.
‘R CMD config’ now make use of personal ‘Makevars’ files under ‘~/.R’ and a site file ‘Makevars.site’, in the same way as ‘R CMD SHLIB’ and ‘R CMD INSTALL’. This makes the utility more useful in package ‘configure’ scripts.
On Windows finding the personal files may require the environment variable ‘HOME’ set.
The old behaviour can be obtained with the new options ‘--no-user-files’ and ‘--no-site-files’.
‘contourLines()’ now checks more comprehensively for conformance of its ‘x’, ‘y’ and ‘z’ arguents (it was used incorrectly in package ‘R2G2’).
Saved graphics display lists are R version-specific. Attempting to load workspaces containing them (or some other version-specific objects) aborted the load in R 3.0.0 and earlier; now it does a partial load and generates a warning instead.
Quotes were handled differently when reading the first line and reading the rest, so ‘read.table()’ misread some files that contained quote characters (PR#15245).
‘.find.package()’ and ‘.path.package()’ are defunct: only the public versions without the initial dot have ever been in the API.
‘unzip(list = TRUE)’ returned a factor and not a character vector (as documented) for ‘Names’ in the internal method. (Noticed by Sean O'Riordain.)
‘cat()’ with ‘sep’ a character vector of length greater than one and more than one argument was using separators inconsistently (PR#15261).
On Windows in R 3.0.0, ‘savePlot()’ failed because of an incorrect check on the argument count.
‘cat()’ with ‘sep’ string vector of length greater than one and more than one argument was using separators inconsistently (PR#15261).
Quotes were handled differently when reading the first line and reading the rest, so ‘read.table()’ misread files that contained quote characters (PR#15245).
‘R CMD config’ now make use of personal ‘Makevars’ files under ‘~/.R’ and a site file ‘Makevars.site’, in the same way as ‘R CMD SHLIB’ and ‘R CMD INSTALL’. This makes the utility more useful in package ‘configure’ scripts.
On Windows the personal files may require the environment variable ‘HOME’ set.
The old behaviour can be obtained with the new options ‘--no-user-files’ and ‘--no-site-files’.
On Windows in R 3.0.0, ‘savePlot()’ failed because of a bad check on the argument count.
‘scan()’ now warns when end-of-file occurs within a quoted string.
‘count.fields()’ is now consistent with ‘scan()’ in handling newlines in quoted strings. Instead of triggering an error, this results in the current line receiving ‘NA’ as the field count, with the next line getting the total count of the two lines.
Quotes were handled differently when reading the first line and reading the rest, so ‘read.table()’ misread files that contained quote characters (PR#15245)
‘R CMD config’ now make use of personal ‘Makevars’ files under ‘~/.R’, in the same way as ‘R CMD SHLIB’ and ‘R CMD INSTALL’. This makes the utility more useful in package ‘configure’ scripts.
On Windows this may require the environment variable ‘HOME’ set.
The old behaviour can be obtained with the new option ‘--no-personal’.
‘citation(pkg)’ dropped the header and footer specified in the ‘CITATION’ file (PR#15257).
Profiling of built-in functions with ‘line.profiling= TRUE’ did not record the line from which they were called.
‘str(d)’ no longer gives an error when ‘names(d)’ contain illegal multibyte strings (PR#15247).
(‘For experts only’, as the introductory manual says.) The use of environment variables ‘R_NSIZE’ and ‘R_VSIZE’ to control the initial (= minimum) garbage collection trigger for number of cons cels and size of heap has been restored: they can be overridden by the command-line options ‘--min-nsize’ and ‘--min-vsize’; see ‘?Memory’.
For consistency, ‘R CMD build’ now matches entries in ‘.Rbuildignore’ and ‘vignettes/.install_extras’ case-insensitively on all platforms (not just on Windows).
For consistency, entries in ‘.Rinstignore’ are now matched case-insensitively on all platforms.
‘mcparallel’ has a new argument ‘mc.interactive’ which can modify the
interactive flag in the child process. The new default is ‘FALSE’ which
makes child processes non-interactive by default (this prevents
lock-ups due to children waiting for interactive input).
‘mcparallel’ has a new argument ‘mc.interactive’ which can modify the interactive flag in the child process. The new default is ‘FALSE’ which makes child processes non-interactive by default (this prevents lock-ups due to children waiting for interactive input).
‘as.POSIXct.numeric’ was coercing ‘origin’ using the ‘tz’ argument and not ‘"GMT"’ as documented (PR#14973).
‘chooseCRANmirror()’ and ‘chooseBioCmirror()’ gain an ‘ind’ argument
(like ‘setRepositories()’).
In the ‘DESCRIPTION’ file,
License: X11
is no longer recognized as valid. Use ‘MIT’ or ‘BSD_2_clause’ instead.
‘chooseCRANmirror()’ and ‘chooseBioCmirror()’ gain an ‘ind’ argument (like ‘setRepositories()’).
‘sys.source()’ did not report error locations when ‘keep.source = TRUE’.
In the ‘DESCRIPTION’ file,
License: X11
is no longer recognized as valid, since it includes ‘Copyright (C) 1996 X Consortium’ which cannot be appropriate for a current R package. Use ‘MIT’ or ‘BSD_2_clause’ instead.
‘tools::Rdiff(useDiff = FALSE)’ is closer to the POSIX definition of ‘diff -b’ (as distinct from the description in the ‘man’ pages of most systems).
In a package's ‘DESCRIPTION’ file,
License: X11
is deprecated, since it includes ‘Copyright (C) 1996 X Consortium’ which cannot be appropriate for a current R package. Use ‘MIT’ or ‘BSD_2_clause’ instead.
R help pages and manuals have no ISBNs because ISBN rules no longer allow constantly changing content to be assigned an ISBN.
‘chooseCRANmirror()’ and ‘chooseBioCmirror()’ gain an ‘ind’ argument (like ‘setRepositories()’).
‘removeClass(cc)’ gave "node stack overflow" for some class definitions containing ‘"array"’ or ‘"matrix"’.
‘sum()’ for integer arguments now uses an integer accumulator of at least 64 bits and so will be more accurate in the very rare case that a cumulative sum exceeds 2^53 (necessarily summing more than 4 million elements).
It is now possible to write custom connection implementations outside core R using ‘R_ext/Connections.h’. Please note that the implementation of connections is still considered internal and may change in the future (see the above file for details).
File ‘share/licenses/licenses.db’ has some clarifications, especially as to which variants of ‘BSD’ and ‘MIT’ is intended and how to apply them to packages. The problematic licence ‘Artistic-1.0’ has been removed.
There is support for vectors longer than 2^31 - 1 elements. This applies to raw, logical, integer, double, complex and character vectors, as well as lists. (Elements of character vectors remain limited to 2^31 - 1 bytes.)
Most operations which can sensibly be done with long vectors work: others may return the error ‘long vectors not supported yet’. Most of these are because they explicitly work with integer indices (e.g. ‘anyDuplicated()’ and ‘match()’) or because other limits (e.g. of character strings or matrix dimensions) would be exceeded or the operations would be extremely slow.
‘serialize()’ to a raw vector is unlimited in size (except by resources).
The C-level function ‘R_alloc’ can now allocate 2^35 or more bytes.
The ‘*.R’ tangled source code for vignettes is now included in tarballs when ‘R CMD build’ is used to produce them. In R 3.0.0, ‘*.R’ files not in the sources will be produced at install time, but eventually this will be dropped.
The package type ‘"mac.binary"’ now looks in a path in the repository without any Mac subtype (which used to be ‘universal’ or ‘leopard’): it looks in ‘bin/macosx/contrib/3.0’ rather than ‘bin/macosx/leopard/contrib/2.15’). This is the type used for the CRAN binary distribution for OS X as from R 3.0.0.
File ‘etc/Makeconf’ makes more use of the macros ‘$(CC)’, ‘$(CXX)’, ‘$(F77)’ and ‘$(FC)’, so the compiler in use can be changed by setting just these (and if necessary the corresponding flags and ‘FLIBS’) in file ‘~/.R/Makevars’.
This is convenient for those working with binary distributions of R, e.g. on OS X.
‘mcparallel’ has a new argument ‘mc.interactive’ which can modify the interactive flag in the child process. The new default is ‘FALSE’ which makes child processes non-interactive by default (this prevents lock-ups due to children waiting for interactive input).
‘type.convert()’ (hence ‘read.table()’) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify ‘colClasses’ in ‘read.table()’ to be ‘"numeric"’.
Partial matching when using the ‘$’ operator _on data frames_ now throws a warning and may become defunct in the future. If partial matching is intended, replace ‘foo$bar’ by ‘foo[["bar", exact = FALSE]]’.
Specifying both ‘rate’ and ‘scale’ to ‘[dpqr]gamma’ is a warning (if they are essentially the same value) or an error.
‘type.convert()’ (hence ‘read.table()’) returns a character vectors or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
‘chol(LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’, ‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK = TRUE)’ use LAPACK and no longer warn.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
Arguments ‘EISPACK’ for ‘eigen()’ and ‘LINPACK’ for ‘chol()’, ‘ch2inv()’, ‘solve()’ and ‘svd()’ are ignored: LAPACK is always used.
Partial matching when using the ‘$’ operator on data frames now throws a warning and may become defunct in the future. If partial matching is intended, replace ‘foo$bar’ with ‘foo[["bar", exact=FALSE]]’.
‘type.convert()’ (hence ‘read.table()’) returns as character string or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs.
The ‘breaks’ argument in ‘hist.default()’ can now be a function that returns the breakpoints to be used (previously it could only return the suggested number of breakpoints).
On Windows, the device name for bitmap devices as reported by ‘.Device’ and ‘.Devices’ no longer includes the file name. This is for consistency with other platforms and was requested by the ‘lattice’ maintainer.
‘win.metafile()’ still uses the file name: the exact form is used by package ‘tkrplot’.
‘set.seed(NULL)’ re-initializes ‘.Random.seed’ as done at the beginning of the session if not already set. (Suggestion of Bill Dunlap.)
(‘For experts only’, as the introductory manual says.) The use of environment variables ‘R_NSIZE’ and ‘R_VSIZE’ to control the initial (= minimum) garbade collection trigger for number of cons cels and size of heap has been restored: they can be overridden by the command-line options ‘--min-nsize’ and ‘--min-vsize’; see ‘?Memory’.
File ‘etc/Makeconf’ makes more use of the macros ‘$(CC)’, ‘$(CXX)’, ‘$(F77)’ and ‘$(FC)’, so the compiler in use can be changed by setting just these (and if necessary the corresponding flags) in file ‘~/.R/Makevars’.
This is convenient for those working with binary distributions of R, e.g. on OS X.
The package type ‘"mac.binary"’ now results in a path without Mac subtype (which used to be ‘"universal"’). This is the type used for the CRAN binary distribution for OS X as from R 3.0.0.
[On Apr 12] ‘.find.package()’ and ‘.path.package()’ are defunct: only the public versions without the dot have ever been in the API.
The package type ‘"mac.binary"’ now results in a path without Mac subtype (which used to be ‘"universal"’).
‘configure’ no longer looks for file ‘~/.Rconfig’: ‘~/.R/config’ has long been preferred.
(‘For experts only’, and the introductory manual says.) The use of environment variables ‘R_NSIZE’ and ‘R_VSIZE’ to control the initial (= minimum) garbade collection trigger for number of cons cels and size of heap has been restored: they can be overridden by the command-line options ‘--min-nsize’ and ‘--min-vsize’; see ‘?Memory’.
On Windows, the stack size is reduced to 16MB on 32-bit systems: misguided users were launching many threads without controlling the stack size.
The minimum versions for ‘--use-system-zlib’ and ‘--use-system-pcre’ are now tested as 1.2.5 and 8.10 respectively.
‘chol(pivot = FALSE, LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’,
‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK =
TRUE)’ no longer warn that LAPACK will be used.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
‘chol(LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’, ‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK = TRUE)’ use LAPACK and no longer warn.
[Intended] The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files has been removed.
[Intended] ‘.find.package()’ and ‘.path.package()’ are defunct: only the public versions without the dot have ever been in the API.
The memory manager now allows the strategy used to balance garbage collection and memory growth to be controlled by setting the environment variable ‘R_GC_MEM_GROW’. See ‘?Memory’ for more details.
‘ftable(x, row.vars, col.vars)’ now also works when the ‘*.vars’ arguments are (integer or character vectors) of length zero.
Calling ‘cat()’ on a malformed UTF-8 string could cause the Windows GUI to lock up. (PR#15227)
Packages need to be (re-)installed under this version (3.0.0) of R.
There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as ‘NA’, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and ‘x[2^31] <- y’ will now extend the vector on a 64-bit platform and give an error on a 32-bit one.
