• ‘R CMD check’ has a new option ‘--as-cran’ to turn on most of the customizations that CRAN uses for its incoming checks.

• For consistency with the ‘logLik()’ method, ‘nobs()’ for ‘"nls"’ files now excludes observations with zero weight. (Reported by Berwin Turlach.)

2.14.2 UTILITIES

• ‘R CMD check’ has a new option ‘-as-cran’ to turn on most of the customizations that CRAN uses for its incoming checks.

2.14.2 BUG FIXES

• For consistency with the ‘logLik()’ method, ‘nobs()’ for ‘"nls"’ files now excludes observations with zero weight. (Reported by Berwin Turlach.)

• The ‘getS3method()’ implementation had an old computation to find an S4 default method.

• ‘R CMD check’ could miss undocumented S4 objects in packages which used S4 classes but did not ‘Depends: methods’ in their ‘DESCRIPTION’ file.

• ‘svg()’ could segfault if called with a non-existent file path. (PR#14790)

• ‘.Primitive()’ could be mis-used to call ‘.Internal()’ entry points.

• ‘R CMD check’ now reports by default on licenses not according to the description in ‘Writing R Extensions’.

• ‘R CMD check’ has a new option ‘-as-cran’ to turn most of the customizations that CRAN uses of their incoming checks.

2.14.2 NEW FEATURES

• ‘R CMD check’ now reports by default on licenses not according to the description in ‘Writing R Extensions’.

2.14.2 BUG FIXES

• ‘.Primitive()’ could be misused to call ‘.Internal()’ entry points.

• ‘format.POSIXlt(x)’ raised an arithmetic exception when ‘x’ was an invalid object of class ‘"POSIXlt"’ and parts were empty.

• ‘installed.packages()’ has some more protection against package installs going on in parallel.

• ‘format.POSIXlt(x)’ raised an arithmetic exception when ‘x’ was an in valid object of class ‘"POSIXlt"’ and parts were empty.

• The internal ‘untar()’ (as used by default by ‘R CMD INSTALL’) now knows about some ‘pax’ headers which ‘bsdtar’ (e.g., the default ‘tar’ for Mac OS >= 10.6) can incorrectly include in ‘tar’ files, and will skip them with a warning.

• PCRE has been upgraded to version 8.21: as well as bug fixes and greater Perl compatibility, this adds a JIT pattern compiler, about which PCRE's news says ‘large performance benefits can be had in many situations’. This is supported on most but not all R platforms.

• Function ‘compactPDF()’ in package ‘tools’ now takes the default for argument ‘gs_quality’ from environment variable ‘GS_QUALITY’: there is a new value ‘"none"’, the ultimate default, which prevents GhostScript being used in preference to ‘qpdf’ just because environment variable ‘R_GSCMD’ is set. If ‘R_GSCMD’ is unset or set to ‘""’, the function will try to find a suitable GhostScript executable.

• The included version of zlib has been updated to 1.2.6.

• ‘R CMD check’ now reports by default on licenses not according to the description in ‘Writing R Extensions’.

2.14.1 patched PACKAGE INSTALLATION

• ‘R CMD INSTALL’ will now no longer install certain file types from ‘inst/doc’: these are almost certainly mistakes and for some packages are wasting a lot of space. These are ‘Makefile’, files generated by running LaTeX, and unless the package uses a ‘vignettes’ directory, PostScript and image bitmap files.

  Note that only PDF vignettes have ever been supported: some of these files come from DVI/PS output from the Sweave defaults prior to R 2.13.0.

2.14.1 patched BUG FIXES

• R configured with ‘--disable-openmp’ would mistakenly set ‘HAVE_OPENMP’ (internal) and ‘SUPPORT_OPENMP’ (in ‘Rconfig.h’) even though no OpenMP flags were populated.

• The ‘getS3method()’ implementation had a very old and incorrect computation to find an S4 default method.

• ‘readLines()’ could overflow a buffer if the last line of the file was not terminated. (PR#14766)

• ‘R CMD check’ could miss undocumented S4 objects in packages which used S4 classes but did not ‘Depends: methods’.

• The HTML Help Search page had malformed links. (PR#14769)

• A couple of instances of lack of protection of ‘SEXP’s have been squashed. (PR#14772, PR#14773)

• ‘image(x, useRaster=TRUE)’ misbehaved on single-column ‘x’. (PR#14774)

• Negative values for ‘options("max.print")’ or the ‘max’ argument to ‘print.default()’ caused crashes. Now the former are ignored and the latter trigger an error. (PR#14779)

• The text of a function body containing more than 4096 bytes was not properly saved by the parser when entered at the console.

• Forgetting the ‘#endif’ tag in an Rd file could cause the parser to go into a loop. (Reported by Hans-Jorg Bibiko.)

• For consistency with the ‘logLik()’ method, ‘nobs()’ for ‘"nls"’ files now excludes observations with zero weight. (Reported by Berwin Turlach.)

• ‘str(*, ....., strict.width="cut")’ now also obeys ‘list.len = n’. (Reported by Sören Vogel.)

• Printing of arrays did not have enough protection (C level), e.g., in the context of ‘capture.output()’. (Reported by Hervé Pagès and Martin Morgan.)

• ‘pdf(file = NULL)’ would produce a spurious file named ‘NA’. (PR#14808)

• ‘list2env()’ did not check the type of its ‘envir’ argument. (PR#14807)

• ‘svg()’ could segfault if called with a non-existent filename. (PR#14790)

• ‘make install’ can install to a path containing ‘+’ characters. (PR#14798)

• The ‘edit()’ function did not respect the ‘options("keep.source")’ setting. (Reported by Cleridy Lennert.)

• ‘predict.lm(*, type="terms", terms=*, se.fit=TRUE)’ did not work. (PR#14817)

• There is a partial workaround for errors in the TRE regular-expressions engine with named classes and repeat counts of at least 2 in a MBCS locale (PR#14408): these are avoided when TRE is in 8-bit mode (e.g. for ‘useBytes = TRUE’ and when all the data are ASCII).

• ‘R_ReplDLLdo1()’ did not call top-level handlers.

• The Quartz device was unable to detect window sessions on Mac OS X 10.7 (Lion) and higher and thus it was not used as the default device on the console. Since Lion any application can use window sessions, so Quartz will now be the default device if user's window session is active and R is not run via ssh which is at least close to the behavior in prior OS X versions.

2.14.2 NEW FEATURES

• The internal ‘untar()’ (as used by default by ‘R CMD INSTALL’) now knows about some ‘pax’ headers which ‘bsdtar’ (e.g., the default ‘tar’ for Mac OS >= 10.6) can incorrectly include in ‘tar’ files, and will skip them with a warning.

• PCRE has been upgraded to version 8.21: as well as bug fixes and greater Perl compatibility, this adds a JIT pattern compiler, about which PCRE's news says ‘large performance benefits can be had in many situations’. This is supported on most but not all R platforms.

• Function ‘compactPDF()’ in package ‘tools’ now takes the default for argument ‘gs_quality’ from environment variable ‘GS_QUALITY’: there is a new value ‘"none"’, the ultimate default, which prevents GhostScript being used in preference to ‘qpdf’ just because environment variable ‘R_GSCMD’ is set. If ‘R_GSCMD’ is unset or set to ‘""’, the function will try to find a suitable GhostScript executable.

• The included version of zlib has been updated to 1.2.6.

• ‘R CMD check’ now reports by default on licenses not according to the description in ‘Writing R Extensions’.

2.14.2 PACKAGE INSTALLATION

• ‘R CMD INSTALL’ will now no longer install certain file types from ‘inst/doc’: these are almost certainly mistakes and for some packages are wasting a lot of space. These are ‘Makefile’, files generated by running LaTeX, and unless the package uses a ‘vignettes’ directory, PostScript and image bitmap files.

  Note that only PDF vignettes have ever been supported: some of these files come from DVI/PS output from the Sweave defaults prior to R 2.13.0.

2.14.2 BUG FIXES

• R configured with ‘--disable-openmp’ would mistakenly set ‘HAVE_OPENMP’ (internal) and ‘SUPPORT_OPENMP’ (in ‘Rconfig.h’) even though no OpenMP flags were populated.

• The ‘getS3method()’ implementation had a very old and incorrect computation to find an S4 default method.

• ‘readLines()’ could overflow a buffer if the last line of the file was not terminated. (PR#14766)

• ‘R CMD check’ could miss undocumented S4 objects in packages which used S4 classes but did not ‘Depends: methods’.

• The HTML Help Search page had malformed links. (PR#14769)

• A couple of instances of lack of protection of ‘SEXP’s have been squashed. (PR#14772, PR#14773)

• ‘image(x, useRaster=TRUE)’ misbehaved on single-column ‘x’. (PR#14774)

• Negative values for ‘options("max.print")’ or the ‘max’ argument to ‘print.default()’ caused crashes. Now the former are ignored and the latter trigger an error. (PR#14779)

• The text of a function body containing more than 4096 bytes was not properly saved by the parser when entered at the console.

• Forgetting the ‘#endif’ tag in an Rd file could cause the parser to go into a loop. (Reported by Hans-Jorg Bibiko.)

• For consistency with the ‘logLik()’ method, ‘nobs()’ for ‘"nls"’ files now excludes observations with zero weight. (Reported by Berwin Turlach.)

• ‘str(*, ....., strict.width="cut")’ now also obeys ‘list.len = n’. (Reported by Sören Vogel.)

• Printing of arrays did not have enough protection (C level), e.g., in the context of ‘capture.output()’. (Reported by Hervé Pagès and Martin Morgan.)

• ‘pdf(file = NULL)’ would produce a spurious file named ‘NA’. (PR#14808)

• ‘list2env()’ did not check the type of its ‘envir’ argument. (PR#14807)

• ‘svg()’ could segfault if called with a non-existent filename. (PR#14790)

• ‘make install’ can install to a path containing ‘+’ characters. (PR#14798)

• The ‘edit()’ function did not respect the ‘options("keep.source")’ setting. (Reported by Cleridy Lennert.)