It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. ‘ulimit’ in a ‘bash’ shell, ‘limit’ in ‘csh’), to set limits on overall memory consumption of an R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load.
64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option ‘--max-mem-size’ or setting environment variable ‘R_MAX_MEM_SIZE’.
Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error.
‘identical()’ has a new argument, ‘ignore.environment’, used when comparing functions (with default ‘FALSE’ as before).
There is a new option, ‘options(CBoundsCheck=)’, which controls how ‘.C()’ and ‘.Fortran()’ pass arguments to compiled code. If true (which can be enabled by setting the environment variable ‘R_C_BOUNDS_CHECK’ to ‘yes’), raw, integer, double and complex arguments are always copied, and checked for writing off either end of the array on return from the compiled code (when a second copy is made). This also checks individual elements of character vectors passed to ‘.C()’.
This is not intended for routine use, but can be very helpful in finding segfaults in package code.
In ‘layout()’, the limits on the grid size have been raised (again).
New simple ‘provideDimnames()’ utility function.
Where methods for ‘length()’ return a double value which is representable as an integer (as often happens for package ‘Matrix’), this is converted to an integer.
Matrix indexing of dataframes by two-column numeric indices is now supported for replacement as well as extraction.
‘setNames()’ now has a default for its ‘object’ argument, useful for a character result.
‘StructTS()’ has a revised additive constant in the ‘loglik’ component of the result: the previous definition is returned as the ‘loglik0’ component. However, the help page has always warned of a lack of comparability of log-likelihoods for non-stationary models. (Suggested by Jouni Helske.)
The logic in ‘aggregate.formula()’ has been revised. It is now possible to use a formula stored in a variable; previously, it had to be given explicitly in the function call.
‘install.packages()’ has a new argument ‘quiet’ to reduce the amount of output shown.
Setting an element of the graphics argument ‘lwd’ to a negative or infinite value is now an error. Lines corresponding to elements with values ‘NA’ or ‘NaN’ are silently omitted.
Previously the behaviour was device-dependent.
Setting graphical parameters ‘cex’, ‘col’, ‘lty’, ‘lwd’ and ‘pch’ in ‘par()’ now requires a length-one argument. Previously some silently took the first element of a longer vector, but not always when documented to do so.
‘Sys.which()’ when used with inputs which would be unsafe in a shell (e.g. absolute paths containing spaces) now uses appropriate quoting.
‘as.tclObj()’ has been extended to handle raw vectors. Previously, it only worked in the other direction. (Contributed by Charlie Friedemann, PR#14939.)
New functions ‘cite()’ and ‘citeNatbib()’ have been added, to allow generation of in-text citations from ‘"bibentry"’ objects. A ‘cite()’ function may be added to ‘bibstyle()’ environments.
A ‘sort()’ method has been added for ‘"bibentry"’ objects.
The ‘bibstyle()’ function now defaults to setting the default bibliography style. The ‘getBibstyle()’ function has been added to report the name of the current default style.
‘scatter.smooth()’ now has an argument ‘lpars’ to pass arguments to ‘lines()’.
‘pairs()’ has a new ‘log’ argument, to allow some or all variables to be plotted on logarithmic scale. (In part, wish of PR#14919.)
‘split()’ gains a ‘sep’ argument.
‘termplot()’ does a better job when given a model with interactions (and no longer attempts to plot interaction terms).
The parser now incorporates code from Romain Francois' ‘parser’ package, to support more detailed computation on the code, such as syntax highlighting, comment-based documentation, etc. Functions ‘getParseData()’ and ‘getParseText()’ access the data.
There is a new function ‘rep_len()’ analogous to ‘rep.int()’ for when speed is required (and names are not).
The undocumented use ‘rep(NULL, length.out = n)’ for ‘n > 0’ (which returns ‘NULL’) now gives a warning.
‘demo()’ gains an ‘encoding’ argument for those packages with non-ASCII demos: it defaults to the package encoding where there is one.
‘strwrap()’ converts inputs with a marked encoding to the current locale: previously it made some attempt to pass through as bytes inputs invalid in the current locale.
Specifying both ‘rate’ and ‘scale’ to ‘[dpar]gamma’ is a warning (if they are essentially the same value) or an error.
‘merge()’ works in more cases where the data frames include matrices. (Wish of PR#14974.)
‘optimize()’ and ‘uniroot()’ no longer use a shared parameter object across calls. (‘nlm()’, ‘nlminb()’ and ‘optim()’ with numerical derivatives still do, as documented.)
The ‘all.equal()’ method for date-times is now documented: times are regarded as equal (by default) if they differ by up to 1 msec.
‘duplicated()’ and ‘unique()’ gain a ‘nmax’ argument which can be used to make them much more efficient when it is known that there are only a small number of unique entries. This is done automatically for factors.
Functions ‘rbinom()’, ‘rgeom()’, ‘rhyper()’, ‘rpois()’, ‘rnbinom(),’ ‘rsignrank()’ and ‘rwilcox()’ now return integer (not double) vectors. This halves the storage requirements for large simulations.
‘sort()’, ‘sort.int()’ and ‘sort.list()’ now use radix sorting for factors of less than 100,000 levels when ‘method’ is not supplied. So does ‘order()’ if called with a single factor, unless ‘na.last = NA’.
‘diag()’ as used to generate a diagonal matrix has been re-written in C for speed and less memory usage. It now forces the result to be numeric in the case ‘diag(x)’ since it is said to have ‘zero off-diagonal entries’.
‘backsolve()’ (and ‘forwardsolve()’) are now internal functions, for speed and support for large matrices.
More matrix algebra functions (e.g. ‘chol()’ and ‘solve()’) accept logical matrices (and coerce to numeric).
‘sample.int()’ has some support for n >= 2^31: see its help for the limitations.
A different algorithm is used for ‘(n, size, replace = FALSE, prob = NULL)’ for ‘n > 1e7’ and ‘size <= n/2’. This is much faster and uses less memory, but does give different results.
‘approxfun()’ and ‘splinefun()’ now return a wrapper to an internal function in the ‘stats’ namespace rather than a ‘.C()’ or ‘.Call()’ call. This is more likely to work if the function is saved and used in a different session.
The functions ‘.C()’, ‘.Call()’, ‘.External()’ and ‘.Fortran()’ now give an error (rather than a warning) if called with a named first argument.
‘Sweave()’ by default now reports the locations in the source file(s) of each chunk.
‘clearPushBack()’ is now a documented interface to a long-existing internal call.
‘aspell()’ gains filters for R code, Debian Control Format and message catalog files, and support for R level dictionaries. In addition, package ‘utils’ now provides functions ‘aspell_package_R_files()’ and ‘aspell_package_C_files()’ for spell checking R and C level message strings in packages.
‘bibentry()’ gains some support for “incomplete” entries with a ‘crossref’ field.
‘gray()’ and ‘gray.colors()’ finally allow ‘alpha’ to be specified.
‘monthplot()’ gains parameters to control the look of the reference lines. (Suggestion of Ian McLeod.)
Added support for new ‘%~%’ relation (“is distributed as”) in plotmath.
‘domain = NA’ is accepted by ‘gettext()’ and ‘ngettext()’, analogously to ‘stop()’ etc.
‘termplot()’ gains a new argument ‘plot = FALSE’ which returns information to allow the plots to be modified for use as part of other plots, but does not plot them. (Contributed by Terry Therneau, PR#15076.)
‘quartz.save()’, formerly an undocumented part of ‘R.app’, is now available to copy a device to a ‘quartz()’ device. ‘dev.copy2pdf()’ optionally does this for PDF output: ‘quartz.save()’ defaults to PNG.
The default method of ‘pairs()’ now allows ‘text.panel = NULL’ and the use of ‘<foo>.panel = NULL’ is now documented.
‘setRefClass()’ and ‘getRefClass()’ now return class generator functions, similar to ‘setClass()’, but still with the reference fields and methods as before (suggestion of Romain Francois).
New functions ‘bitwNot()’, ‘bitwAnd()’, ‘bitwOr()’ and ‘bitwXor()’, using the internal interfaces previously used for classes ‘"octmode"’ and ‘"hexmode"’.
Also ‘bitwShiftL()’ and ‘bitwShiftR()’ for shifting bits in elements of integer vectors.
New option ‘"deparse.cutoff"’ to control the deparsing of language objects such as calls and formulae when printing. (Suggested by a comment of Sarah Goslee.)
‘colors()’ gains an argument ‘distinct’.
New ‘demo(colors)’ and ‘demo(hclColors)’, with utility functions.
‘list.files()’ (aka ‘dir()’) gains a new optional argument ‘no..’ which allows to exclude ‘"."’ and ‘".."’ from listings.
Multiple time series are also of class ‘"matrix"’; consequently, ‘head()’, e.g., is more useful.
‘encodeString()’ preserves UTF-8 marked encodings. Thus if factor levels are marked as UTF-8 an attempt is made to print them in UTF-8 in ‘RGui’ on Windows.
‘readLines()’ and ‘scan()’ (and hence ‘read.table()’) in a UTF-8 locale now discard a UTF-8 byte-order-mark (BOM). Such BOMs are allowed but not recommended by the Unicode Standard: however Microsoft applications can produce them and so they are sometimes found on websites.
The encoding name ‘"UTF-8-BOM"’ for a connection will ensure that a UTF-8 BOM is discarded.
‘mapply(FUN, a1, ..)’ now also works when ‘a1’ (or a further such argument) needs a ‘length()’ method (which the documented arguments never do). (Requested by Hervé Pagès; with a patch.)
‘.onDetach()’ is supported as an alternative to ‘.Last.lib’. Unlike ‘.Last.lib’, this does not need to be exported from the package's namespace.
The ‘srcfile’ argument to ‘parse()’ may now be a character string, to be used in error messages.
The ‘format()’ method for ‘ftable’ objects gains a ‘method’ argument, propagated to ‘write.ftable()’ and ‘print()’, allowing more compact output, notably for LaTeX formatting, thanks to Marius Hofert.
The ‘utils::process.events()’ function has been added to trigger immediate event handling.
‘Sys.which()’ now returns ‘NA’ (not ‘""’) for ‘NA’ inputs (related to PR#15147).
The ‘print()’ method for class ‘"htest"’ gives fewer trailing spaces (wish of PR#15124).
Also print output from ‘HoltWinters()’, ‘nls()’ and others.
‘loadNamespace()’ allows a version specification to be given, and this is used to check version specifications given in the ‘Imports’ field when a namespace is loaded.
‘setClass()’ has a new argument, ‘slots’, clearer and less ambiguous than ‘representation’. It is recommended for future code, but should be back-compatible. At the same time, the allowed slot specification is slightly more general. See the documentation for details.
‘mget()’ now has a default for ‘envir’ (the frame from which it is called), for consistency with ‘get()’ and ‘assign()’.
‘close()’ now returns an integer status where available, invisibly. (Wish of PR#15088.)
The internal method of ‘tar()’ can now store paths too long for the ‘ustar’ format, using the (widely supported) GNU extension. It can also store long link names, but these are much less widely supported. There is support for larger files, up to the ‘ustar’ limit of 8GB.
Local reference classes have been added to package ‘methods’. These are a technique for avoiding unneeded copying of large components of objects while retaining standard R functional behavior. See ‘?LocalReferenceClasses’.
‘untar()’ has a new argument ‘restore_times’ which if false (not the default) discards the times in the tarball. This is useful if they are incorrect (some tarballs submitted to CRAN have times in a local timezone or many years in the past even though the standard required them to be in UTC).
‘replayplot()’ cannot (and will not attempt to) replay plots recorded under R < 3.0.0. It may crash the R session if an attempt is made to replay plots created in a different build of R >= 3.0.0.
Palette changes get recorded on the display list, so replaying plots (including when resizing screen devices and using ‘dev.copy()’) will work better when the palette is changed during a plot.
‘chol(pivot = TRUE)’ now defaults to LAPACK, not LINPACK.
The ‘parse()’ function has a new parameter ‘keep.source’, which defaults to ‘options("keep.source")’.
Profiling via ‘Rprof()’ now optionally records information at the statement level, not just the function level.
The ‘Rprof()’ function now quotes function names in in its output file on Windows, to be consistent with the quoting in Unix.
Profiling via ‘Rprof()’ now optionally records information about time spent in GC.
The HTML help page for a package now displays non-vignette documentation files in a more accessible format.
To support ‘options(stringsAsFactors = FALSE)’, ‘model.frame()’, ‘model.matrix()’ and ‘replications()’ now automatically convert character vectors to factors without a warning.
The ‘print’ method for objects of class ‘"table"’ now detects tables with 0-extents and prints the results as, e.g., ‘< table of extent 0 x 1 x 2 >’. (Wish of PR#15198.)
Deparsing involving calls to anonymous functions and has been made closer to reversible by the addition of extra parentheses.
The function ‘utils::packageName()’ has been added as a lightweight version of ‘methods::getPackageName()’.
‘find.package(lib.loc = NULL)’ now treats loaded namespaces preferentially in the same way as attached packages have been for a long time.
In Windows, the Change Directory dialog now defaults to the current working directory, rather than to the last directory chosen in that dialog.
‘available.packages()’ gains a ‘"license/restricts_use"’ filter which retains only packages for which installation can proceed solely based on packages which are guaranteed not to restrict use.
New ‘check_packages_in_dir()’ function in package ‘tools’ for conveniently checking source packages along with their reverse dependencies.
R's completion mechanism has been improved to handle help requests (starting with a question mark). In particular, help prefixes are now supported, as well as quoted help topics. To support this, completion inside quotes are now handled by R by default on all platforms.
There is support for vectors longer than 2^31 - 1 elements on 64-bit platforms. This applies to raw, logical, integer, double, complex and character vectors, as well as lists. (Elements of character vectors remain limited to 2^31 - 1 bytes.)
Not all aspects of such vectors are completely implemented (nor completely tested).
Most operations which can sensibly be done with long vectors now work: others may return the error ‘long vectors not supported yet’. Most of these are because they explicitly work with integer indices (e.g. ‘anyDuplicated()’ and ‘match()’) or because of other limits (e.g. of character strings or matrix dimensions) would be exceeded or the operations would be extremely slow.
‘length()’ returns a double for long vectors, and lengths can be set to 2^31 or more by the replacement function with a double value.
Most aspects of indexing are available. Generally double-valued indices can be used to access elements beyond 2^31 - 1.
There is some support for matrices and arrays with each dimension less than 2^31 but total number of elements more than that. Only some aspects of matrix algebra work for such matrices, often taking a very long time. In other cases the underlying Fortran code has an unstated restriction (as was found for complex ‘svd()’).
‘dist()’ can produce dissimilarity objects for more than 65536 rows (but for example ‘hclust()’ cannot process such objects).
‘serialize()’ to a raw vector is no longer limited in size (except by resources) on 64-bit platforms.
The C-level function ‘R_alloc’ can now allocate 2^35 or more bytes on 64-bit platforms.
‘agrep()’ and ‘grep()’ will return double vectors of indices for long vector inputs.
Many calls to ‘.C()’ have been replaced by ‘.Call()’ to allow long vectors to be supported (now or in the future). Regrettably several packages had copied the non-API ‘.C()’ calls and so failed.
‘.C()’ and ‘.Fortran()’ do not accept long vector inputs. This is a precaution as it is very unlikely that existing code will have been written to handle long vectors (and the R wrappers often assume that ‘length(x)’ is an integer).
Most of the methods for ‘sort()’ work for long vectors.
‘rank()’, ‘sort.list()’ and ‘order()’ support long vectors (slowly except for radix sorting).
‘sample()’ can do uniform sampling from a long vector.
More use has been made of R objects representing registered entry points, which is more efficient as the address is provided by the loader once only when the package is loaded.
This has been done for packages ‘base’, ‘methods’, ‘splines’ and ‘tcltk’: it was already in place for the other standard packages.
Since these entry points are always accessed by the R entry points they do not need to be in the load table which can be substantially smaller and hence searched faster. This does mean that ‘.C’ / ‘.Fortran’ / ‘.Call’ calls copied from earlier versions of R may no longer work - but they were never part of the API.
Many ‘.Call()’ calls in package ‘base’ have been migrated to ‘.Internal()’ calls.
‘solve()’ makes fewer copies, especially when ‘b’ is a vector rather than a matrix.
‘eigen()’ makes fewer copies if the input has dimnames.
Most of the linear algebra functions make fewer copies when the input(s) are not double (e.g. integer or logical).
A foreign function call (‘.C()’ etc) in a package without a ‘PACKAGE’ argument will only look in the first DLL specified in the ‘NAMESPACE’ file of the package rather than searching all loaded DLLs. A few packages needed ‘PACKAGE’ arguments added.
The ‘@<-’ operator is now implemented as a primitive, which should reduce some copying of objects when used. Note that the operator object must now be in package ‘base’: do not try to import it explicitly from package ‘methods’.
The transitional support for installing packages without namespaces (required since R 2.14.0) has been removed. ‘R CMD build’ will still add a namespace, but a ‘.First.lib()’ function will need to be converted.
‘R CMD INSTALL’ no longer adds a namespace (so installation will fail), and a ‘.First.lib()’ function in a package will be ignored (with an installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’ file can still be installed.
Packages can specify in their ‘DESCRIPTION file’ a line like
Biarch: yes
to be installed on Windows with ‘--force-biarch’.
Package vignettes can now be processed by other engines besides ‘Sweave’; see ‘Writing R Extensions’ and the ‘tools::vignetteEngine’ help topic for details.
‘R CMD check’ now gives a warning rather than a note if it finds calls to ‘abort’, ‘assert’ or ‘exit’ in compiled code, and has been able to find the ‘.o’ file in which the calls occur.
Such calls can terminate the R process which loads the package.
The location of the build and check environment files can now be specified by the environment variables ‘R_BUILD_ENVIRON’ and ‘R_CHECK_ENVIRON’, respectively.
‘R CMD Sweave’ gains a ‘--compact’ option to control possibly reducing the size of the PDF file it creates when ‘--pdf’ is given.
‘R CMD build’ now omits Eclipse's ‘.metadata’ directories, and ‘R CMD check’ warns if it finds them.
‘R CMD check’ now does some checks on functions defined within reference classes, including of ‘.Call()’ etc calls.
‘R CMD check --as-cran’ notes assignments to the global environment, calls to ‘data()’ which load into the global environment, and calls to ‘attach()’.
‘R CMD build’ by default uses the internal method of ‘tar()’ to prepare the tarball. This is more likely to produce a tarball compatible with ‘R CMD INSTALL’ and ‘R CMD check’: an external ‘tar’ program, including options, can be specified _via_ the environment variable ‘R_BUILD_TAR’.
‘tools::massageExamples()’ is better protected against packages which re-define base functions such as ‘cat()’ and ‘get()’ and so can cause ‘R CMD check’ to fail when checking examples.
‘R CMD javareconf’ has been enhanced to be more similar to the code used by ‘configure’.
There is now a test that a JNI program can be compiled (like ‘configure’ did) and only working settings are used.
It makes use of custom settings from configuration recorded in ‘etc/javaconf’.
The ‘--no-vignettes’ argument of ‘R CMD build’ has been renamed to the more accurate ‘--no-build-vignettes’: its action has always been to (re)build vignettes and never omitted them.
‘R CMD check’ accepts ‘--no-build-vignettes’ as a preferred synonym for ‘--no-rebuild-vignettes’.
The ‘ENCODING’ argument to ‘.C()’ is defunct. Use ‘iconv()’ instead.
The ‘.Internal(eval.with.vis)’ non-API function has been removed.
Support for the converters for use with ‘.C()’ has been removed, including the oft misused non-API header ‘R_ext/RConverters.h’.
The previously deprecated uses of ‘array()’ with a 0-length ‘dim’ argument and ‘tapply()’ with a 0-length ‘INDEX’ list are now errors.
‘Translation’ packages are defunct.
Calling ‘rep()’ or ‘rep.int()’ on a pairlist or other non-vector object is now an error.
Several non-API entry points have been transferred to packages (e.g. ‘R_zeroin2’) or replaced by different non-API entry points (e.g. ‘R_tabulate’).
The ‘internal’ graphics device invoked by ‘.Call("R_GD_nullDevice", package = "grDevices")’ has been removed: use ‘pdf(file = NULL)’ instead.
The ‘.Fortran()’ entry point ‘"dqrls"’ which has not been used by R since version 2.15.1 is no longer available.
Functions ‘traceOn()’ and ‘traceOff()’ in package ‘methods’ are now defunct.
Function ‘CRAN.packages()’ is finally defunct.
Use of ‘col2rgb(0)’ is defunct: use ‘par("bg")’ or ‘NA’ instead.
The long-defunct functions ‘Rd_parse()’, ‘anovalist.lm()’, ‘categpry()’, ‘clearNames()’, ‘gammaCody()’, ‘glm.fit.null()’, ‘lm.fit.null()’, ‘lm.wfit.null()’, ‘manglePackageNames()’, ‘mauchley.test()’, ‘package.contents()’, ‘print.coefmat()’, ‘reshapeLong()’, ‘reshapeWide()’, ‘tkclose()’, ‘tkcmd()’, ‘tkfile.dir()’, ‘tkfile.tail()’, ‘tkopen()’, ‘tkputs()’, ‘tkread()’, ‘trySilent()’ and ‘zip.file.extract()’ have been removed entirely (but are still documented in the help system).
The unused ‘dataPath’ argument to ‘attachNamespace()’ has been removed.
‘grid.prompt()’ has been removed: use ‘devAskNewPage()’ instead.
The long-deprecated ‘intensities’ component is no longer returned by ‘hist()’.
‘mean()’ for data frames and ‘sd()’ for data frames and matrices are defunct.
‘chol(pivot = FALSE, LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’, ‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK = TRUE)’ are defunct: LAPACK will be used, with a warning.
The ‘keep.source’ argument to ‘library()’ and ‘require()’ is defunct. This option needs to be set at install time.
Documentation for ‘real()’, ‘as.real()’ and ‘is.real()’ has been moved to ‘defunct’ and the functions removed.
The ‘maxRasters’ argument of ‘pdf()’ (unused since R 2.14.0) has been removed.
The unused ‘fontsmooth’ argument has been removed from the ‘quartz()’ device.
All the (non-API) EISPACK entry points in R have been removed.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is deprecated.
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files will be removed in R 3.1.0.
‘.find.package()’ and ‘.path.package()’ are deprecated: only the public versions without the dot have ever been in the API.
The C code underlying base graphics has been migrated to the ‘graphics’ package (and hence no longer uses ‘.Internal()’ calls).
Most of the ‘.Internal()’ calls used in the ‘stats’ package have been migrated to C code in that package.
This means that a number of ‘.Internal()’ calls which have been used by packages no longer exist, including ‘.Internal(cor)’ ‘.Internal(cov)’, ‘.Internal(optimhess)’ and ‘.Internal(update.formula)’.
Some ‘.External()’ calls to the ‘base’ package (really to the R executable or shared library) have been moved to more appropriate packages. Packages should not have been using such calls, but some did (mainly those used by ‘integrate()’).
There is a new function ‘mcaffinity()’ which allows getting or setting the CPU affinity mask for the current R process on systems that supports this (currently only Linux has been tested successfully). It has no effect on systems which do not support process affinity. Users are not expected to use this function directly (with the exception of fixing libraries that break affinity settings like OpenBLAS) - the function is rather intended to support affinity control in high-level parallel functions. In the future, R may supplement lack of affinity control in the OS by its own bookkeeping via ‘mcaffinity()’ related to processes and threads it spawns.
‘mcparallel()’ has a new argument ‘mc.affinity’ which attempts to set the affinity of the child process according to the specification contained therein.
The port used by socket clusters is chosen randomly: this should help to avoid clashes observed when two users of a multi-user machine try to create a cluster at the same time. To reproduce the previous behaviour set environment variable ‘R_PARALLEL_PORT’ to ‘10187’.
There has been some minor re-organization of the non-API header files. In particular, ‘Rinternals.h’ no longer includes the non-API header ‘R_exts/PrtUtil.h’, and that no longer includes ‘R_exts/Print.h’.
Passing ‘NULL’ to ‘.C()’ is now an error.
‘.C()’ and ‘.Fortran()’ now warn if ‘"single"’ arguments are used with ‘DUP = FALSE’, as changes to such arguments are not returned to the caller.
C entry points ‘R_qsort’ and ‘R_qsort_I’ now have ‘start’ and ‘end’ as ‘size_t’ to allow them to work with longer vectors on 64-bit platforms. Code using them should be recompiled.
A few recently added C entry points were missing the remapping to ‘Rf_’, notably ‘[dpq]nbinom_mu’.
Some of the interface pointers formerly available only to ‘R.app’ are now available to front-ends on all Unix-alikes: one has been added for the interface to ‘View()’.
‘PACKAGE = ""’ is now an error in ‘.C()’ etc calls: it was always contrary to the documentation.
Entry point ‘rcont2’ has been migrated to package ‘stats’ and so is no longer available.
‘R_SVN_REVISION’ in ‘Rversion.h’ is now an integer (rather than a string) and hence usable as e.g. ‘#if R_SVN_REVISION < 70000’.
The entry points ‘rgb2hsv’ and ‘hsv2rgb’ have been migrated to package ‘grDevices’ and so are no longer available.