• ‘predict.lm(*, type="terms", terms=*, se.fit=TRUE)’ did not work. (PR#14817)

• There is a partial workaround for errors in the TRE regular-expressions engine with named classes and repeat counts of at least 2 in a MBCS locale (PR#14408): these are avoided when TRE is in 8-bit mode (e.g. for ‘useBytes = TRUE’ and when all the data are ASCII).

• The C function ‘R_ReplDLLdo1()’ did not call top-level handlers.

• The Quartz device was unable to detect window sessions on Mac OS X 10.7 (Lion) and higher and thus it was not used as the default device on the console. Since Lion any application can use window sessions, so Quartz will now be the default device if the user's window session is active and R is not run via ‘ssh’ which is at least close to the behavior in prior OS X versions.

• ‘mclapply()’ would fail in code assembling the translated error message if some (but not all) cores encountered an error.

• ‘format.POSIXlt(x)’ raised an arithmetic exception when parts of ‘x’ were empty.

• ‘bitmap()’ and ‘dev2bitmap()’ look for ‘gswin64c.exe’ (as used by 64-bit GhostScript), in preference to ‘gswin32c.exe’.

2.14.1 patched INSTALLATION (Windows)

• The sources (and packages) can now be compiled using the multilib toolchain developed for R 2.15.x: see the ‘MULTI’ macro in ‘MkRules.dist’. This toolchain is used for the CRAN binary distribution.

2.14.1 patched PACKAGE INSTALLATION (Windows)

• The preferred toolchain has changed since the one used for R 2.12.0 to 2.14.1: see the‘R Installation and Administration manual’. Compiled code (except DLLs) may be incompatible with previous toolchains (and compiled C++ code almost certainly will be: users of ‘Rcpp’ take care).

  Ensure that the settings in ‘MkRules.local’ are appropriate to the toolchain you use.

• There is a new macro (aka make variable) ‘SHLIB_PTHREAD_FLAGS’. This is set to ‘-pthread’ on builds using toolchains which support it, and should be included in both ‘PKG_CPPFLAGS’ (or the Fortran or F9x equivalents) and ‘PKG_LIBS’.

2.14.1 patched BUG FIXES (Windows)

• Using a prompt of more than 80 characters in ‘readline()’ could cause a buffer overflow in Rterm. (Reported by Henrik Bengtsson.)

2.14.2 NEW FEATURES (Windows)

• ‘bitmap()’ and ‘dev2bitmap()’ look for ‘gswin64c.exe’ (as used by 64-bit GhostScript), in preference to ‘gswin32c.exe’.

2.14.2 INSTALLATION (Windows)

• The sources (and packages) can now be compiled using the multilib toolchain developed for R 2.15.x: see the ‘MULTI’ macro in ‘MkRules.dist’. This toolchain is used for the CRAN binary distribution.

2.14.2 PACKAGE INSTALLATION (Windows)

• The preferred toolchain has changed since the one used for R 2.12.0 to 2.14.1: see the‘R Installation and Administration manual’. Compiled code (except DLLs) may be incompatible with previous toolchains (and compiled C++ code almost certainly will be: users of ‘Rcpp’ take care).

  Ensure that the settings in ‘MkRules.local’ are appropriate to the toolchain you use.

• There is a new macro (aka make variable) ‘SHLIB_PTHREAD_FLAGS’. This is set to ‘-pthread’ on builds using toolchains which support it, and should be included in both ‘PKG_CPPFLAGS’ (or the Fortran or F9x equivalents) and ‘PKG_LIBS’.

2.14.2 BUG FIXES (Windows)

• Using a prompt of more than 80 characters in ‘readline()’ could cause a buffer overflow in Rterm. (Reported by Henrik Bengtsson.)

• Some of the custom messages in the installer were corrupted: add a BOM mark to the file as now required by Unicode Inno Setup. (PR#14816)

• ‘R_ReplDLLdo1()’ did not call top-level handlers.

• The Quartz device was unable to detect window sessions on Mac OS X 10.7 (Lion) and higher and thus it was not used as the default device on the console. Since Lion any application can use window sessions, so Quartz will now be the default device if user's window session is active and R is not run via ssh which is at least close to the behavior in prior OS X versions.

• ‘predict.lm(*, type="terms", terms=*, se.fit=TRUE)’ did not work. (PR#14817)

• There is a partial workaround for errors in the TRE regular-expressions engine with named classes and repeat counts of at least 2 in a MBCS locale (PR#14408): these are avoided when TRE is in 8-bit mode (e.g. for ‘useBytes = TRUE’ and when all the data are ASCII).

• ‘str(*, ....., strict.width="cut")’ now also obeys ‘list.len = n’. (Reported by Sören Vogel.)

• The ‘edit()’ function did not respect the ‘options("keep.source")’ setting. (Reported by Cleridy Lennert.)

• ‘pdf(file = NULL)’ would produce a spurious file named ‘NA’. (PR#14808)

• ‘list2env()’ did not check the type of its ‘envir’ argument. (PR#14807)

• ‘svg()’ could segfault if called with a non-existent filename. (PR#14790)

• ‘make install’ can install to a path containing ‘+’ characters. (PR#14798)

• ‘readLines()’ could overflow a buffer if the last line of the file was not terminated. (PR#14766)

• The text of a function body containing more than 4096 bytes was not properly saved by the parser when entered at the console.

• ‘R CMD check’ now reports by default on licenses not according to the description in ‘Writing R Extensions’.

2.14.1 patched BUG FIXES

• Printing of arrays did not have enough protection (C level), e.g., in the context of ‘capture.output()’. (Reported by Hervé Pagès and Martin Morgan.)

• str(*, ....., strict.width="cut") now also obeys ‘list.len = n’. (Reported by Sören Vogel.)

• The included version of zlib has been updated to 1.2.6.

• str(*, ....., strict.width="cut") now also obeys ‘list.len = n’ (Reported by Sören Vogel.)

• PCRE has been upgraded to version 8.21: as well as bug fixes and greater Perl compatibility, this adds a JIT pattern compiler, about which PCRE's news says ‘large performance benefits can be had in many situations’. This is supported on most but not all R platforms.

• Function ‘compactPDF()’ in package ‘tools’ now takes the default for argument ‘gs_quality’ from environment variable ‘GS_QUALITY’: there is a new value ‘"none"’, the ultimate default, which prevents GhostScript being used in preference to ‘qpdf’ just because environment variable ‘R_GSCMD’ is set. If ‘R_GSCMD’ is unset or set to ‘""’, the function will try to find a suitable GhostScript executable.

• The internal ‘untar()’ (as used by default by ‘R CMD INSTALL’) now knows about some ‘pax’ headers which ‘bsdtar’ (e.g., the default ‘tar’ for Mac OS >= 10.6) can incorrectly include in ‘tar’ files, and will skip them with a warning.

• PCRE has been upgraded to version 8.21: as well as bug fixes and greater Perl compatibility, this adds a JIT pattern compiler, about which PCRE's news says ‘large performance benefits can be had in many situations’.

• Function ‘compactPDF()’ in package ‘tools’ now takes the default for argument ‘gs_quality’ from environment variable ‘GS_QUALITY’: there is a new value ‘"none"’, the ultimate default, which prevents GhostScript being used in preference to ‘qpdf’ just because environment variable ‘R_GSCMD’ is set.

• Using a prompt of more than 80 characters in ‘readline()’ could cause a buffer overflow in Rterm. (Reported by Henrik Bengtsson.)

• Using a prompt of more than 80 characters in ‘readline()’ could cause a buffer overflow in Rterm. (Reported by Henrik Bengtsson.)

2.14.1 patched PACKAGE INSTALLATION (Windows)

• The preferred toolchain has changed since the one used for R 2.12.0 to 2.14.1: see the‘R Installation and Administration manual’. Compiled code (except DLLs) may be incompatible with previous toolchains (and compiled C++ code almost certainly will be: users of ‘Rcpp’ take care).

  Ensure that the settings in ‘MkRules.local’ are appropriate to the toolchain you use.

• There is a new macro (aka make variable) ‘SHLIB_PTHREAD_FLAGS’. This is set to ‘-pthread’ on builds using toolchains which support it, and should be included in both ‘PKG_CPPFLAGS’ (or the Fortran or F9x equivalents) and ‘PKG_LIBS’.

2.14.1 patched INSTALLATION (Windows)

• The sources (and packages) can now be compiled using the multilib toolchain developed for R 2.15.x: see the ‘MULTI’ macro in ‘MkRules.dist’. This toolchain is used for the CRAN binary distribution.

• The internal ‘untar()’ (as used by default by ‘R CMD INSTALL’) now knows about some ‘pax’ headers which ‘bsdtar’ (e.g., the default ‘tar’ for Mac OS >= 10.6) can incorrectly include in ‘tar’ files, and will skip them with a warning.

• PCRE has been upgraded to version 8.21: as well as bug fixes and greater Perl compatibility, this adds a JIT pattern compiler, about which PCRE's news says ‘large performance benefits can be had in many situations’.

2.14.0 NEW FEATURES

• ‘vector(len)’ and ‘length(x) <- len’ no longer accept ‘TRUE’/‘FALSE’ for ‘len’ (not that they were ever documented to, but there was special-casing in the C code).

2.14.0 GRAPHICS DEVICES

• There is a new type ‘X11(type = "dbcairo")’ which updates the screen less frequently: see its help page.

2.13.0 NEW FEATURES

• The internal (C) function ‘scientific()’, at the heart of R's ‘format.info(x)’, ‘format(x)’, ‘print(x)’, etc, for numeric ‘x’, has been re-written in order to provide slightly more correct results, fixing PR#14491, notably in border cases including when ‘digits >= 16’, thanks to substantial contributions (code and experiments) from Petr Savicky. This affects a noticeable amount of numeric output from R.

• There is an additional marked encoding ‘"bytes"’ for character strings. This is intended to be used for non-ASCII strings which should be treated as a set of bytes, and never re-encoded as if they were in the encoding of the current locale: ‘useBytes = TRUE’ is automatically selected in functions such as ‘writeBin()’, ‘writeLines()’, ‘grep()’ and ‘strsplit()’.