‘R_GE_version’ has been increased to ‘10’ and ‘name2col’ removed (use ‘R_GE_str2col’ instead). R internal colour codes are now defined using the typedef ‘rcolor’.
The ‘REPROTECT’ macro now checks that the protect index is valid.
Several non-API entry points no longer used by R have been removed, including the Fortran entry points ‘chol’, ‘chol2inv’, ‘cg’, ‘ch’ and ‘rg’, and the C entry points ‘Brent_fmin’, ‘fft_factor’ and ‘fft_work’.
If a ‘.External’ call is registered with a number of arguments (other than ‘-1’), the number of arguments passed is checked for each call (as for other foreign function calls).
The management of translations has been converted to R code: see ‘?tools::update_pkg_po’.
The translations for the R interpreter and ‘RGui.exe’ are now part of the ‘base’ package (rather than having sources in directory ‘po’ and being installed to ‘share/locale’). Thus the ‘base’ package supports three translation domains, ‘R-base’, ‘R’ and ‘RGui’.
The compiled translations which ship with R are all installed to the new package ‘translations’ for easier updating. The first package of that name found on ‘.libPaths()’ at the start of the R session will be used. (It is possible messages will be used before ‘.libPaths()’ is set up in which case the default translations will be used: set environment variable ‘R_TRANSLATIONS’ to point to the location of the intended ‘translations’ package to use this right from the start.)
The translations form a separate group in the Windows installer, so can be omitted if desired.
The markup for many messages has been changed to make them easier to translate, incorporating suggestions from Łukasz Daniel.
There is again support for building without using the C ‘long double’ type. This is required by C99, but system implementations can be slow or flawed. Use ‘configure’ option ‘--disable-long-double’.
‘make pdf’ and ‘make install-pdf’ now make and install the full reference index (including all base and recommended packages).
The 'reference manual' on the Windows GUI menu and included in the installer is now the full reference index, including all base and recommended packages.
The Windows installer no longer installs a Start Menu link to the static help pages; as most pages are generated dynamically, this led to a lot of broken links.
Any custom settings for Java configuration are recorded in file ‘etc/javaconf’ for subsequent use by ‘R CMD javareconf’.
There is now support for ‘makeinfo’ version 5.0 (which requires a slightly different ‘.texi’ syntax).
When ‘R CMD build’ is run in an encoding other than the one specified in the package's ‘DESCRIPTION’ file it tries harder to expand the ‘authors@R’ field in the specified encoding. (PR#14958)
If ‘R CMD INSTALL’ is required to expand the ‘authors@R’ field of the ‘DESCRIPTION’ file, it tries harder to do so in the encoding specified for the package (rather than using ASCII escapes).
Fix in package ‘grid’ for pushing a viewport into a layout cell, where the layout is within a viewport that has zero physical width OR where the layout has zero total relative width (likewise for height). The layout column widths (or row heights) in this case were being calculated with non-finite values. (Reported by Winston Chang.)
‘solve(A, b)’ for a vector ‘b’ gave the answer names from ‘colnames(A)’ for ‘LINPACK = TRUE’ but not in the default case.
‘La.svd()’ accepts logical matrices (as documented, and as ‘svd()’ did).
‘legend()’ now accepts negative ‘pch’ values, in the same way ‘points()’ long has.
Parse errors when installing files now correctly display the name of the file containing the bad code.
In Windows, tcltk windows were not always properly constructed. (PR#15150)
The internal functions implementing ‘parse()’, ‘tools::parseLatex()’ and ‘tools::parse_Rd()’ were not reentrant, leading to errors in rare circumstances such as a garbage collection triggering a recursive call.
Field assignments in reference class objects via ‘$<-’ were not being checked because the magic incantation to turn methods on for that primitive operator had been inadvertently omitted.
‘setHook(hookname, value, action="replace")’ set the hook to be the value, rather than a list containing the value as documented. (PR#15167)
If a package used a ‘NEWS.Rd’ file, the main HTML package index page did not link to it. (Reported by Dirk Eddelbuettel.)
The primitive implementation of ‘@<-’ was not checking the class of the replacement. It now does a check, quicker but less general than ‘slot<-’. See the help.
‘split(x, f)’ now recycles classed objects ‘x’ in the same way as vectors. (Reported by Martin Morgan.)
‘pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)’ is no longer ‘-Inf’; ditto for corresponding ‘pt()’ and ‘pf()’ calls, such as ‘pt(45, df=5000, lower.tail=FALSE, log.p=TRUE)’. (PR#15162)
The Windows graphics device would crash R if a user attempted to load the graphics history from a variable that was not a saved history. (PR#15230)
The workspace size for the ‘predict()’ method for ‘loess()’ could exceed the maximum integer size. (Reported by Hiroyuki Kawakatsu.)
It is intended that this version will be released as R 3.0.0.
Packages need to have been installed under this version of R.
There is a subtle change in behaviour for numeric index values 2^31 and
larger. These never used to be legitimate and so were treated as ‘NA’,
sometimes with a warning. They are now legal for long vectors so there
is no longer a warning, and ‘x[2^31] <- y’ will now extend the vector
on a 64-bit platform and give an error on a 32-bit one.
It is now possible for 64-bit builds to allocate amounts of memory
limited only by the OS. It may be wise to use OS facilities (e.g.
‘ulimit’ in a ‘bash’ shell, ‘limit’ in ‘csh’), to set limits on overall
memory consumption of an R process, particularly in a multi-user
environment. A number of packages need a limit of at least 4GB of
virtual memory to load.
64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option ‘--max-mem-size’ or setting environment variable ‘R_MAX_MEM_SIZE’.
Negative numbers for colours are consistently an error: previously they
were sometimes taken as transparent, sometimes mapped into the current
palette and sometimes an error.
‘identical()’ has a new argument, ‘ignore.environment’, used when
comparing functions (with default ‘FALSE’ as before).
There is a new option, ‘options(CBoundsCheck=)’, which controls how
‘.C()’ and ‘.Fortran()’ pass arguments to compiled code. If true
(which can be enabled by setting the environment variable
‘R_C_BOUNDS_CHECK’ to ‘yes’), raw, integer, double and complex
arguments are always copied, and checked for writing off either end of
the array on return from the compiled code (when a second copy is
made). This also checks individual elements of character vectors
passed to ‘.C()’.
This is not intended for routine use, but can be very helpful in finding segfaults in package code.
In ‘layout()’, the limits on the grid size have been raised (again).
New simple ‘provideDimnames()’ utility function.
Where methods for ‘length()’ return a double value which is
representable as an integer (as often happens for package ‘Matrix’),
this is converted to an integer.
Matrix indexing of dataframes by two-column numeric indices is now
supported for replacement as well as extraction.
‘setNames()’ now has a default for its ‘object’ argument, useful for a
character result.
‘StructTS()’ has a revised additive constant in the ‘loglik’ component
of the result: the previous definition is returned as the ‘loglik0’
component. However, the help page has always warned of a lack of
comparability of log-likelihoods for non-stationary models. (Suggested
by Jouni Helske.)
The logic in ‘aggregate.formula()’ has been revised. It is now
possible to use a formula stored in a variable; previously, it had to
be given explicitly in the function call.
‘install.packages()’ has a new argument ‘quiet’ to reduce the amount of
output shown.
Setting an element of the graphics argument ‘lwd’ to a negative or
infinite value is now an error. Lines corresponding to elements with
values ‘NA’ or ‘NaN’ are silently omitted.
Previously the behaviour was device-dependent.
Setting graphical parameters ‘cex’, ‘col’, ‘lty’, ‘lwd’ and ‘pch’ in
‘par()’ now requires a length-one argument. Previously some silently
took the first element of a longer vector, but not always when
documented to do so.
‘Sys.which()’ when used with inputs which would be unsafe in a shell
(e.g. absolute paths containing spaces) now uses appropriate quoting.
‘as.tclObj()’ has been extended to handle raw vectors. Previously, it
only worked in the other direction. (Contributed by Charlie
Friedemann, PR#14939.)
New functions ‘cite()’ and ‘citeNatbib()’ have been added, to allow
generation of in-text citations from ‘"bibentry"’ objects. A ‘cite()’
function may be added to ‘bibstyle()’ environments.
A ‘sort()’ method has been added for ‘"bibentry"’ objects.
The ‘bibstyle()’ function now defaults to setting the default
bibliography style. The ‘getBibstyle()’ function has been added to
report the name of the current default style.
‘scatter.smooth()’ now has an argument ‘lpars’ to pass arguments to
‘lines()’.
‘pairs()’ has a new ‘log’ argument, to allow some or all variables to
be plotted on logarithmic scale. (In part, wish of PR#14919.)
‘split()’ gains a ‘sep’ argument.
‘termplot()’ does a better job when given a model with interactions
(and no longer attempts to plot interaction terms).
The parser now incorporates code from Romain Francois' ‘parser’
package, to support more detailed computation on the code, such as
syntax highlighting, comment-based documentation, etc. Functions
‘getParseData()’ and ‘getParseText()’ access the data.
There is a new function ‘rep_len()’ analogous to ‘rep.int()’ for when
speed is required (and names are not).
The undocumented use ‘rep(NULL, length.out = n)’ for ‘n > 0’ (which
returns ‘NULL’) now gives a warning.
‘demo()’ gains an ‘encoding’ argument for those packages with non-ASCII
demos: it defaults to the package encoding where there is one.
‘strwrap()’ converts inputs with a marked encoding to the current
locale: previously it made some attempt to pass through as bytes inputs
invalid in the current locale.
Specifying both ‘rate’ and ‘scale’ to ‘[dpar]gamma’ is a warning (if
they are essentially the same value) or an error.
‘merge()’ works in more cases where the data frames include matrices.
(Wish of PR#14974.)
‘optimize()’ and ‘uniroot()’ no longer use a shared parameter object
across calls. (‘nlm()’, ‘nlminb()’ and ‘optim()’ with numerical
derivatives still do, as documented.)
The ‘all.equal()’ method for date-times is now documented: times are
regarded as equal (by default) if they differ by up to 1 msec.
‘duplicated()’ and ‘unique()’ gain a ‘nmax’ argument which can be used
to make them much more efficient when it is known that there are only a
small number of unique entries. This is done automatically for
factors.
Functions ‘rbinom()’, ‘rgeom()’, ‘rhyper()’, ‘rpois()’, ‘rnbinom(),’
‘rsignrank()’ and ‘rwilcox()’ now return integer (not double) vectors.
This halves the storage requirements for large simulations.
‘sort()’, ‘sort.int()’ and ‘sort.list()’ now use radix sorting for
factors of less than 100,000 levels when ‘method’ is not supplied. So
does ‘order()’ if called with a single factor, unless ‘na.last = NA’.
‘diag()’ as used to generate a diagonal matrix has been re-written in C
for speed and less memory usage. It now forces the result to be
numeric in the case ‘diag(x)’ since it is said to have ‘zero
off-diagonal entries’.
‘backsolve()’ (and ‘forwardsolve()’) are now internal functions, for
speed and support for large matrices.
More matrix algebra functions (e.g. ‘chol()’ and ‘solve()’) accept
logical matrices (and coerce to numeric).
‘sample.int()’ has some support for n >= 2^31: see its help for the
limitations.
A different algorithm is used for ‘(n, size, replace = FALSE, prob = NULL)’ for ‘n > 1e7’ and ‘size <= n/2’. This is much faster and uses less memory, but does give different results.
‘approxfun()’ and ‘splinefun()’ now return a wrapper to an internal
function in the ‘stats’ namespace rather than a ‘.C()’ or ‘.Call()’
call. This is more likely to work if the function is saved and used in
a different session.
The functions ‘.C()’, ‘.Call()’, ‘.External()’ and ‘.Fortran()’ now
give an error (rather than a warning) if called with a named first
argument.
‘Sweave()’ by default now reports the locations in the source file(s)
of each chunk.
‘clearPushBack()’ is now a documented interface to a long-existing
internal call.
‘aspell()’ gains filters for R code, Debian Control Format and message
catalog files, and support for R level dictionaries. In addition,
package ‘utils’ now provides functions ‘aspell_package_R_files()’ and
‘aspell_package_C_files()’ for spell checking R and C level message
strings in packages.
‘bibentry()’ gains some support for “incomplete” entries with a
‘crossref’ field.
‘gray()’ and ‘gray.colors()’ finally allow ‘alpha’ to be specified.
‘monthplot()’ gains parameters to control the look of the reference
lines. (Suggestion of Ian McLeod.)
Added support for new ‘%~%’ relation (“is distributed as”) in plotmath.
‘domain = NA’ is accepted by ‘gettext()’ and ‘ngettext()’, analogously
to ‘stop()’ etc.