  Only a few character operations are supported (such as ‘substr()’).

  Printing, ‘format()’ and ‘cat()’ will represent non-ASCII bytes in such strings by a ‘\xab’ escape.

2.12.2 SIGNIFICANT USER-VISIBLE CHANGES

• Complex arithmetic (notably ‘z^n’ for complex ‘z’ and integer ‘n’) gave incorrect results since R 2.10.0 on platforms without C99 complex support. This and some lesser issues in trigonometric functions have been corrected.

  Such platforms were rare (we know of Cygwin and FreeBSD). However, because of new compiler optimizations in the way complex arguments are handled, the same code was selected on x86_64 Linux with ‘gcc 4.5.x’ at the default ‘-O2’ optimization (but not at ‘-O’).

2.11.1 BUG FIXES

• ‘do.call()’ing ‘NextMethod’ in erroneous ways no longer segfaults. (PR#13487)

2.11.0 SIGNIFICANT USER-VISIBLE CHANGES

• A port to 64-bit Windows is now available as well as binary package repositories: see the ‘R Administration and Installation Manual’.

2.11.0 BUG FIXES

• Internal function ‘matchArgs()’ no longer modifies the general purpose bits of the ‘SEXP’s that make up the formals list of R functions. This fixes an invalid error message that would occur when a garbage collection triggered a second call to ‘matchArgs’ for the same function _via_ a finalizer.

2.10.1 BUG FIXES

• ‘qchisq(p, df, ncp, lower.tail = FALSE)’ with ‘ncp >= 80’ was inaccurate for small ‘p’ (as the help page said): it is now less inaccurate. (In part, PR#13999.)

  For ‘ncp’ less than but close to 80, ‘pchisq()’ and ‘qchisq()’ are more accurate for probabilities very close to 1 (a series expansion was truncated slightly too early).

  ‘pchisq(x, df, ncp)’ can no longer return values just larger than one for large values of ‘ncp’.

• Forgetting the ‘#endif’ tag in an Rd file could cause the parser to go into a loop. (Reported by Hans-Jorg Bibiko.)

• For consistency with the ‘logLik()’ method, ‘nobs()’ for ‘"nls"’ files now excludes observations with zero weight. (Reported by Berwin Turlach.)

• The sources (and packages) can now be compiled using the multilib toolchain recommended for R 2.15.x: see the ‘MULTI’ macro in ‘MkRules.dist’.

2.14.1 BUG FIXES (Windows)

• The fix for PR#14543 caused stack problems with outputting large R objects (e.g. data frames of 25,000 items). (PR#14698)

• ‘R CMD INSTALL’ will now no longer install certain file types from ‘inst/doc’: these are almost certainly mistakes and for some packages are wasting a lot of space. These are ‘Makefile’, files generated by running LaTeX, and unless the package uses a ‘vignettes’ directory, PostScript and image bitmap files.

  Note that only PDF vignettes have ever been supported: some of these files come from DVI/PS output from the Sweave defaults prior to R 2.13.0.

• The text of a function body containing more than 4096 characters was not properly saved by the parser when entered at the console.

• Negative values for ‘options("max.print")’ or the ‘max’ argument to ‘print.default()’ caused crashes. Now the former are ignored and the latter trigger an error. (PR#14779)

• The text of function bodies containing more than 4096 characters were not properly saved by the parser when entered at the console.

• A couple of instances of lack of protection of ‘SEXP’s have been squashed. (PR#14772, PR#14773)

• ‘image(x, useRaster=TRUE)’ misbehaved on single-column ‘x’. (PR#14774)

• ‘R CMD check’ could miss undocumented S4 objects in packages which used S4 classes but did not ‘Depends: methods’.

• The HTML Help Search page had malformed links. (PR#14769)

• ‘readLines()’ could overflow a buffer if the last line was not terminated. (PR#14766)

2.14.0 BUG FIXES

• Several stack trampling and overflow issues have been fixed in TRE, triggered by ‘agrep’ and friends with long patterns. (PR#14627)

2.13.1 NEW FEATURES

• ‘persp(box = TRUE)’ now warns if the surface extends outside the box (since occlusion for the box and axes is computed assuming the box is a bounding box). (PR#202)

• Using a prompt of more than 80 characters in ‘readline()’ could cause a buffer overflow in Rterm. (Reported by Henrik Bengtsson.)

• ‘tempfile()’ on a Unix-alike now takes the process ID into account. This is needed with ‘multicore’ (and as part of ‘parallel’) because the parent and all the children share a session temporary directory, and they can share the C random number stream used to produce the unique part. Further, two children can call ‘tempfile()’ simultaneously.

2.14.1 BUG FIXES

• ‘options(warn = 0)’ failed to end a (C-level) context with more than 50 accumulated warnings. (Spotted by Jeffrey Horner.)

2.14.0 NEW FEATURES

• Automatic printing for reference classes is now done by the ‘$show()’ method. A method is defined for class ‘envRefClass’ and may be overridden for user classes (see the ‘?ReferenceClasses’ example). S4 ‘show()’ methods should no longer be needed for reference classes.

• The body of a closure can be one of further types of R objects, including environments and external pointers.

2.14.0 PACKAGE INSTALLATION

• A dependency on SVN revision is allowed for ‘R’, e.g. ‘R (>= r56550)’. This should be used in conjunction with a version number, e.g. ‘R (>= 2.14.0), R (>= r56550)’ to distinguish between R-patched and R-devel versions with the same SVN revision.

2.13.1 BUG FIXES

• ‘pbirthday()’ and ‘qbirthday()’ did not implement the algorithm exactly as given in their reference and so were unnecessarily inaccurate.

  ‘pbirthday()’ now solves the approximate formula analytically rather than using ‘uniroot()’ on a discontinuous function.

  The description of the problem was inaccurate: the probability is a tail probability (‘2 _or more_ people share a birthday’)

• Rd conversion to latex mishandled multi-line titles (including cases where there was a blank line in the ‘\title’ section). (It seems this happened only in 2.13.0 patched.)

• ‘parallel::detectCores()’ is now able to find the number of physical cores (rather than CPUs) on Sparc Solaris.

  It can also do so on most versions of Windows; however the default remains ‘detectCores(logical = TRUE)’ on that platform.

• Reference classes now keep a record of which fields are locked. ‘$lock()’ with no arguments returns the names of the locked fields.

• ‘HoltWinters()’ reports a warning rather than an error for some optimization failures (where the answer might be a reasonable one).

• ‘tools::dependsOnPkg()’ now accepts the shorthand ‘dependencies = "all"’.

• ‘parallel::clusterExport()’ now allows specification of an environment from which to export.

• The ‘quartz()’ device now does tilde expansion on its ‘file’ argument.

• ‘tempfile()’ on a Unix-alike now takes the process ID into account. This is needed with ‘multicore’ (and as part of ‘parallel’) because the parent and all the children share a session temporary directory, and they can share the C random number stream used to produce the uniaue part. Further, two children can call ‘tempfile()’ simultaneously.

• Option ‘print’ in Sweave's ‘RweaveLatex()’ driver now emulates auto-printing rather than printing (which can differ for an S4 object by calling ‘show()’ rather than ‘print()’).

• ‘filled.contour()’ now accepts infinite values: previously it might have generated invalid graphics files (e.g. containing NaN values).

2.14.1 INSTALLATION

• On 64-bit Linux systems, ‘configure’ now only sets ‘LIBnn’ to ‘lib64’ if ‘/usr/lib64’ exists. This may obviate setting ‘LIBnn’ explicitly on Debian-derived systems.

  It is still necessary to set ‘LIBnn = lib’ (or ‘lib32’) for 32-bit builds of R on a 64-bit OS on those Linux distributions capable for supporting that concept.

• ‘configure’ looks for ‘inconsolata.sty’, and if not found adjusts the default ‘R_RD4PDF’ to not use it (with a warning, since it is needed for high-quality rendering of manuals).

2.14.1 PACKAGE INSTALLATION

• ‘R CMD INSTALL’ will now do a test load for all sub-architectures for which code was compiled (rather than just the primary sub-architecture).

2.14.1 UTILITIES

• When checking examples under more than one sub-architecture, ‘R CMD check’ now uses a separate directory ‘examples_arch’ for each sub-architecture, and leaves the output in file ‘pkgname-Ex_arch.Rout’. Some packages expect their examples to be run in a clean directory ....

2.14.1 BUG FIXES

• ‘stack()’ now gives an error if no vector column is selected, rather than returning a 1-column data frame (contrary to its documentation).

• ‘summary.mlm()’ did not handle objects where the formula had been specified by an expression. (Reported by Helios de Rosario Martinez).

• ‘tools::deparseLatex(dropBraces=TRUE)’ could drop text as well as braces.

• ‘colormodel = "grey"’ (new in R 2.14.0)) did not always work in ‘postscript()’ and ‘pdf()’.

• ‘file.append()’ could return ‘TRUE’ for failures. (PR#14727)

• ‘gzcon()’ connections are no longer subject to garbage collection: it was possible for this to happen when unintended (e.g. when calling ‘load()’).

• ‘nobs()’ does not count zero-weight observations for ‘glm()’ fits, for consistency with ‘lm()’. This affects the ‘BIC()’ values reported for such ‘glm()’ fits. (Spotted by Bill Dunlap.)

• ‘options(warn = 0)’ failed to end a (C-level) context with more than 50 accumulated warnings. (Spotted by Jeffery Horner.)

• The internal ‘plot.default()’ code did not do sanity checks on a ‘cex’ argument, so invalid input could cause problems. (Reported by Ben Bolker.)

• ‘anyDuplicated(<array>, MARGIN=0)’ no longer fails. (Reported by Hervé Pagès.)

• ‘read.dcf()’ removes trailing blanks: unfortunately on some platforms this included ‘\xa0’ (non-breaking space) which is the trailing byte of a UTF-8 character. It now only considers ASCII space and tab to be ‘blank’.

• There was a sign error in part of the calculations for the variance returned by ‘KalmanSmooth()’. (PR#14738)

• ‘pbinom(10, 1e6, 0.01, log.p = TRUE)’ was ‘NaN’ thanks to the buggy fix to PR#14320 in R 2.11.0. (PR#14739)

• ‘RweaveLatex()’ now emulates auto-printing rather than printing, by calling ‘methods::show()’ when auto-printing would.

• ‘duplicated()’ ignored ‘fromLast’ for a one-column data frame. (PR#14742)

• ‘source()’ and related functions did not put the correct timestamp on the source references; ‘srcfilecopy()’ has gained a new argument ‘timestamp’ to support this fix. (PR#14750)

• LaTeX conversion of Rd files did not correctly handle preformatted backslashes. (PR#14751)

• HTML conversion of Rd files did not handle markup within tabular cells properly. (PR#14708)

• ‘source()’ on an empty file with ‘keep.source = TRUE’ tried to read from ‘stdin()’, in R 2.14.0 only. (PR#14753)

• The code to check Rd files in packages would abort if duplicate description sections were present.

2.14.1 patched BUG FIXES

• R configured with ‘--disable-openmp’ would mistakenly set ‘HAVE_OPENMP’ (internal) and ‘SUPPORT_OPENMP’ (in ‘Rconfig.h’) even though no OpenMP flags were populated.

• The ‘getS3method()’ implementation had a very old and incorrect computation to find an S4 default method.

• The ‘Save as’ menu item on the script editor adds extension ‘.R’ to a file name without an extension.

• In package ‘parallel’, ‘detectCores(logical = FALSE)’ makes an OS-dependent attempt to find the number of physical cores. It usually succeeds, even on XP.

2.14.1 PACKAGE INSTALLATION (Windows)

• The directory pointed to by ‘USER_LOCAL’ can now have architecture-specific sub-directories ‘lib/i386’ and ‘lib/x64’.

2.14.1 BUG FIXES (Windows)

• The fix for PR#14543 caused stack problems with outputing large R objects (e.g. data frames of 25,000 items). (PR#14698)

• In a double-byte locale (Chinese, Japanese, Korean), ‘grep()’ and friends might have used byte-wise matching of strings in the native encoding. (PR#14622)

2.14.1 patched NEW FEATURES (Windows)

• ‘bitmap()’ and ‘dev2bitmap()’ look for ‘gswin64c.exe’ (as used by 64-bit GhostScript), in preference to ‘gswin32c.exe’.

• The code to check Rd files in packages would abort if duplicate description sections were present.

• ‘source()’ on an empty file with ‘keep.source = TRUE’ tried to read from ‘stdin()’, in R 2.14.0 only. (PR#14753)

• ‘source()’ and related functions did not put the correct timestamp on the source references; ‘srcfilecopy()’ has gained a new argument ‘timestamp’ to support this fix. (PR#14750)

• LaTeX conversion of Rd files did not correctly handle preformatted backslashes. (PR#14751)

• HTML conversion of Rd files did not handle markup within tabular cells properly. (PR#14708)

• ‘duplicated()’ ignored ‘fromLast’ for a one-column data frame. (PR#14742)

• ‘filled.contour()’ now accepts infinite values: previously it might have generated invalid graphics files (e.g. containing NaN values).

• Option ‘print’ in Sweave's ‘RweaveLatex()’ driver now emulates auto-printing rather than printing (which can differ for an S4 object by calling ‘show()’ rather than ‘print()’).

2.14.0 patched BUG FIXES

• ‘RweaveLatex()’ now emulates auto-printing rather than printing, by calling ‘methods::show()’ when auto-printing would.

• ‘pbinom(10, 1e6, 0.01, log.p = TRUE)’ was ‘NaN’ thanks to the buggy fix to PR#14320 in R 2.11.0. (PR#14739)

• There was a sign error in part of the calculations for the variance returned by ‘KalmanSmooth()’. (PR#14738)

2.14.0 NEW FEATURES

• The ‘"source"’ attribute on functions created with ‘keep.source=TRUE’ has been replaced with a ‘"srcref"’ attribute. The ‘"srcref"’ attribute references an in-memory copy of the source file using the ‘"srcfilecopy"’ class or the new ‘"srcfilealias"’ class.

  *NB:* This means that functions sourced with ‘keep.source = TRUE’ and saved (e.g., by ‘save()’ or ‘readRDS()’) in earlier versions of R will no longer show the original sources (including comments).

• ‘tempfile()’ on a Unix-alike now takes the process ID into account. This is needed with ‘multicore’ (and as part of ‘parallel’) because the parent and all the children share a session temporary directory, and they can share the C random number stream used to produce the uniaue part. Further, two children can call ‘tempfile()’ simultaneously.

• There was sign error in part of the calculations for the variance returned by ‘KalmanSmooth()’. (PR#14738)

• The ‘quartz()’ device now does tilde expansion on its ‘file’ argument.

2.14.0 patched BUG FIXES

• ‘read.dcf()’ removes trailing blanks: unfortunately on some platforms this included ‘\xa0’ (non-breaking space) which is the trailing byte of a UTF-8 character. It now only considers ASCII space and tab to be ‘blank’.

• The internal ‘plot.default()’ code did not do sanity checks on a ‘cex’ argument, so invalid input could cause problems. (Reported by Ben Bolker.)

• ‘tools::dependsOnPkg()’ now accepts the shorthand ‘dependencies = "all"’.

• ‘parallel::clusterExport()’ now allows specification of an environment from which to export.

2.14.0 patched UTILITIES

• When checking examples under more than one sub-architecture, ‘R CMD check’ now uses a separate directory ‘examples_arch’ for each sub-architecture, and leaves the output in file ‘pkgname-Ex_arch.Rout’. Some packages expect their examples to be run in a clean directory ....

• The directory pointed to by ‘USER_LOCAL’ can now have architecture-specific sub-directories ‘lib/i386’ and ‘lib/x64’.

• When checking examples under more than one sub-architecture, ‘R CMD check’ now uses a separate directory ‘examples-arch’ for each sub-architecture, and leaves the output in file ‘pkgname-Ex_arch.Rout’. Some packages expect their examples to be run in a clean directory ....

• ‘R CMD INSTALL’ will now do a test load for all sub-architectures for which code was compiled (rather than just the primary sub-architecture).

2.14.0 patched NEW FEATURES

• ‘parallel::clusterExport’ now allows specification of an environment from which to export.

2.14.0 patched BUG FIXES

• The internal ‘plot.default()’ code did not do sanity checks on ‘cex’, so invalid input could cause problems. (Reported by Ben Bolker.)

• ‘anyDuplicated(<array>, MARGIN=0)’ no longer fails. (Reported by Hervé Pagès.)

• ‘options(warn = 0)’ failed to end a (C-level) context with more than 50 accumulated warnings. (Spotted by Jeffery Horner.)

• The ‘Save as’ menu item on the script editor adds extension ‘.R’ to a file name without an extension.

• In package ‘parallel’, ‘detectCores(logical = FALSE)’ makes an OS-dependent attempt to find the number of physical cores. It usually succeeds, even on XP.

2.14.0 patched BUG FIXES (Windows)

• The fix for PR#14543 caused stack problems with outputing large R objects (e.g. data frames of 25,000 items). (PR#14698)

• In a double-byte locale (Chinese, Japanese, Korean), ‘grep()’ and friends might have used byte-wise matching of strings in the native encoding. (PR#14622)

• ‘options(warn = 0)’ failed to end a (C-level) contest with more than 50 accumulated warnings. (Spotted by Jeffery Horner.)

• ‘nobs()’ does not count zero-weight observations for ‘glm()’ fits, for consistency with ‘lm()’. This affects the ‘BIC()’ values reported for such ‘glm()’ fits. (Spotted by Bill Dunlap.)

• ‘parallel::detectCores()’ is now able to find the number of physical cores (rather than CPUs) on Sparc Solaris.

  It can also do so on most versions of Windows; however the default remains ‘detectCores(logical = TRUE)’ on that platform.

• Reference classes now keep a record of which fields are locked. ‘$lock()’ with no arguments returns the names of the locked fields.

2.14.0 BUG FIXES

• The creation of ticks on log axes (including ‘axTicks()’ sometimes incorrectly omitted a tick at one end

• ‘mapply()’ now gives an explicit error message (rather than an obscure one) if inputs of zero and positive length are mixed.

• On 64-bit Linux systems, ‘configure’ now only sets ‘LIBnn’ to ‘lib64’ if ‘/usr/lib64’ exists. This may obviate setting ‘LIBnn’ explicitly on Debian-derived systems.

  It is still necessary to set ‘LIBnn = lib’ (or ‘lib32’) for 32-bit builds of R on a 64-bit OS on those Linux distributions capable for supporting that concept.

• ‘configure’ looks for ‘inconsolata.sty’, and if not found adjusts the default ‘R_RD4PDF’ to not use it (with a warning, since it is needed for high-quality rendering of manuals).

2.14.0 patched BUG FIXES

• ‘file.append()’ could return ‘TRUE’ for failures. (PR#14727)

• ‘gzcon()’ connections are no longer subject to garbage collection: it was possible for this to happen when unintended (e.g. when calling ‘load()’).

• ‘configure’ looks for ‘inconsolata.sty’, and if not found adjusts the default ‘R_RD4PDF’ to not use it (with a warning, since it is needed for high-quality manuals).

• On 64-bit Linux systems, ‘configure’ now only sets ‘LIBnn’ to ‘lib64’ if ‘/usr/lib64’ exists. This may obviate setting ‘LIBnn’ explicitly on Debian-derived systems.

  It is still necessary to set ‘LIBnn = lib’ (or ‘lib32’)for 32-bit builds of R on a 64-bit OS on those Linux distributions capable for supporting that concept.

2.14.0 patched BUG FIXES

• ‘colormodel = "grey"’ (new in R 2.14.0)) did not always work in ‘postscript()’ and ‘pdf()’.