‘termplot()’ gains a new argument ‘plot = FALSE’ which returns
information to allow the plots to be modified for use as part of other
plots, but does not plot them. (Contributed by Terry Therneau,
PR#15076.)
‘quartz.save()’, formerly an undocumented part of ‘R.app’, is now
available to copy a device to a ‘quartz()’ device. ‘dev.copy2pdf()’
optionally does this for PDF output: ‘quartz.save()’ defaults to PNG.
The default method of ‘pairs()’ now allows ‘text.panel = NULL’ and the
use of ‘<foo>.panel = NULL’ is now documented.
‘setRefClass()’ and ‘getRefClass()’ now return class generator
functions, similar to ‘setClass()’, but still with the reference fields
and methods as before (suggestion of Romain Francois).
New functions ‘bitwNot()’, ‘bitwAnd()’, ‘bitwOr()’ and ‘bitwXor()’,
using the internal interfaces previously used for classes ‘"octmode"’
and ‘"hexmode"’.
Also ‘bitwShiftL()’ and ‘bitwShiftR()’ for shifting bits in elements of integer vectors.
New option ‘"deparse.cutoff"’ to control the deparsing of language
objects such as calls and formulae when printing. (Suggested by a
comment of Sarah Goslee.)
‘colors()’ gains an argument ‘distinct’.
New ‘demo(colors)’ and ‘demo(hclColors)’, with utility functions.
‘list.files()’ (aka ‘dir()’) gains a new optional argument ‘no..’ which
allows to exclude ‘"."’ and ‘".."’ from listings.
Multiple time series are also of class ‘"matrix"’; consequently,
‘head()’, e.g., is more useful.
‘encodeString()’ preserves UTF-8 marked encodings. Thus if factor
levels are marked as UTF-8 an attempt is made to print them in UTF-8 in
‘RGui’ on Windows.
‘readLines()’ and ‘scan()’ (and hence ‘read.table()’) in a UTF-8 locale
now discard a UTF-8 byte-order-mark (BOM). Such BOMs are allowed but
not recommended by the Unicode Standard: however Microsoft applications
can produce them and so they are sometimes found on websites.
The encoding name ‘"UTF-8-BOM"’ for a connection will ensure that a UTF-8 BOM is discarded.
‘mapply(FUN, a1, ..)’ now also works when ‘a1’ (or a further such
argument) needs a ‘length()’ method (which the documented arguments
never do). (Requested by Hervé Pagès; with a patch.)
‘.onDetach()’ is supported as an alternative to ‘.Last.lib’. Unlike
‘.Last.lib’, this does not need to be exported from the package's
namespace.
The ‘srcfile’ argument to ‘parse()’ may now be a character string, to
be used in error messages.
The ‘format()’ method for ‘ftable’ objects gains a ‘method’ argument,
propagated to ‘write.ftable()’ and ‘print()’, allowing more compact
output, notably for LaTeX formatting, thanks to Marius Hofert.
The ‘utils::process.events()’ function has been added to trigger
immediate event handling.
‘Sys.which()’ now returns ‘NA’ (not ‘""’) for ‘NA’ inputs (related to
PR#15147).
The ‘print()’ method for class ‘"htest"’ gives fewer trailing spaces
(wish of PR#15124).
Also print output from ‘HoltWinters()’, ‘nls()’ and others.
‘loadNamespace()’ allows a version specification to be given, and this
is used to check version specifications given in the ‘Imports’ field
when a namespace is loaded.
‘setClass()’ has a new argument, ‘slots’, clearer and less ambiguous
than ‘representation’. It is recommended for future code, but should
be back-compatible. At the same time, the allowed slot specification
is slightly more general. See the documentation for details.
‘mget()’ now has a default for ‘envir’ (the frame from which it is
called), for consistency with ‘get()’ and ‘assign()’.
‘close()’ now returns an integer status where available, invisibly.
(Wish of PR#15088.)
The internal method of ‘tar()’ can now store paths too long for the
‘ustar’ format, using the (widely supported) GNU extension. It can
also store long link names, but these are much less widely supported.
There is support for larger files, up to the ‘ustar’ limit of 8GB.
Local reference classes have been added to package ‘methods’. These
are a technique for avoiding unneeded copying of large components of
objects while retaining standard R functional behavior. See
‘?LocalReferenceClasses’.
‘untar()’ has a new argument ‘restore_times’ which if false (not the
default) discards the times in the tarball. This is useful if they are
incorrect (some tarballs submitted to CRAN have times in a local
timezone or many years in the past even though the standard required
them to be in UTC).
‘replayplot()’ cannot (and will not attempt to) replay plots recorded
under R < 3.0.0. It may crash the R session if an attempt is made to
replay plots created in a different build of R >= 3.0.0.
Palette changes get recorded on the display list, so replaying plots
(including when resizing screen devices and using ‘dev.copy()’) will
work better when the palette is changed during a plot.
‘chol(pivot = TRUE)’ now defaults to LAPACK, not LINPACK.
The ‘parse()’ function has a new parameter ‘keep.source’, which
defaults to ‘options("keep.source")’.
Profiling via ‘Rprof()’ now optionally records information at the
statement level, not just the function level.
The ‘Rprof()’ function now quotes function names in in its output file
on Windows, to be consistent with the quoting in Unix.
Profiling via ‘Rprof()’ now optionally records information about time
spent in GC.
The HTML help page for a package now displays non-vignette
documentation files in a more accessible format.
To support ‘options(stringsAsFactors = FALSE)’, ‘model.frame()’,
‘model.matrix()’ and ‘replications()’ now automatically convert
character vectors to factors without a warning.
The ‘print’ method for objects of class ‘"table"’ now detects tables
with 0-extents and prints the results as, e.g., ‘< table of extent 0 x
1 x 2 >’. (Wish of PR#15198.)
Deparsing involving calls to anonymous functions and has been made
closer to reversible by the addition of extra parentheses.
The function ‘utils::packageName()’ has been added as a lightweight
version of ‘methods::getPackageName()’.
‘find.package(lib.loc = NULL)’ now treats loaded namespaces
preferentially in the same way as attached packages have been for a
long time.
In Windows, the Change Directory dialog now defaults to the current
working directory, rather than to the last directory chosen in that
dialog.
‘available.packages()’ gains a ‘"license/restricts_use"’ filter which
retains only packages for which installation can proceed solely based
on packages which are guaranteed not to restrict use.
New ‘check_packages_in_dir()’ function in package ‘tools’ for
conveniently checking source packages along with their reverse
dependencies.
R's completion mechanism has been improved to handle help requests
(starting with a question mark). In particular, help prefixes are now
supported, as well as quoted help topics. To support this, completion
inside quotes are now handled by R by default on all platforms.
There is support for vectors longer than 2^31 - 1 elements on 64-bit
platforms. This applies to raw, logical, integer, double, complex and
character vectors, as well as lists. (Elements of character vectors
remain limited to 2^31 - 1 bytes.)
Not all aspects of such vectors are completely implemented (nor completely tested).
Most operations which can sensibly be done with long vectors now work:
others may return the error ‘long vectors not supported yet’. Most of
these are because they explicitly work with integer indices (e.g.
‘anyDuplicated()’ and ‘match()’) or because of other limits (e.g. of
character strings or matrix dimensions) would be exceeded or the
operations would be extremely slow.
‘length()’ returns a double for long vectors, and lengths can be set to
2^31 or more by the replacement function with a double value.
Most aspects of indexing are available. Generally double-valued
indices can be used to access elements beyond 2^31 - 1.
There is some support for matrices and arrays with each dimension less
than 2^31 but total number of elements more than that. Only some
aspects of matrix algebra work for such matrices, often taking a very
long time. In other cases the underlying Fortran code has an unstated
restriction (as was found for complex ‘svd()’).
‘dist()’ can produce dissimilarity objects for more than 65536 rows
(but for example ‘hclust()’ cannot process such objects).
‘serialize()’ to a raw vector is no longer limited in size (except by
resources) on 64-bit platforms.
The C-level function ‘R_alloc’ can now allocate 2^35 or more bytes on
64-bit platforms.
‘agrep()’ and ‘grep()’ will return double vectors of indices for long
vector inputs.
Many calls to ‘.C()’ have been replaced by ‘.Call()’ to allow long
vectors to be supported (now or in the future). Regrettably several
packages had copied the non-API ‘.C()’ calls and so failed.
‘.C()’ and ‘.Fortran()’ do not accept long vector inputs. This is a
precaution as it is very unlikely that existing code will have been
written to handle long vectors (and the R wrappers often assume that
‘length(x)’ is an integer).
Most of the methods for ‘sort()’ work for long vectors.
‘rank()’, ‘sort.list()’ and ‘order()’ support long vectors (slowly except for radix sorting).
‘sample()’ can do uniform sampling from a long vector.
More use has been made of R objects representing registered entry
points, which is more efficient as the address is provided by the
loader once only when the package is loaded.
This has been done for packages ‘base’, ‘methods’, ‘splines’ and ‘tcltk’: it was already in place for the other standard packages.
Since these entry points are always accessed by the R entry points they do not need to be in the load table which can be substantially smaller and hence searched faster. This does mean that ‘.C’ / ‘.Fortran’ / ‘.Call’ calls copied from earlier versions of R may no longer work - but they were never part of the API.
Many ‘.Call()’ calls in package ‘base’ have been migrated to
‘.Internal()’ calls.
‘solve()’ makes fewer copies, especially when ‘b’ is a vector rather
than a matrix.
‘eigen()’ makes fewer copies if the input has dimnames.
Most of the linear algebra functions make fewer copies when the
input(s) are not double (e.g. integer or logical).
A foreign function call (‘.C()’ etc) in a package without a ‘PACKAGE’
argument will only look in the first DLL specified in the ‘NAMESPACE’
file of the package rather than searching all loaded DLLs. A few
packages needed ‘PACKAGE’ arguments added.
The ‘@<-’ operator is now implemented as a primitive, which should
reduce some copying of objects when used. Note that the operator
object must now be in package ‘base’: do not try to import it
explicitly from package ‘methods’.
The transitional support for installing packages without namespaces
(required since R 2.14.0) has been removed. ‘R CMD build’ will still
add a namespace, but a ‘.First.lib()’ function will need to be
converted.
‘R CMD INSTALL’ no longer adds a namespace (so installation will fail), and a ‘.First.lib()’ function in a package will be ignored (with an installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’ file can still be installed.
Packages can specify in their ‘DESCRIPTION file’ a line like
Biarch: yes
to be installed on Windows with ‘--force-biarch’.
Package vignettes can now be processed by other engines besides
‘Sweave’; see ‘Writing R Extensions’ and the ‘tools::vignetteEngine’
help topic for details.
‘R CMD check’ now gives a warning rather than a note if it finds calls
to ‘abort’, ‘assert’ or ‘exit’ in compiled code, and has been able to
find the ‘.o’ file in which the calls occur.
Such calls can terminate the R process which loads the package.
The location of the build and check environment files can now be
specified by the environment variables ‘R_BUILD_ENVIRON’ and
‘R_CHECK_ENVIRON’, respectively.
‘R CMD Sweave’ gains a ‘--compact’ option to control possibly reducing
the size of the PDF file it creates when ‘--pdf’ is given.
‘R CMD build’ now omits Eclipse's ‘.metadata’ directories, and ‘R CMD
check’ warns if it finds them.
‘R CMD check’ now does some checks on functions defined within
reference classes, including of ‘.Call()’ etc calls.
‘R CMD check --as-cran’ notes assignments to the global environment,
calls to ‘data()’ which load into the global environment, and calls to
‘attach()’.
‘R CMD build’ by default uses the internal method of ‘tar()’ to prepare
the tarball. This is more likely to produce a tarball compatible with
‘R CMD INSTALL’ and ‘R CMD check’: an external ‘tar’ program, including
options, can be specified _via_ the environment variable ‘R_BUILD_TAR’.
‘tools::massageExamples()’ is better protected against packages which
re-define base functions such as ‘cat()’ and ‘get()’ and so can cause
‘R CMD check’ to fail when checking examples.
‘R CMD javareconf’ has been enhanced to be more similar to the code
used by ‘configure’.
There is now a test that a JNI program can be compiled (like ‘configure’ did) and only working settings are used.
It makes use of custom settings from configuration recorded in ‘etc/javaconf’.
The ‘--no-vignettes’ argument of ‘R CMD build’ has been renamed to the
more accurate ‘--no-build-vignettes’: its action has always been to
(re)build vignettes and never omitted them.
‘R CMD check’ accepts ‘--no-build-vignettes’ as a preferred synonym for ‘--no-rebuild-vignettes’.
The C code underlying base graphics has been migrated to the ‘graphics’
package (and hence no longer uses ‘.Internal()’ calls).
Most of the ‘.Internal()’ calls used in the ‘stats’ package have been
migrated to C code in that package.