• ‘HoltWinters()’ reports a warning rather than an error for some optimization failures (where the answer might be a reasonable one).

• Reference classes now keep a record of which fields are locked. ‘\$lock()’ with no arguments returns the names of the locked fields.

• The fix for PR#14543 caused stack problems with outputing large R objects (e.g. data frames of 25,000 items). (PR#14698)

  In a double-byte locale (Chinese, Japanese, Korean), ‘grep()’ and friends might have used byte-wise matching of strings in the native encoding. (PR#14622)

2.14.0 patched NEW FEATURES (Windows)

• In package ‘parallel’, ‘detectCores(logical = FALSE)’ makes an OS-dependent attempt to find the number of physical cores. It usually succeeds, even on XP.

• ‘tools::deparseLatex(dropBraces=TRUE)’ could drop text as well as braces.

• ‘parallel::detectCores()’ is now able to find the number of physical cores (rather than CPUs) on Sparc Solaris.

  It can also do so on recent versions of Windows; however the default remains ‘detectCores(logical = TRUE)’ on that platform.

• The ‘Save as’ menu item on the script editor appends ‘.R’ to a file name without an extension.

• In package ‘parallel’, ‘detectCores(logical = FALSE)’ makes an OS-dependent attempt to find the number of physical cores.

• ‘parallel::detectCores()’ is now able to find the number of physical cores (rather than CPUs) on Sparc Solaris.

  It can also do so on recent versions of Windows (but not Windows XP); however the default remains ‘detectCores(logical = TRUE)’ on that platform.

2.14.0 patched INSTALLATION

• On 64-bit Linux systems, ‘configure’ now only sets ‘LIBnn’ to ‘lib64’ if ‘/usr/lib64’ exists. This may obviate setting ‘LIBnn’ explicitly on Debian-derived systems.

  It is still necessary to set ‘LIBnn = lib’ for 32-bit builds of R on a 64-bit OS on those Linux distributions capable for supporting that concept.

2.14.0 patched BUG FIXES

• ‘stack()’ now gives an error if no vector column is selected, rather than returning a 1-column data frame (contrary to its documentation).

• ‘summary.mlm()’ did not handle objects where the formula had been specified by an expression. (Reported by Helios de Rosario Martinez).

• There are two new options for typesetting PDF manuals from Rd files. These are ‘beramono’ and ‘inconsolata’, and used the named font for monospaced output. They are intended to be used in combination with ‘times’, and ‘times,inconsolata,hyper’ is now the default for the reference manual and package manuals. If you do not have that font installed, you can set ‘R_RD4PF’ to one of the other options: see the ‘R Installation and Administration Manual’.

2.14.0 UTILITIES

• ‘R CMD check’ now checks line-endings of makefiles and C/C++/Fortran sources in subdirectories of ‘src’ as well as in ‘src’ itself.

• It is deprecated to use ‘mean(x)’ and ‘sd(x)’ directly on data frames (or also matrices, for ‘sd’) ‘x’, instead of simply using ‘sapply’.

  In the same spirit, ‘median(x)’ now gives an error for a data frame ‘x’ (it often gave nonsensical results).

2.14.0 BUG FIXES

• Setting a Hershey font family followed by string height query would crash R.

• ‘R CMD javareconf -e’ would fail for some shells due to a shift error. Also the resulting paths will no longer contain ‘$(JAVA_HOME)’ as that can result in an unintended substitution based on ‘Makeconf’ instead of the shell setting.

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use the higher-level API functions in those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’, and links explicitly to ‘multicore’ or ‘snow’ on help pages).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters. This replaces functions like ‘clusterSetupRNG()’ from ‘snow’ (which are not in ‘parallel’).

  The version released for R 2.14.0 contains base functionality: higher-level convenience functions are planned (and some are already available in the ‘R-devel’ version of R).

2.14.0 DEPRECATED AND DEFUNCT

• Using a false value for the ‘DESCRIPTION’ field ‘LazyLoad’ is deprecated.

2.14.0 BUG FIXES

• ‘mapply()’ now gives an explicit error message (rather than an obscure one) is inputs of zero and positive length are mixed.

• ‘socketConnection()’ now has a ‘timeout’ argument. It is now documented that large values (package ‘snow’ used a year) do not work on some OSes.

2.14.0 BUG FIXES

• ‘qgamma()’ for small ‘shape’ underflows to ‘0’ rather than sometimes giving ‘NaN’. (PR#8528, PR#14710)

• All packages must have a namespace, and one is created on installation if not supplied in the sources. This means that any package without a namespace must be re-installed under this version of R (but previously-installed data-only packages without R code can still be used).

2.14.0 NEW FEATURES

• ‘socketConnection()’ now has a ‘timeout’ argument. It is now documented that large values (package ‘snow’ uses a year) do not work on some OSes.

2.14.0 GRAPHICS DEVICES

• The default ‘colormodel’ for ‘pdf()’ and ‘postscript()’ is now called ‘"srgb"’ to more accurately describe it. (Instead of ‘"rgb"’, and in the case of ‘postscript()’ it no longer switches to and from the gray colorspace, by default.)

  The ‘colormodel’ for ‘postscript()’ which does use both gray and sRGB colorspaces is now called ‘"srgb+gray"’.

  Plots which are known to use only black/white/transparent can advantageously use ‘colormodel = "gray"’ (just as before, but there is now slightly more advantage in doing so).

2.14.0 DEPRECATED AND DEFUNCT

• It is eprecated to use ‘mean(x)’ and ‘sd(x)’ directly on data frames (or also matrices, for ‘sd’) ‘x’, instead of simply using ‘sapply’.

  In the same spirit, ‘median(x)’ now gives an error for a data frame ‘x’ (it often gave nonsensical results).

2.14.0 BUG FIXES

• A late change in R 2.13.2 broke ‘\Sexpr’ expressions in Rd files.

• The creation of ticks on log axes (including ‘axTicks()’ sometimes incorrectly omitted a tick at one end

• The creation of ticks on log axes (including by ‘axTicks()’) sometimes incorrectly omitted a tick at one end of the range by rounding error in a platform-dependent way. This could be seen in the examples for ‘axTicks()’, where with axis limits ‘c(0.2, 88)’ the tick for ‘0.2’ was sometimes omitted.

• The ‘X11()’ device's cairo back-end produced incorrect capture snapshot images on big-endian machines.

• ‘loglin()’ gave a spurious error when argument ‘margin’ consisted of a single element of length one. (PR#14690)

• ‘stack()’ and ‘unstack()’ converted character columns to factors.

  ‘unstack()’ sometimes produced incorrect results (a list or a vector) if the factor on which to un-split had only one level.

• Non-blocking listening socket connections continued to report ‘isIncomplete()’ as true even when the peer had closed down and all available input had been read.

• ‘help.search()’ and ‘??’ can now display vignettes and demos as well as help pages. The new option ‘"help.search.types"’ controls the types of documentation and the order of their display.

  This also applies to HTML searches, which now give results in all of help pages, vignettes and demos.

2.14.0 BUG FIXES

• The revised HTML search system now generates better hyperlinks to help topics found: previously it gave problems with help pages with names containing e.g. spaces and slashes.

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use the higher-level API functions in those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’, and links explicitly to ‘multicore’ or ‘snow’ on help pages).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters. This replaces functions like ‘clusterSetupRNG()’ from ‘snow’ (which are not in ‘parallel’).

2.14.0 NEW FEATURES

• Using ‘fix()’ or ‘edit()’ on a R object (except perhaps a matrix or data frame) writes its temporary file with extension ‘.R’ so editors which select their mode based on the extension will select a suitable mode.

2.14.0 INSTALLATION

• Java detection (‘R CMD javareconf’) works around bogus ‘java.library.path’ property in recent Oracle Java binaries.

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use the higher-level API functions in those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters. This replaces functions like ‘clusterSetupRNG()’ from ‘snow’ (which are not in ‘parallel’).

2.14.0 BUG FIXES

• On some systems ‘help(".C", help_type = "pdf")’ and similar generated file names that TeX was unable to handle.

• Non-blocking listening socket connections continued to report ‘isIncomplete’ as true even when the peer had closed down.

• ‘stack()’ and ‘unstack()’ converted character columns to factors. ‘unstack()’ sometimes produced incorrect results (a list or a vector) if the factor on which to un-split had only one level.

• The ‘"table"’ method for ‘Axis()’ hardcoded ‘side = 1’, hence calls to ‘plot(<vector>, <table>)’ labelled the wrong axis. (PR#14699)

• Creating a connection might fail under ‘gctorture(TRUE)’.

• The ‘keep.source’ argument to ‘library()’ and ‘require()’ is deprecated: it was only used for packages installed without lazy-loading, and now all packages are lazy-loaded.

2.14.0 BUG FIXES

• Creating almost any connection would fail under ‘gctorture()’.

• Where both 32- and 64-bit versions of R are installed, the file association for ‘.RData’ files defaults to 64-bit R (it defaulted to 32-bit in R 2.12.x and 2.13.x).

• Reference output for a vignette can be supplied when checking a package by ‘R CMD check’: see ‘Writing R Extensions’.

• Raster drawing on ‘win.metafile()’ (or copying a plot that includes a raster image from another device to a Metafile) now does not crash. (Reported by Stefan Gelissen.)

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters. This replaces functions like ‘clusterSetupRNG()’ from ‘snow’ (which are not in ‘parallel’).

2.14.0 GRAPHICS DEVICES

• The default ‘colormodel’ for ‘pdf()’ and ‘postscript()’ is now called ‘"srgb"’ to more accurately describe it. (Instead of ‘"rgb"’, and in the case of ‘postscript()’ it no longer switches to and from the gray colorspace, by default.)

  The ‘colormodel’ for ‘postscript()’ which does use both gray and sRGB colorspace is now called ‘"srgb+gray"’.

  Plots which are known to use only black/white/transparent can advantageously use ‘colormodel = "gray"’ (just as before, but there is now slightly more advantage in doing so).

• It is deprecated now to use ‘mean(x)’ and ‘sd(x)’ directly on data frames (or also matrices, for ‘sd’) ‘x’, instead of simply using ‘sapply’. In the same spirit, ‘median(x)’ now gives an error for a data frame ‘x’ (it often gave nonsensical results).

• Use of ‘library.dynam()’ without specifying all the first three arguments is deprecated. (It is often called from a namespace, and the defaults are only appropriate to a package.)

  Use of ‘chname’ in ‘library.dynam()’ with the extension ‘.so’ or ‘.dll’ (which is clearly not allowed according to the help page) is deprecated. This also applies to ‘library.dynam.unload()’ and ‘useDynLib’ directives in ‘NAMESPACE’ files.

2.14.0 BUG FIXES

• The ‘"table"’ method for ‘Axis()’ hardcoded ‘side = 1’, hence calls ‘plot(<vector>, <table>)’ labelled the wrong axis. (PR#14699)

• ‘round(x, -Inf)’ now does something sensible (return zero rather than ‘NA’).

• ‘signif(x, -Inf)’ now behaves as documented (‘signif(x, 1)’) rather than giving zero.

• There is a Danish translation of the RGui menus.

• Use of ‘library.dynam()’ without specifying all the first three arguments is deprecated. (It is often called from a namespace, and the defaults are only appropriate to a package.)

  Use of ‘chname’ in ‘library.dynam()’ with the extension ‘.so’ or ‘.dll’ (which is clearly not allowed according to the help page) is deprecated. This also applies to ‘library.dynam.unload()’ and ‘useDynLib’ directives in ‘NAMESPACE’ files.

  It is deprecated now to use ‘mean(x)’ and ‘sd(x)’ directly on data frames (or also matrices, for ‘sd’) ‘x’, instead of simply using ‘sapply’.

  In the same spirit, ‘median(x)’ now gives an error for a data frame ‘x’, rather than often non-sense.

• The (undocumented) inclusion of superclass objects in default initializing of reference classes overwrote explicit field arguments. The bug is fixed, the feature documented and a test added.

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters.

  (It is not yet complete: some enhancements are planned by R 2.14.0.)

• ‘R CMD Rd2dvi’ without the ‘--pdf’ option is now deprecated: only PDF output will be supported in future releases (since this allows the use of fonts only supported for PDF), and only ‘R CMD Rd2pdf’ will be available.

• Use of ‘library.dynam()’ without specifying all the first three arguments is deprecated. (It is often called from a namespace, and the defaults are only appropriate to a package.)

  Use of ‘chname’ in ‘library.dynam()’ with the extension ‘.so’ or ‘.dll’ (which is clearly not allowed according to the help page) is deprecated. This also applies to ‘library.dynam.unload()’ and ‘useDynLib’ directives in ‘NAMESPACE’ files.

2.14.0 BUG FIXES

• ‘HoltWinters()’ checks that the optimization succeeded. (PR#14694)

• The ‘yLineBias’ of the ‘windows()’ family of devices has been changed from 0.1 to 0.2: this changes slightly the vertical positioning of text (including axis annotations). This can be overridden by setting the new ‘"ylbias"’ graphical parameter. This was done for consistency with other devices such as ‘pdf()’.

• ‘R CMD build’ once again attempts to preserve file permissions on Windows.

• There is support for cairographics-based devices using the same code as on Unix-alikes. This can be selected by the new ‘type’ argument of the bitmap devices ‘bmp()’, ‘jpeg()’, ‘png()’ and ‘tiff()’, and devices ‘svg()’, ‘cairo_pdf()’ and ‘cairo_ps()’ are now available on Windows.

  These are not compiled in by default when building from source: see the instructions in the ‘R Installation and Administration Manual’.

• All the Windows-specific graphics devices now have a ‘family’ argument. If non-empty this specifies an initial family to be used for fonts 1-4. If empty the fonts specified in the ‘Rdevga’ configuration file are used for the Windows GDI devices and ‘"sans"’ for cairographics-based devices.

  This will generally be a Windows font name such as ‘"Lucida Bright"’ or one of the device-independent names (‘"sans"’, ‘"serif"’ and ‘"mono"’). Outside Western Europe you may need to select a family that better supports your locale such as ‘"Arial MS Unicode"’ or one specific to Chinese/Korean/Thai ....

• There is a new ‘antialias’ argument to ‘windows()’, ‘win.print()’ and the bitmap devices. This is an option that can be set in ‘windows.options()’ to set the default for ‘windows()’ (and ‘win.graph()’).

  This gives a hint to the Windows plotting system. Whether anti-aliasing is actually used principally depends on the OS settings: this argument should at least be able to turn it off. The default behaviour (unchanged from before) is that Windows will use anti-aliasing for screen devices (and bitmap devices, as they plot on a hidden screen) if ClearType has been enabled. For those not using ClearType, ‘windows.options(antialias = "cleartype")’ will make this the default, and it will probably give more legible plots.

  The argument can also be used for the cairographics-based versions of the bitmap devices.

• The ‘Update packages ...’ menu item now runs ‘update.packages(ask="graphics", checkBuilt=TRUE)’.

• ‘R CMD INSTALL’ preserves the package-directory modification time when it restores an earlier install of the package.

• File extensions ‘.xz’, ‘.rda’ and ‘.RData’ have been added to those which default to binary transfer for ‘download.file()’.

• ‘install.packages()’ and ‘R CMD check’ have a small delay after removing a directory to counteract some interference from anti-virus software.

CHANGES IN R-devel INSTALLATION (Windows)

• Compilation of C and Fortran code now uses the optimization flag ‘-mtune=core2’: this will improve performance a few percent on recent CPUs at the expense of those which are several years old. Its effect is particularly evident on 64-bit builds.

  This can be overridden when building from the sources: see the ‘EOPTS’ macro defined in file ‘MkRules.dist’.

• Where both 32- and 64-bit versions of R are installed, the file association for @file.RData files defaults to 64-bit R (it defaulted to 32-bit in R 2.12.x and 2.13.x).

• There is preliminary support for ‘multilib’ toolchains which use options ‘--m32’ or ‘--m64’ to select the architecture; set the appropriate macros in ‘MkRules.local’.

  It is the intention to move to such a toolchain when they become mature enough.

CHANGES IN R-devel PACKAGE INSTALLATION (Windows)

• ‘Rzlib.dll’ (sometimes used in packages _via_ ‘$(ZLIB_LIBS)’) does not include the buggy gzio interface from zlib 1.2.5.

CHANGES IN R-devel DEFUNCT (Windows)

• zip.unpack() (deprecated in R 2.13.0) is defunct: use ‘unzip()’ instead.

2.14.0 NEW FEATURES (Windows)

• The ‘yLineBias’ of the ‘windows()’ family of devices has been changed from 0.1 to 0.2: this changes slightly the vertical positioning of text (including axis annotations). This can be overridden by setting the new ‘"ylbias"’ graphical parameter. This was done for consistency with other devices such as ‘pdf()’.

• ‘R CMD build’ once again attempts to preserve file permissions on Windows.

• There is support for cairographics-based devices using the same code as on Unix-alikes. This can be selected by the new ‘type’ argument of the bitmap devices ‘bmp()’, ‘jpeg()’, ‘png()’ and ‘tiff()’, and devices ‘svg()’, ‘cairo_pdf()’ and ‘cairo_ps()’ are now available on Windows.

  These are not compiled in by default when building from source: see the instructions in the ‘R Installation and Administration Manual’.

• All the Windows-specific graphics devices now have a ‘family’ argument. If non-empty this specifies an initial family to be used for fonts 1-4. If empty the fonts specified in the ‘Rdevga’ configuration file are used for the Windows GDI devices and ‘"sans"’ for cairographics-based devices.

  This will generally be a Windows font name such as ‘"Lucida Bright"’ or one of the device-independent names (‘"sans"’, ‘"serif"’ and ‘"mono"’). Outside Western Europe you may need to select a family that better supports your locale such as ‘"Arial MS Unicode"’ or one specific to Chinese/Korean/Thai ....

• There is a new ‘antialias’ argument to ‘windows()’, ‘win.print()’ and the bitmap devices. This is an option that can be set in ‘windows.options()’ to set the default for ‘windows()’ (and ‘win.graph()’).

  This gives a hint to the Windows plotting system. Whether anti-aliasing is actually used principally depends on the OS settings: this argument should at least be able to turn it off. The default behaviour (unchanged from before) is that Windows will use anti-aliasing for screen devices (and bitmap devices, as they plot on a hidden screen) if ClearType has been enabled. For those not using ClearType, ‘windows.options(antialias = "cleartype")’ will make this the default, and it will probably give more legible plots.

  The argument can also be used for the cairographics-based versions of the bitmap devices.

• The ‘Update packages ...’ menu item now runs ‘update.packages(ask="graphics", checkBuilt=TRUE)’.

• ‘R CMD INSTALL’ preserves the package-directory modification time when it restores an earlier install of the package.

• File extensions ‘.xz’, ‘.rda’ and ‘.RData’ have been added to those which default to binary transfer for ‘download.file()’.

• ‘install.packages()’ and ‘R CMD check’ have a small delay after removing a directory to counteract some interference from anti-virus software.

2.14.0 INSTALLATION (Windows)

• Compilation of C and Fortran code now uses the optimization flag ‘-mtune=core2’: this will improve performance a few percent on recent CPUs at the expense of those which are several years old. Its effect is particularly evident on 64-bit builds.

  This can be overridden when building from the sources: see the ‘EOPTS’ macro defined in file ‘MkRules.dist’.

• Where both 32- and 64-bit versions of R are installed, the file association for @file.RData files defaults to 64-bit R (it defaulted to 32-bit in R 2.12.x and 2.13.x).

• There is preliminary support for ‘multilib’ toolchains which use options ‘--m32’ or ‘--m64’ to select the architecture; set the appropriate macros in ‘MkRules.local’.

  It is the intention to move to such a toolchain when they become mature enough.