This means that a number of ‘.Internal()’ calls which have been used by packages no longer exist, including ‘.Internal(cor)’ ‘.Internal(cov)’, ‘.Internal(optimhess)’ and ‘.Internal(update.formula)’.
Some ‘.External()’ calls to the ‘base’ package (really to the R
executable or shared library) have been moved to more appropriate
packages. Packages should not have been using such calls, but some did
(mainly those used by ‘integrate()’).
There is a new function ‘mcaffinity()’ which allows getting or setting
the CPU affinity mask for the current R process on systems that
supports this (currently only Linux has been tested successfully). It
has no effect on systems which do not support process affinity. Users
are not expected to use this function directly (with the exception of
fixing libraries that break affinity settings like OpenBLAS) - the
function is rather intended to support affinity control in high-level
parallel functions. In the future, R may supplement lack of affinity
control in the OS by its own bookkeeping via ‘mcaffinity()’ related to
processes and threads it spawns.
‘mcparallel()’ has a new argument ‘mc.affinity’ which attempts to set
the affinity of the child process according to the specification
contained therein.
The port used by socket clusters is chosen randomly: this should help
to avoid clashes observed when two users of a multi-user machine try to
create a cluster at the same time. To reproduce the previous behaviour
set environment variable ‘R_PARALLEL_PORT’ to ‘10187’.
There has been some minor re-organization of the non-API header files.
In particular, ‘Rinternals.h’ no longer includes the non-API header
‘R_exts/PrtUtil.h’, and that no longer includes ‘R_exts/Print.h’.
Passing ‘NULL’ to ‘.C()’ is now an error.
‘.C()’ and ‘.Fortran()’ now warn if ‘"single"’ arguments are used with
‘DUP = FALSE’, as changes to such arguments are not returned to the
caller.
C entry points ‘R_qsort’ and ‘R_qsort_I’ now have ‘start’ and ‘end’ as
‘size_t’ to allow them to work with longer vectors on 64-bit platforms.
Code using them should be recompiled.
A few recently added C entry points were missing the remapping to
‘Rf_’, notably ‘[dpq]nbinom_mu’.
Some of the interface pointers formerly available only to ‘R.app’ are
now available to front-ends on all Unix-alikes: one has been added for
the interface to ‘View()’.
‘PACKAGE = ""’ is now an error in ‘.C()’ etc calls: it was always
contrary to the documentation.
Entry point ‘rcont2’ has been migrated to package ‘stats’ and so is no
longer available.
‘R_SVN_REVISION’ in ‘Rversion.h’ is now an integer (rather than a
string) and hence usable as e.g. ‘#if R_SVN_REVISION < 70000’.
The entry points ‘rgb2hsv’ and ‘hsv2rgb’ have been migrated to package
‘grDevices’ and so are no longer available.
‘R_GE_version’ has been increased to ‘10’ and ‘name2col’ removed (use
‘R_GE_str2col’ instead). R internal colour codes are now defined using
the typedef ‘rcolor’.
The ‘REPROTECT’ macro now checks that the protect index is valid.
Several non-API entry points no longer used by R have been removed,
including the Fortran entry points ‘chol’, ‘chol2inv’, ‘cg’, ‘ch’ and
‘rg’, and the C entry points ‘Brent_fmin’, ‘fft_factor’ and ‘fft_work’.
If a ‘.External’ call is registered with a number of arguments (other
than ‘-1’), the number of arguments passed is checked for each call (as
for other foreign function calls).
The management of translations has been converted to R code: see
‘?tools::update_pkg_po’.
The translations for the R interpreter and ‘RGui.exe’ are now part of
the ‘base’ package (rather than having sources in directory ‘po’ and
being installed to ‘share/locale’). Thus the ‘base’ package supports
three translation domains, ‘R-base’, ‘R’ and ‘RGui’.
The compiled translations which ship with R are all installed to the
new package ‘translations’ for easier updating. The first package of
that name found on ‘.libPaths()’ at the start of the R session will be
used. (It is possible messages will be used before ‘.libPaths()’ is
set up in which case the default translations will be used: set
environment variable ‘R_TRANSLATIONS’ to point to the location of the
intended ‘translations’ package to use this right from the start.)
The translations form a separate group in the Windows installer, so can
be omitted if desired.
The markup for many messages has been changed to make them easier to
translate, incorporating suggestions from Łukasz Daniel.
There is again support for building without using the C ‘long double’
type. This is required by C99, but system implementations can be slow
or flawed. Use ‘configure’ option ‘--disable-long-double’.
‘make pdf’ and ‘make install-pdf’ now make and install the full
reference index (including all base and recommended packages).
The 'reference manual' on the Windows GUI menu and included in the
installer is now the full reference index, including all base and
recommended packages.
The Windows installer no longer installs a Start Menu link to the
static help pages; as most pages are generated dynamically, this led to
a lot of broken links.
Any custom settings for Java configuration are recorded in file
‘etc/javaconf’ for subsequent use by ‘R CMD javareconf’.
There is now support for ‘makeinfo’ version 5.0 (which requires a
slightly different ‘.texi’ syntax).
When ‘R CMD build’ is run in an encoding other than the one specified
in the package's ‘DESCRIPTION’ file it tries harder to expand the
‘authors@R’ field in the specified encoding. (PR#14958)
If ‘R CMD INSTALL’ is required to expand the ‘authors@R’ field of the
‘DESCRIPTION’ file, it tries harder to do so in the encoding specified
for the package (rather than using ASCII escapes).
Fix in package ‘grid’ for pushing a viewport into a layout cell, where
the layout is within a viewport that has zero physical width OR where
the layout has zero total relative width (likewise for height). The
layout column widths (or row heights) in this case were being
calculated with non-finite values. (Reported by Winston Chang.)
‘solve(A, b)’ for a vector ‘b’ gave the answer names from ‘colnames(A)’
for ‘LINPACK = TRUE’ but not in the default case.
‘La.svd()’ accepts logical matrices (as documented, and as ‘svd()’
did).
‘legend()’ now accepts negative ‘pch’ values, in the same way
‘points()’ long has.
Parse errors when installing files now correctly display the name of
the file containing the bad code.
In Windows, tcltk windows were not always properly constructed.
(PR#15150)
The internal functions implementing ‘parse()’, ‘tools::parseLatex()’
and ‘tools::parse_Rd()’ were not reentrant, leading to errors in rare
circumstances such as a garbage collection triggering a recursive call.
Field assignments in reference class objects via ‘$<-’ were not being
checked because the magic incantation to turn methods on for that
primitive operator had been inadvertently omitted.
‘setHook(hookname, value, action="replace")’ set the hook to be the
value, rather than a list containing the value as documented.
(PR#15167)
If a package used a ‘NEWS.Rd’ file, the main HTML package index page
did not link to it. (Reported by Dirk Eddelbuettel.)
The primitive implementation of ‘@<-’ was not checking the class of the
replacement. It now does a check, quicker but less general than
‘slot<-’. See the help.
‘split(x, f)’ now recycles classed objects ‘x’ in the same way as
vectors. (Reported by Martin Morgan.)
‘pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)’ is no longer
‘-Inf’; ditto for corresponding ‘pt()’ and ‘pf()’ calls, such as
‘pt(45, df=5000, lower.tail=FALSE, log.p=TRUE)’. (PR#15162)
The ‘ENCODING’ argument to ‘.C()’ is defunct. Use ‘iconv()’ instead.
The ‘.Internal(eval.with.vis)’ non-API function has been removed.
Support for the converters for use with ‘.C()’ has been removed,
including the oft misused non-API header ‘R_ext/RConverters.h’.
The previously deprecated uses of ‘array()’ with a 0-length ‘dim’
argument and ‘tapply()’ with a 0-length ‘INDEX’ list are now errors.
Calling ‘rep()’ or ‘rep.int()’ on a pairlist or other non-vector object
is now an error.
Several non-API entry points have been transferred to packages (e.g.
‘R_zeroin2’) or replaced by different non-API entry points (e.g.
‘R_tabulate’).
The ‘internal’ graphics device invoked by ‘.Call("R_GD_nullDevice",
package = "grDevices")’ has been removed: use ‘pdf(file = NULL)’
instead.
The ‘.Fortran()’ entry point ‘"dqrls"’ which has not been used by R
since version 2.15.1 is no longer available.
Functions ‘traceOn()’ and ‘traceOff()’ in package ‘methods’ are now
defunct.
Function ‘CRAN.packages()’ is finally defunct.
Use of ‘col2rgb(0)’ is defunct: use ‘par("bg")’ or ‘NA’ instead.
The long-defunct functions ‘Rd_parse()’, ‘anovalist.lm()’,
‘categpry()’, ‘clearNames()’, ‘gammaCody()’, ‘glm.fit.null()’,
‘lm.fit.null()’, ‘lm.wfit.null()’, ‘manglePackageNames()’,
‘mauchley.test()’, ‘package.contents()’, ‘print.coefmat()’,
‘reshapeLong()’, ‘reshapeWide()’, ‘tkclose()’, ‘tkcmd()’,
‘tkfile.dir()’, ‘tkfile.tail()’, ‘tkopen()’, ‘tkputs()’, ‘tkread()’,
‘trySilent()’ and ‘zip.file.extract()’ have been removed entirely (but
are still documented in the help system).
The unused ‘dataPath’ argument to ‘attachNamespace()’ has been removed.
‘grid.prompt()’ has been removed: use ‘devAskNewPage()’ instead.
The long-deprecated ‘intensities’ component is no longer returned by
‘hist()’.
‘mean()’ for data frames and ‘sd()’ for data frames and matrices are
defunct.
The ‘keep.source’ argument to ‘library()’ and ‘require()’ is defunct.
This option needs to be set at install time.
Documentation for ‘real()’, ‘as.real()’ and ‘is.real()’ has been moved
to ‘defunct’ and the functions removed.
The ‘maxRasters’ argument of ‘pdf()’ (unused since R 2.14.0) has been
removed.
The unused ‘fontsmooth’ argument has been removed from the ‘quartz()’
device.
All the (non-API) EISPACK entry points in R have been removed.
‘.find.package()’ and ‘.path.package()’ are deprecated: only the public
versions without the dot have ever been in the API.
‘.find.package()’ and ‘.path.package()’ are defunct: only the public versions without the dot have ever been in the API.
‘chol(pivot = FALSE, LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’, ‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK = TRUE)’ no longer warn that LAPACK will be used.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files has been removed.
R's completion mechanism has been improved to handle help requests (starting with a question mark). In particular, help prefixes are now supported, as well as quoted help topics. To support this, completion inside quotes are now handled by R by default on all platforms.
‘pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)’ is no longer ‘-Inf’; ditto for corresponding ‘pt()’ and ‘pf()’ calls, such as ‘pt(45, df=5000, lower.tail=FALSE, log.p=TRUE)’. (PR#15162)
‘available.packages()’ gains a ‘"license/restricts_use"’ filter which retains only packages for which installation can proceed solely based on packages which are guaranteed not to restrict use.
New ‘check_packages_in_dir()’ function in package ‘tools’ for conveniently checking source packages along with their reverse dependencies.
In Windows, the Change Directory dialog now defaults to the current working directory, rather than to the last directory chosen in that dialog.
All the (non-API) EISPACK entry points in R have been removed.
The ‘--no-vignettes’ argument of ‘R CMD build’ has been renamed to the more accurate ‘--no-build-vignettes’: its action has always been to (re)build vignettes and never omitted them.
‘R CMD check’ accepts ‘--no-build-vignettes’ as a preferred synonym for ‘--no-rebuild-vignettes’.
On Windows, ‘basename()’, ‘dirname()’ and ‘file.choose()’ have more support for long non-ASCII file names with 260 or more bytes when expressed in UTF-8.
‘find.package(lib.loc = NULL)’ now treats loaded namespaces preferentially in the same way as attached packages have been for a long time.
‘.find.package()’ and ‘.path.package()’ are deprecated: only the public versions without the dot have ever been in the API.
The function ‘utils::packageName()’ has been added as a lightweight version of ‘methods::getPackageName()’.
All the (non-API) EISPACK entry points in R except ‘rs’ have been removed: that is liable to be removed at any time.
This is formal notice that the non-API EISPACK entry points in R will be removed shortly.
Expressions involving user defined operators were not always deparsed faithfully. (PR#15179)
There is now support for ‘makeinfo’ version 5.0 (which requires a slightly different ‘.texi’ syntax).
The ‘tcltk’ namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child from package ‘parallel’ (as in e.g. ‘mclapply()’).
On unix ‘Rscript’ will pass the ‘r_arch’ setting it was compiled with on to the R process so that the architecture of ‘Rscript’ and that of R will match unless overridden.
The long-defunct functions ‘Rd_parse()’, ‘anovalist.lm()’, ‘categpry()’, ‘clearNames()’, ‘gammaCody()’, ‘glm.fit.null()’, ‘lm.fit.null()’, ‘lm.wfit.null()’, ‘manglePackageNames()’, ‘mauchley.test()’, ‘package.contents()’, ‘print.coefmat()’, ‘reshapeLong()’, ‘reshapeWide()’, ‘tkclose()’, ‘tkcmd()’, ‘tkfile.dir()’, ‘tkfile.tail()’, ‘tkopen()’, ‘tkputs()’, ‘tkread()’, ‘trySilent()’ and ‘zip.file.extract()’ have been removed entirely (but are still documented in the help system).
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files will be removed in R 3.1.0.
The ‘maxRasters’ argument of ‘pdf()’ (unused since R 2.14.0) has been removed.
The unused ‘fontsmooth’ argument has been removed from the ‘quartz()’ device.
‘split(x, f)’ now recycles classed objects ‘x’ in the same way as vectors. (Reported by Martin Morgan.)
The long-defunct functions ‘Rd_parse()’, ‘anovalist.lm()’, ‘clearNames()’, ‘gammaCody()’, ‘glm.fit.null()’, ‘lm.fit.null()’, ‘lm.wfit.null()’, ‘manglePackageNames()’, ‘mauchley.test()’, ‘package.contents()’, ‘print.coefmat()’, ‘reshapeLong()’, ‘reshapeWide()’, ‘tkclose()’, ‘tkcmd()’, ‘tkfile.dir()’, ‘tkfile.tail()’, ‘tkopen()’, ‘tkputs()’, ‘tkread()’, ‘trySilent()’ and ‘zip.file.extract()’ have been removed entirely (but are still documented in the help system).
‘chol(pivot = TRUE, LINPACK = TRUE)’ is deprecated.
The long deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files will be removed in R 3.1.0.
‘lgamma(x)’ for very small ‘x’ (in the denormalized range) is no longer
‘Inf’ with a warning.
‘image()’ now sorts an unsorted ‘breaks’ vector, with a warning.
The internal methods for ‘tar()’ and ‘untar()’ do a slightly more
general job for ‘ustar’-style handling of paths of more than 100 bytes.
Packages ‘compiler’ and ‘parallel’ have been added to the reference
index (‘refman.pdf’).
‘untar(tar = "internal")’ has some support for ‘pax’ headers as
produced by e.g. ‘gnutar --posix’ (which seems prevalent on OpenSUSE
12.2) or ‘bsdtar --format pax’, including long path and link names.
‘sQuote()’ and ‘dQuote()’ now handle 0-length inputs. (Suggestion of
Ben Bolker.)
‘summaryRprof()’ returns zero-row data frames rather than throw an
error if no events are recorded, for consistency.
The included version of PCRE has been updated to 8.32.
The ‘tcltk’ namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child (as in e.g. ‘mclapply()’.
The default for ‘TAR’ on Windows for ‘R CMD build’ has been changed to
be ‘internal’ if no ‘tar’ command is on the path.
This enables most packages to be built ‘out of the box’ without ‘Rtools’: the main exceptions are those which need to be installed to re-build vignettes and need ‘Rtools’ for installation (usually because they contain compiled code).
On a 64-bit Windows platform with enough RAM, ‘R_alloc’ can now
allocate up to just under 32GB like other 64-bit platforms.
Use of ‘col2rgb(0)’ is deprecated (see the help page for its
limitations).
The deprecated ‘intensities’ component returned by ‘hist()’ is no
longer recognized by the ‘plot()’ method and will be removed in R
3.0.0.
‘real()’, ‘as.real()’ and ‘is.real()’ are now formally deprecated and
give a warning.
The ‘configure’ tests for Objective C and Objective C++ now work on Mac
OS 10.8 with Xcode 4.5.2 (PR#15107).
The cairo-based versions of ‘X11()’ now work with current versions of
cairographics (e.g. 1.12.10). (PR#15168)
A workaround for earlier versions of R is to use ‘X11.options(type = "nbcairo")’.
Configuration and ‘R CMD javareconf’ now come up with a smaller set of
library paths for Java on Oracle-format JDK (including OpenJDK). This
helps avoid conflicts between libraries (such as ‘libjpeg’) supplied in
the JDK and system libraries. This can always be overridden if needed:
see the ‘R Installation and Administration’ manual.
‘beta(a, b)’ could overflow to infinity in its calculations when one of
‘a’ and ‘b’ was less than one. (PR#15075)
‘lbeta(a, b)’ no longer gives ‘NaN’ if ‘a’ or ‘b’ is very small (in the
denormalized range).
‘bquote()’ is now able to substitute default arguments in
single-argument functions. (PR#15077)
‘browseEnv(html = FALSE)’ would segfault if called from R (not ‘R.app’)
on a CRAN-style Mac OS X build of R.
‘[[<-’ for lists (generic vectors) needed to increment ‘NAMED’ count
when RHS is used more than once. (PR#15098)
On Windows, warnings about opening a file or pipe with a non-ASCII
description were sometimes output in UTF-8 rather than in the current
locale's character set.
The ‘call()’ function did not duplicate its arguments. (PR#15115)
‘TukeyHSD()’ could give ‘NA’ results with some ‘na.action’ methods such
as ‘na.exclude()’. (Hinted at on R-help by John Fox.)
The deprecated ‘svd(X, LINPACK = TRUE)’ could alter ‘X’ in R 2.15.[12].
(Reported by Bill Dunlap.)
Under Windows, ‘file.link()’ and ‘file.symlink()’ used the link name
twice, so would always fail. (Reported by Rui Barradas/Oliver Soong).
‘summaryRprof(memory = "both")’ mixed up the units of Vcells and
Ncells: it now works in bytes. (PR#15138)
‘tools::Rd2HTML()’ would sometimes delete text. (PR#15134)
‘plot()’ failed for ‘"table"’ objects containing just one entry.
(PR#15118)
‘embedFonts()’ needed to quote some filepaths. (PR#15149)
‘parallel::mccollect()’ handled ‘NULL’ returns incorrectly (removing
the element rather than setting it to ‘NULL’).
The full reference index (‘fullrefman.pdf’) was missing packages
‘compiler’ and ‘parallel’.
The report for ‘optim(method = "L-BFGS-B", control = list(trace = 1))’
reported the last completed and not the current iteration, unlike other
methods and trace levels. (PR#15103)
‘qt(1e-12, 1.2)’ no longer gives ‘NaN’.
‘dt(1e160, 1.2, log=TRUE)’ no longer gives ‘-Inf’.
On Windows the ‘untar()’ function now quotes the directory name when
using an external ‘tar’ utility, so ‘R CMD check’ will handle pathnames
containing spaces.
The version for Windows 8 and Windows Server 2012 is now displayed by
‘win.version()’. (Reported by Gabor Grothendieck.)
The custom Windows installer target ‘myR’ in the installer ‘Makefile’
did not work in 2.15.2. (Reported by Erich Neuwirth.)
‘aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), "A")’ no longer
segfaults.
Expressions involving user defined operators were not always deparsed
faithfully (PR#15179).
The ‘enc2utf8()’ function converted ‘NA_character_’ to ‘"NA"’ in
non-UTF-8 locales. (PR#15201)
The ‘exclude’ argument to ‘xtabs()’ was ignored for ‘"factor"’
arguments.
On Windows, work around an event-timing problem when the RGui console
was closed from the ‘X’ control and the closure cancelled. (This would
on some 64-bit systems crash R, typically those with a slow GPU
relative to the CPU.)
‘lgamma(x)’ for very small ‘x’ (in the denormalized range) is no longer ‘Inf’ with a warning.
‘image()’ now sorts an unsorted ‘breaks’ vector, with a warning.
The internal methods for ‘tar()’ and ‘untar()’ do a slightly more general job for ‘ustar’-style handling of paths of more than 100 bytes.
Packages ‘compiler’ and ‘parallel’ have been added to the reference index (‘refman.pdf’).
‘untar(tar = "internal")’ has some support for ‘pax’ headers as produced by e.g. ‘gnutar --posix’ (which seems prevalent on OpenSUSE 12.2) or ‘bsdtar --format pax’, including long path and link names.
‘sQuote()’ and ‘dQuote()’ now handle 0-length inputs. (Suggestion of Ben Bolker.)
‘summaryRprof()’ returns zero-row data frames rather than throw an error if no events are recorded, for consistency.
The included version of PCRE has been updated to 8.32.
The ‘tcltk’ namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child from package ‘parallle’ (as in e.g. ‘mclapply()’.
‘parallel::makeCluster()’ recognizes the value ‘random’ for the environment variable ‘R_PARALLEL_PORT’: this chooses a random value for the port and reduces the chance of conflicts when multiple users start a cluster at the same time.
The default for ‘TAR’ on Windows for ‘R CMD build’ has been changed to be ‘internal’ if no ‘tar’ command is on the path.
This enables most packages to be built ‘out of the box’ without ‘Rtools’: the main exceptions are those which need to be installed to re-build vignettes and need ‘Rtools’ for installation (usually because they contain compiled code).
On a 64-bit Windows platform with enough RAM, ‘R_alloc’ can now allocate up to just under 32GB like other 64-bit platforms.
Use of ‘col2rgb(0)’ is deprecated (see the help page for its limitations).
The deprecated ‘intensities’ component returned by ‘hist()’ is no longer recognized by the ‘plot()’ method and will be removed in R 3.0.0.
‘real()’, ‘as.real()’ and ‘is.real()’ are now formally deprecated and give a warning.
The ‘configure’ tests for Objective C and Objective C++ now work on Mac OS 10.8 with Xcode 4.5.2 (PR#15107).
The cairo-based versions of ‘X11()’ now work with current versions of cairographics (e.g. 1.12.10). (PR#15168)
A workaround for earlier versions of R is to use ‘X11.options(type = "nbcairo")’.
Configuration and ‘R CMD javareconf’ now come up with a smaller set of library paths for Java on Oracle-format JDK (including OpenJDK). This helps avoid conflicts between libraries (such as ‘libjpeg’) supplied in the JDK and system libraries. This can always be overridden if needed: see the ‘R Installation and Administration’ manual.
‘beta(a, b)’ could overflow to infinity in its calculations when one of ‘a’ and ‘b’ was less than one. (PR#15075)
‘lbeta(a, b)’ no longer gives ‘NaN’ if ‘a’ or ‘b’ is very small (in the denormalized range).
‘bquote()’ is now able to substitute default arguments in single-argument functions. (PR#15077)
‘browseEnv(html = FALSE)’ would segfault if called from R (not ‘R.app’) on a CRAN-style Mac OS X build of R.
‘[[<-’ for lists (generic vectors) needed to increment ‘NAMED’ count when RHS is used more than once. (PR#15098)
On Windows, warnings about opening a file or pipe with a non-ASCII description were sometimes output in UTF-8 rather than in the current locale's character set.
The ‘call()’ function did not duplicate its arguments. (PR#15115)
‘TukeyHSD()’ could give ‘NA’ results with some ‘na.action’ methods such as ‘na.exclude()’. (Hinted at on R-help by John Fox.)
The deprecated ‘svd(X, LINPACK = TRUE)’ could alter ‘X’ in R 2.15.[12]. (Reported by Bill Dunlap.)
Under Windows, ‘file.link()’ and ‘file.symlink()’ used the link name twice, so would always fail. (Reported by Rui Barradas/Oliver Soong).
‘summaryRprof(memory = "both")’ mixed up the units of Vcells and Ncells: it now works in bytes. (PR#15138)
‘tools::Rd2HTML()’ would sometimes delete text. (PR#15134)
‘plot()’ failed for ‘"table"’ objects containing just one entry. (PR#15118)
‘embedFonts()’ needed to quote some filepaths. (PR#15149)
‘parallel::mccollect()’ handled ‘NULL’ returns incorrectly (removing the element rather than setting it to ‘NULL’).
The full reference index (‘fullrefman.pdf’) was missing packages ‘compiler’ and ‘parallel’.
The report for ‘optim(method = "L-BFGS-B", control = list(trace = 1))’ reported the last completed and not the current iteration, unlike other methods and trace levels. (PR#15103)
‘qt(1e-12, 1.2)’ no longer gives ‘NaN’.
‘dt(1e160, 1.2, log=TRUE)’ no longer gives ‘-Inf’.
On Windows the ‘untar()’ function now quotes the directory name when using an external ‘tar’ utility, so ‘R CMD check’ will handle pathnames containing spaces.
The version for Windows 8 and Windows Server 2012 is now displayed by ‘win.version()’. (Reported by Gabor Grothendieck.)
The custom Windows installer target ‘myR’ in the installer ‘Makefile’ did not work in 2.15.2. (Reported by Erich Neuwirth.)