2.14.0 PACKAGE INSTALLATION (Windows)

• ‘Rzlib.dll’ (sometimes used in packages _via_ ‘$(ZLIB_LIBS)’) does not include the buggy gzio interface from zlib 1.2.5.

2.14.0 DEFUNCT (Windows)

• zip.unpack() (deprecated in R 2.13.0) is defunct: use ‘unzip()’ instead.

• All packages must have a namespace, and one is created on installation if not supplied in the sources. This means that any package without a namespace must be re-installed under this version of R (but data-only packages without R code can still be used).

• The ‘yLineBias’ of the ‘X11()’ and ‘windows()’ families of devices has been changed from 0.1 to 0.2: this changes slightly the vertical positioning of text in the margins (including axis annotations). This is mainly for consistency with other devices such as ‘quartz()’ and ‘pdf()’. (Wish of PR#14538.)

  There is a new graphics parameter ‘"ylbias"’ which allows the y-line bias of the graphics device to be tweaked, including to reproduce output from earlier versions of R.

• Labeling of the p-values in various anova tables has been rationalized to be either ‘"Pr(>F)"’ or ‘"Pr(>Chi)"’ (i.e. the ‘"Pr(F)"’, ‘"Pr(Chi)"’ and ‘"P(>|Chi|)"’ variants have been eliminated). Code which extracts the p value _via_ indexing by name may need adjustment.

• ‘::’ can now be used for datasets made available for lazy-loading in packages with namespaces (which makes it consistent with its use for data-only packages without namespaces in earlier versions of R).

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters.

  (It is still incomplete/experimental.)

• Building PDF manuals (for R itself or packages, e.g. _via_ ‘R CMD check’) by default requires the LaTeX package ‘inconsolata’: see the section on ‘Making the manuals’ in the ‘R Installation and Administration Manual’.

• ‘axTicks(*, log=TRUE)’ has changed in some cases to satisfy the documented behavior and be consistent.

CHANGES IN R-devel NEW FEATURES

• ‘txtProgressBar()’ can write to an open connection instead of the console.

• Non-portable package names ending in ‘.’ are no longer allowed. Nor are single-character package names (‘R’ was already disallowed).

• ‘regexpr()’ and ‘gregexpr()’ with ‘perl = TRUE’ allows Python-style named captures. (Wish and contribution of PR#14518.)

• The placement of ‘plotmath’ text in the margins of plots done by base graphics now makes the same vertical adjustment as ordinary text, so using ordinary and plotmath text on the same margin line will seem better aligned (but not exactly aligned, since ordinary text has descenders below the baseline and plotmath places them on the baseline). (Related to PR#14537.)

• ‘sunflowerplot()’ now has a formula interface. (Wish of PR#14541.)

• ‘iconv()’ has a new argument ‘toRaw’ to handle encodings such as ‘UTF-16’ with embedded nuls (as was possible before the ‘CHARSXP’ cache was introduced).

  It will also accept as input the type of list generated with ‘toRaw = TRUE’.

• Garbage-collecting an unused input text connection no longer gives a warning (since it ‘connects’ to nothing outside R).

• ‘read.table()’ and ‘scan()’ have gained a ‘text’ argument, to allow reading data from a (possibly literal) character string.

• ‘optim(*, method = .)’ now allows ‘method = "Brent"’ as an interface to ‘optimize()’, for use in cases such as ‘mle()’ where ‘optim()’ is used internally.

• ‘mosaicplot()’ gains a ‘border’ argument. (Wish of PR#14550.)

• ‘smooth.spline()’ gains a ‘tol’ argument which controls how different ‘x’ values need to be to be treated as distinct. The default has been changed to be more reliable for inputs whose range is small compared to their maximum absolute value. (Wish of PR#14452.)

• ‘gl()’ runs faster by avoiding calling ‘factor()’.

• The ‘print()’ method for ‘object.size()’ accepts ‘B’ as well as ‘b’ as an abbreviation for ‘bytes’.

• ‘unlink()’ gains a ‘force’ argument to work like ‘rm -f’ and if possible override restrictive permissions.

• ‘pbirthday()’ and ‘qbirthday()’ now use exact calculations for ‘coincident = 2’.

• ‘unzip()’ and ‘unz()’ connections have been updated with support for more recent Zip64 features (including large file sizes and ‘bzip2’ compression, but not UTF-8 file names).

  ‘unzip()’ has a new option to restore file times from those recorded (in an unknown timezone) in the zip file.

• ‘update.packages()’ now accepts a character vector of package names for the ‘oldPkgs’ argument. (Suggestion of Tal Galili.)

• The special reference class fields ‘.self’ and ‘.refClassDef’ are now read-only to prevent corrupting the object.

• ‘decompose()’ now returns the original series as part of its value, so it can be used (rather than reconstructed) when plotting. (Suggestion of Rob Hyndman.)

• Rao's efficient score test has been implemented for ‘glm’ objects. Specifically, the ‘add1’, ‘drop1’, and ‘anova’ methods now allow ‘test = "Rao"’.

• If a saved workspace (e.g. ‘.RData’) contains objects that cannot be loaded, R will now start with an warning message and an empty workspace, rather than failing to start.

• ‘strptime()’ now accepts times such as ‘24:00’ for midnight at the end of the day, for although these are disallowed by POSIX 1003.1-2008, ISO 8601:2004 allows them.

• Assignment of ‘names()’ to S4 objects now checks for a corresponding ‘"names"’ slot, and generates a warning or an error if that slot is not defined. See the section on slots in ‘?Classes’.

• The default methods for ‘is.finite()’, ‘is.infinite()’ and ‘is.nan()’ now signal an error if their argument is not an atomic vector.

• The formula method for ‘plot()’ no longer places package ‘stats’ on the search path (it loads the namespace instead).

• There now is a genuine ‘"function"’ method for ‘plot()’ rather than the generic dispatching internally to ‘graphics::plot.function()’. It is now exported, so can be called directly as ‘plot.function()’.

• The one-sided ‘ks.test()’ allows ‘exact = TRUE’ to be specified in the presence of ties (but the approximate calculation remains the default: the ‘exact’ computation makes assumptions known to be invalid in the presence of ties).

• The behaviour of ‘curve(add = FALSE)’ has changed: it now no longer takes the default x limits from the previous plot (if any): rather they default to ‘c(0, 1)’ just as the ‘"function"’ method for ‘plot()’. To get the previous behaviour use ‘curve(add = NA)’, which also takes the default for log-scaling of the x-axis from the previous plot.

• Both ‘curve()’ and the ‘plot()’ method for functions have a new argument ‘xname’ to facilitate plots such as ‘sin(t)’ _vs_ ‘t’.

• The ‘local’ argument to ‘source()’ can specify an environment as well as ‘TRUE’ (‘parent.env()’) and ‘FALSE’ (‘.GlobalEnv’). It gives better error messages for other values, such as ‘NA’.

• ‘vcov()’ gains methods for classes ‘"summary.lm"’ and ‘"summary.glm"’.

• The ‘plot()’ method for class ‘"profile.nls"’ gains ‘ylab’ and ‘lty’ arguments, and passes ‘...’ on to ‘plot.default’.

• Character-string arguments such as the ‘mode’ argument of ‘vector()’, ‘as.vector()’ and ‘is.vector()’ and the ‘description’ argument of ‘file()’ are required to be of length exactly one, rather than any further elements being silently discarded. This helps catch incorrect usage in programming.

• The ‘length’ argument of ‘vector()’ and its wrappers such as ‘numeric()’ is required to be of length exactly one (other values are now an error rather than giving a warning as previously).

• ‘vector(len)’ and ‘length(x) <- len’ no longer acccept ‘TRUE’/‘FALSE’ for ‘len’ (not that they were ever documented to, but there was special-casing in the C code).

• There is a new function ‘Sys.setFileTime()’ to set the time of a file (including a directory). See its help for exactly which times it sets on various OSes.

• The file times reported by ‘file.info()’ are reported to sub-second resolution on systems which support it. (Currently the POSIX 2008 and FreeBSD/Darwin/NetBSD methods are detected.)

• New function ‘getCall(m)’ as an abstraction for ‘m$call’, enabling ‘update()’'s default method to apply more universally. (NB: this can be masked by existing functions in packages.)

• ‘Sys.info()’ gains a ‘euser’ component to report the ‘effective’ user on OSes which have that concept.

• The result returned by ‘try()’ now contains the original error condition object as the ‘"condition"’ attribute.

• All packages with R code are lazy-loaded irrespective of the ‘LazyLoad’ field in the ‘DESCRIPTION’ file. A warning is given if the ‘LazyLoad’ field is overridden.

• ‘Rd’ markup has a new ‘\figure’ tag so that figures can be included in help pages when converted to HTML or LaTeX. There are examples on the help pages for ‘par()’ and ‘points()’.

• The built-in httpd server now allows access to files in the session temporary directory ‘tempdir()’, addressed as the ‘/session’ directory on the httpd server.

• Development versions of R are no longer referred to by the number under which they might be released, e.g. in the startup banner, ‘R --version’ and ‘sessionUtils()’. The correct way to refer to a development version of R is ‘R-devel’, preferably with the date and SVN version number. E.g. ‘R-devel (2011-07-04 r56266)’

• There is a new function ‘texi2pdf()’ in package ‘tools’, currently a convenience wrapper for ‘texi2dvi(pdf = TRUE)’.

• There are two new options for typesetting PDF manuals from Rd files. These are ‘beramono’ and ‘inconsolata’, and used the named font for mononspaced output. They are intended to be used in combination with ‘times’, and ‘times,inconsolata,hyper’ is now the default for the reference manual and package manuals. If you do not have that font installed, you can set ‘R_RD4PF’ to one of the other options: see the ‘R Installation and Administration Manual’.

• Automatic printing for reference classes is now done by the ‘$show()’ method. A method is defined for class ‘envRefClass’ and may be overriden for user classes (see the ‘?ReferenceClasses’ example). S4 ‘show()’ methods should no longer be needed for reference classes.