‘aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), "A")’ no longer segfaults.
Expressions involving user defined operators were not always deparsed faithfully (PR#15179).
The ‘enc2utf8()’ function converted ‘NA_character_’ to ‘"NA"’ in non-UTF-8 locales. (PR#15201)
The ‘exclude’ argument to ‘xtabs()’ was ignored for ‘"factor"’ arguments.
On Windows, work around an event-timing problem when the RGui console was closed from the ‘X’ control and the closure cancelled. (This would on some 64-bit systems crash R, typically those with a slow GPU relative to the CPU.)
The obsolete use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files will be removed in R 3.1.0.
The port used by socket clusters is chosen randomly: this should help to avoid clashes observed when two users of a multi-user machine try to create a cluster at the same time. To reproduce the previous behaviour set environment variable ‘R_PARALLEL_PORT’ to ‘10187’.
Deparsing involving calls to anonymous functions and has been made closer to reversible by the addition of extra parentheses.
Deparsing involving calls to anonymous functions and formula expressions has been made closer to reversible by the addition of extra parentheses.
The ‘print’ method for objects of class ‘"table"’ now detects tables with 0-extents and prints the results as, e.g., ‘< table of extent 0 x 1 x 2 >’. (Wish of PR#15198.)
The port of socket clusters is chosen randomly: this should help to avoid clashes when two users of a multi-user machine try to create a cluster at the same time.
Expressions involving user defined operators were not always deparsed
faithfully (PR#15179), nor were those involving calls to anonymous
functions (the latter reported by Hadley Wickham).
Expressions involving user defined operators were not always deparsed faithfully (PR#15179).
The long-defunct functions ‘Rd_parse()’, ‘anovalist.lm()’, ‘clearNames()’, ‘gammaCody()’, ‘glm.fit.null()’, ‘lm.fit.null()’, ‘lm.wfit.null()’, ‘manglePackageNames()’, ‘mauchley.test()’, ‘package.contents()’, ‘print.coefmat()’, ‘reshapeLong()’, ‘resapeWide()’, ‘tkclose()’, ‘tkcmd()’, ‘tkfile.dir()’, ‘tkfile.tail()’, ‘tkopen()’, ‘tkputs()’, ‘tkread()’, ‘trySilent()’ and ‘zip.file.extract()’ have been removed entirely (but are still documented in the help system).
Expressions involving user defined operators were not always deparsed faithfully (PR#15179), nor were those involving calls to anonymous functions (the latter reported by Hadley Wickham).
On Windows, work around an event-timing problem when the RGui console was closed from the ‘X’ control and the closure cancelled. (This would on some 64-bit systems crash R, typically those with a slow GPU relative to the CPU.)
‘R CMD javareconf’ has been enhanced to be more similar to the code used by ‘configure’.
There is now a test that a JNI program can be compiled (like ‘configure’ did) and only working settings are used.
It makes use of custom settings from configuration recorded in ‘etc/javaconf’.
Configuration and ‘R CMD javareconf’ now come up with a smaller set of library paths for Java on Oracle-format JDK (including OpenJDK). This helps avoid conflicts between libraries (such as ‘libjpeg’) supplied in the JDK and system libraries. This can always be overridden if needed: see the ‘R Installation and Administration’ manual.
The print method for objects of class ‘"table"’ now detects tables with 0-extents and prints the results as, e.g., ‘< table of extent 0 x 1 x 2 >’. (Wish of PR#15198.)
‘R CMD javareconf’ has been enhanced to be more similar to the code used by ‘configure’.
There is now a test that a JNI program can be compiled (like ‘configure’ did) and only working settings are used.
It makes use of custom settings from configuration in ‘etc/javaconf’.
Any custom settings for Java configuration are recorded in file ‘etc/javaconf’ for subsequent use by ‘R CMD javareconf’.
The ‘exclude’ argument to ‘xtabs()’ was ignored for ‘"factor"’ arguments.
To support ‘options(stringsAsFactors = FALSE)’, ‘model.frame()’, ‘model.matrix()’ and ‘replications()’ now automatically convert character vectors to factors without a warning.
The ‘enc2utf8()’ function converted ‘NA_character_’ to ‘"NA"’ in non-UTF-8 locales. (PR#15201)
Documentation for ‘real()’, ‘as.real()’ and ‘is.real()’ has been moved to ‘defunct’ and the functions removed.
‘R CMD check --as-cran’ notes assignments to the global environment, calls to ‘data()’ which load into the global environment, and calls to ‘attach()’.
The ‘tcltk’ namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child (as in e.g. ‘mclapply()’.
The ‘tcltk’ namespace can now be re-loaded after unloading on Unix-alike.
The Tcl/Tk event loop is inhibited in a forked child (as in e.g. ‘mclapply()’.
The ‘@<-’ operator is now implemented as a primitive, which should reduce some copying of objects when used. Note that the operator object must now be in package ‘base’: do not try to import it explicitly from package ‘methods’.
The primitive implementation of ‘@<-’ was not checking the class of the replacement. It now does a check, quicker but less general than ‘slot<-’. See the help.
The HTML help page for a package now displays non-vignette documentation files in a more accessible format.
Documentation for ‘real()’, ‘as.real()’ and ‘is.real()’ has been moved to ‘defunct’: the functions will be removed before release.
Package vignettes can now be processed by other engines besides ‘Sweave’; see ‘Writing R Extensions’ and the ‘tools::vignetteEngine’ help topic for details.
‘tools::massageExamples()’ is better protected against packages which re-define base functions such as ‘cat()’ and ‘get()’ and so can cause ‘R CMD check’ to fail when checking examples.
Profiling via ‘Rprof()’ now optionally records information about time spent in GC.
The included version of PCRE has been updated to 8.32.
It is intended that this version will be released as R 3.0.0.
Packages need to have been installed under this version of R.
‘setClass()’ has a new argument, ‘slots’, clearer and less ambiguous than ‘representation’. It is recommended for future code, but should be back-compatible. At the same time, the allowed slot specification is slightly more general. See the documentation for details.
The internal method of ‘tar()’ can now store paths too long for the ‘ustar’ format, using the (widely supported) GNU extension. It can also store long link names, but these are much less widely supported. There is support for larger files, up to the ‘ustar’ limit of 8GB.
If a ‘.External’ call is registered with a number of arguments (other than ‘-1’), the number of arguments passed is checked for each call (as for other foreign function calls).
When ‘R CMD build’ is run in an encoding other than the one specified in the package's ‘DESCRIPTION’ file it tries harder to expand the ‘authors@R’ field in the specified encoding. (PR#14958)
Expressions involving user defined operators were not always deparsed faithfully. (PR#15179)
‘qgeom()’ could return ‘-1’ for extremely small ‘q’. (PR#14967)
‘smooth.spline()’ used ‘DUP = FALSE’ which allowed its compiled C code to change the function: this was masked by the default byte-compilation. (PR#14965)
On OS X, the Quartz versions of the bitmap devices did not respect ‘antialias = "none"’. (PR#15006)
The detection of the C stack direction is better protected against compiler optimization. (PR#15011)
Long custom line types would sometimes segfault on the cairographics-based devices. (PR#15055)
Closed the ‘<li>’ tag in pages generated by ‘ Rd2HTML()’. (PR#14841)
Axis tick marks could go out of range when a log scale was used. (PR#14833)
If a ‘.External’ call is registered with a number of arguments (other than ‘-1’), this is checked.
The cairo-based versions of ‘X11()’ now work with current versions of cairographics (e.g. 1.12.10). (PR#15168)
A workaround for earlier versions of R is to use ‘X11.options(type = "nbcairo")’.
The ‘configure’ tests for Objective C and Objective C++ now work on Mac OS 10.8 with Xcode 4.5.2 (PR#15107).
‘aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), "A")’ no longer segfaults.
The ‘Rprof()’ function now quotes function names in in its output file on Windows, to be consistent with the quoting in Unix.
The version for Windows 8 and Windows Server 2012 is now displayed by ‘win.version()’. (Reported by Gabor Grothendieck.)
The custom Windows installer target ‘myR’ in the installer ‘Makefile’ did not work in 2.15.2. (Reported by Erich Neuwirth.)
Profiling via ‘Rprof()’ now optionally records information at the statement level, not just the function level.
The ‘Rprof()’ function now quotes function names in Windows, consistent with the quoting in Unix.
The ‘parse()’ function has a new parameter ‘keep.source’, which defaults to ‘options("keep.source")’.
The ‘keep.source’ argument to ‘library()’ and ‘require()’ is defunct. This option needs to be set at install time.
Several non-API entry points no longer used by R have been removed, including the Fortran entry points ‘chol’, ‘chol2inv’, ‘cg’, ‘ch’ and ‘rg’, and the C entry points ‘Brent_fmin’, ‘fft_factor’ and ‘fft_work’.
If a package used a ‘NEWS.Rd’ file, the main HTML package index page did not link to it. (Reported by Dirk Eddelbuettel.)
‘setHook(hookname, value, action="replace")’ set the hook to be the value, rather than a list containing the value as documented. (PR#15167)
‘chol(pivot = TRUE)’ now defaults to LAPACK, not LINPACK.
‘chol(pivot = FALSE, LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’, ‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK = TRUE)’ are defunct: LAPACK will be used, with a warning.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is deprecated (the ‘pivot = FALSE’ case has been since R 2.15.2).
‘mean()’ for data frames and ‘sd()’ for data frames and matrices are defunct.
Several non-API entry points no longer used by R have been removed, including the Fortran entry points ‘chol’, ‘chol2inv’, ‘cg’, ‘ch’ and ‘rg’.
The Windows installer no longer installs a Start Menu link to the static help pages; as most pages are generated dynamically, this led to a lot of broken links.
‘summaryRprof()’ returns zero-row data frames rather than throw an error if no events are recorded, for consistency.
‘real()’, ‘as.real()’ and ‘is.real()’ are now formally deprecated and give a warning.
‘summaryRprof()’ returns zero-row data frames rather than tnrow an error if no events are recorded, for consistency.
The default for ‘TAR’ on Windows for ‘R CMD build’ has been changed to be ‘internal’ if no ‘tar’ command is on the path.
This enables most packages to be built ‘out of the box’ without ‘Rtools’: the main exceptions are those which need to be installed to re-build vignettes and need ‘Rtools’ for installation (usually because they contain compiled code).
‘untar()’ has a new argument ‘restore_times’ which if false (not the default) discards the times in the tarball. This is useful if they are incorrect (some tarballs submitted to CRAN have times in a local timezone or many years in the past even though the standard required them to be in UTC).
The long-deprecated ‘intensities’ component is no longer returned by ‘hist()’.
‘mean()’ for data frame and ‘sd()’ for data frames and matrices are defunct.
The deprecated ‘intensities’ component returned by ‘hist()’ is no longer recognized by the ‘plot()’ method and will be removed in R 3.0.0.
‘untar()’ has a new arguemnt ‘restore_times’ which if false (not the default) discards the times in the tarball. This is useful if they are incorrect (some tarballs submitted to CRAN have times in a local timzeone or many years in the past even though the standard required them to be in UTC).
‘replayplot()’ cannot (and will not attempt to) replay plots recorded under R < 3.0.0. It may crash the R session if an attempt is made to replay plots created in a different build of R >= 3.0.0.
Palette changes get recorded on the display list, so replaying plots (including when resizing screen devices and using ‘dev.copy()’) will work better when the palette is changed during a plot.
Local reference classes have been added to package ‘methods’. These are a technique for avoiding unneeded copying of large components of objects while retaining standard R functional behavior. See ‘?LocalReferenceClasses’.
‘grid.prompt()’ has been removed: use ‘devAskNewPage()’ instead.
The ‘@<-’ operator is now implemented as a primitive, which should reduce some copying of objects when used. Note that the operator object must now be in base: do not try to import it explicitly from package ‘methods’. Its validity test has been changed: previously it was that the slot name was part of the class definition: it is now that the slot already exists on the object.
‘sQuote()’ and ‘dQuote()’ now handle 0-length inputs. (Suggestion of Ben Bolker.)
‘untar(tar = "internal")’ has some support for ‘pax’ headers as
produced by e.g. ‘gnutar --posix’ or ‘bsdtar --format pax’, including
long path and link names.
The internal method of ‘tar()’ can now store paths too long for the ‘ustar’ format, using the (widely supported) GNU extension.
Local reference classes are a technique for avoiding unneeded copying of large components of objects while retaining standard R functional behavior. See ‘?LocalReferenceClasses’.
‘untar(tar = "internal")’ has some support for ‘pax’ headers as produced by e.g. ‘gnutar --posix’ (which seems prevalent on OpenSUSE 12.2) or ‘bsdtar --format pax’, including long path and link names.