• ‘tools::Rdiff’ (by default) and ‘R CMD Rdiff’ now ignore differences in pointer values when comparing printed environments, compiled byte code, etc.

• The ‘"source"’ attribute on functions created with ‘keep.source=TRUE’ has been replaced with a ‘"srcref"’ attribute. The ‘"srcref"’ attribute references an in-memory copy of the source file using the ‘"srcfilecopy"’ class or the new ‘"srcfilealias"’ class.

• New items User Manuals and Technical Papers have been added to the HTML help main page. These link to vignettes in the base and recommended packages and to a collection of papers about R issues, respectively.

• Documentation and messages have been standardized to use “namespace” rather than “name space”.

• ‘setGeneric()’ now looks in the default packages for a non-generic version of a function if called from a package with a namespace. (It always did for packages without a namespace.)

• Setting the environment variable ‘_R_WARN_ON_LOCKED_BINDINGS_’ will give a warning if an attempt is made to change a locked binding.

• ‘\SweaveInput’ is now supported when generating concordances in ‘Sweave()’.

• ‘findLineNum()’ and ‘setBreakpoint()’ now allow the environment to be specified indirectly; the latter gains a ‘clear’ argument to allow it to call ‘untrace()’.

• The body of a closure can be one of further types of R objects, including enviroments and external pointers.

• The ‘Rd2HTML()’ function in package ‘tools’ now has a ‘stylesheet’ argument, allowing pages to be displayed in alternate formats.

• New function ‘requireNamespace()’ analogous to ‘require()’, returning a logical value after attempting to load a namespace.

• There is a new type of RNG, ‘"L'Ecuyer-CMRG"’, implementing L'Ecuyer (1999)'s ‘combined multiple-recursive generator’ ‘MRG32k3a’. See the comments on ‘?RNG’.

• ‘help.search()’ and ‘??’ can now display vignettes and demos as well as help pages. The new option ‘"help.search.types"’ controls the types of documentation and the order of their display.

• ‘socketConnection()’ now has a ‘timeout’ argument.

• The initialization of the random-number generator now uses the process ID as well as the current time, just in case two R processes are launched very rapidly on a machine with low-resolution wall clock (some have a resolution of a second; modern systems have microsecond-level resolution).

• New function ‘pskill()’ in the ‘tools’ package to send a terminate signal to one or more processes, plus constants such as ‘SIGTERM’ to provide a portable way to refer to signals (since the numeric values are OS-dependent).

• New function ‘psnice()’ in the ‘tools’ package to return or change the ‘niceness’ of a process. (Refers to the ‘priority class’ on Windows.)

• ‘list.dirs()’ gains a ‘recursive’ argument.

• An ‘Authors@R’ field in a package ‘DESCRIPTION’ file can now be used to generate ‘Author’ and ‘Maintainer’ fields if needed, and to auto-generate package citations.

• New utility ‘getElement()’ for accessing either a list component or a slot in an S4 object.

• ‘stars()’ gains a ‘col.lines’ argument, thanks to Dustin Sallings. (Wish of PR#14657.)

• New function ‘regmatches()’ for extracting or replacing matched or non-matched substrings from match data obtained by ‘regexpr()’, ‘gregexpr()’ and ‘regexec()’.

• ‘help(package = "pkg_name", help_type = "HTML")’ now gives HTML help on the package rather than text help. (This gives direct access to the HTML version of the package manual shown _via_ ‘help.start()’'s ‘Packages’ menu.)

• ‘agrep()’ gains a ‘fixed’ argument to optionally allow approximate regular expression matching, and a ‘costs’ argument to specify possibly different integer match costs for insertions, deletions and substitutions.

• ‘read.dcf()’ and ‘write.dcf()’ gain a ‘keep.white’ argument to indicate fields where whitespace should be kept as is.

• ‘available.packages()’ now works around servers that fail to return an error code when ‘PACKAGES.gz’ does not exist. (Patch submitted by Seth Schommer.)

• ‘readBin()’ can now read more than 2^31 - 1 bytes in a single call (the previously documented limitation).

• New function ‘regexec()’ for finding the positions of matches as well as all substrings corresponding to parenthesized subexpressions of the given regular expression.

• New function ‘adist()’ in package ‘utils’ for computing ‘edit’ (generalized Levenshtein) distances between strings.

• Class ‘"raster"’ gains an ‘is.na’ method to avoid confusion from the misuse of the matrix method (such as PR#14618).

• The ‘identical()’ function gains an ‘ignore.bytecode’ argument to control comparison of compiled functions.

• ‘pmin’ and ‘pmax’ now warn if an argument is partially recycled (wish of PR#14638).

• The default for ‘image(useRaster=)’ is now taken from option ‘"preferRaster"’: for the small print see ‘?image’.

• ‘str()’ now displays reference class objects and their fields, rather than treating them as classical S4 classes.

• New function ‘aregexec()’ in package ‘utils’ for finding the positions of approximate string matches as well as all substrings corresponding to parenthesized subexpressions of the given regular expression.

• ‘download.file()’ has an ‘extra’ argument to pass additional command-line options to the non-default methods using command-line utilities.

  ‘cacheOK = FALSE’ is now supported for ‘method = "curl"’.

• ‘interaction.plot(*, type = .)’ now also allows type ‘"o"’ or ‘"c"’.

• ‘axTicks(*, log=TRUE)’ did sometimes give more values than the ticks in the corresponding ‘graphics::axis()’. By default, it now makes use of the new (‘graphics’-package independent) ‘axisTicks()’ which can make use of a new utility ‘.axisPars()’. Further, it now returns a decreasing sequence (as for ‘log=FALSE’) when ‘usr’ is decreasing.

CHANGES IN R-devel GRAPHICS DEVICES

• The ‘pdf()’ device makes use of Flate compression: this is controlled by the new logical argument ‘compress’, and is enabled by default.

• Devices ‘svg()’, ‘cairo_pdf()’ and ‘cairo_ps()’ gain a ‘family’ argument.

  On a Unix-alike ‘X11()’ gains a ‘family’ argument. This is one of the ‘x11.options()’ and so can be passed as an argument to the ‘bmp()’, ‘jpeg()’, ‘png()’ and ‘tiff()’ devices.

  Analogous changes have been made on Windows, so all built-in R graphics devices now have a ‘family’ argument except ‘pictex()’ (which has no means to change fonts).

• The ‘bmp()’, ‘jpeg()’, ‘png()’ and ‘tiff()’ devices now make use of the ‘antialias’ argument for ‘type = "quartz"’.

• There are several new built-in font mappings for ‘X11(type = "Xlib")’: see the help on ‘X11Fonts()’.

• There is a new type ‘X11(type = "dbcairo")’ which updates the screeen less frequently: see its help page.

• The ‘X11()’ device now makes use of cursors to distinguish its states. The normal cursor is an arrow (rather than a crosshair); the crosshair is used when the locator is in use, and a watch cursor is shown when plotting computations are being done. (These are the standard names for X11 cursors: how they are actually displayed depends on the window manager.)

• New functions ‘dev.hold()’ and ‘dev.flush()’ for use with graphics devices with buffering. These are used for most of the high-level graphics functions such as ‘boxplot()’, so that the plot is only displayed when the page is complete.

  Currently implemented for ‘windows(buffered = TRUE)’, ‘quartz()’ and the cairographics-based ‘X11()’ types with buffering (which are the default on-screen devices).

• New function ‘dev.capture()’ for capture of bitmap snapshots of image-based devices (a superset of the functionality provided by ‘grid.cap()’ in ‘grid’).

• The default ‘colormodel’ for ‘pdf()’ and ‘postscript()’ is now called ‘"srgb"’ to more accurately describe it. (Instead of ‘"rgb"’, and in the case of ‘postscript()’ it no longer switches to and from the gray colorspace, by default.)

  The‘colormodel’ for ‘postscript()’ which does use both gray and sRGB colorspace is now called ‘"srgb+gray"’.

  Plots which are known to use only black/white/transparent can advantageously use ‘colormodel = "gray"’ (just as before, but there is now slightly more advantage in doing so).

• ‘postscript()’ with values ‘colormodel = "rgb"’ and ‘colormodel = "rgb-nogray"’ give the behaviour prior to R 2.13.0 of uncalibrated RGB, which under some circumstances can be rendered much faster by a viewer.

  ‘pdf(colormodel = "rgb")’ gives the behaviour prior to R 2.13.0 of uncalibrated RGB, which under some circumstances can be rendered faster by a viewer, and the files will be smaller (by about 9KB if compression is not used).

• The ‘postscript()’ device only includes the definition of the sRGB colorspace in the output file for the colormodels which use it.

• The ‘postscript()’ and ‘pdf()’ devices now output greyscale raster images (and not RGB) when ‘colormodel = "gray"’.

• ‘postscript(colormodel = "gray")’ now accepts non-grey colours and uses their luminance (as ‘pdf()’ long has).

• ‘colormodel = "grey"’ is allowed as an alternative name for ‘postscript()’ and ‘pdf()’.

• ‘pdf()’ in the default sRGB colorspace outputs many fewer changes of colorspace, which may speed up rendering in some viewing applications.

• There is a new function ‘dev.capabilities()’ to query the capabilities of the current device. The initial set of capabilities are support for semi-transparent colours, rendering and capturing raster images, the locator and for interactive events.

• For ‘pdf()’, ‘maxRasters’ is increased as needed so the argument is no longer used.

CHANGES IN R-devel SWEAVE & VIGNETTES

• Options ‘keep.source = TRUE, figs.only = FALSE’ are now the default.

• The way the type of user-defined options is determined has changed. Previously they were all regarded as logical: now the type is determined by the value given at first use.

• The allowed values of logical options are now precisely those allowed for character inputs to ‘as.logical()’: this means that ‘t’ and ‘f’ are no longer allowed (although ‘T’ and ‘F’ still are).

• The preferred location for vignette sources is now the directory ‘vignettes’ and not ‘inst/doc’: ‘R CMD build’ will now re-build vignettes in directory ‘vignettes’ and copy the ‘.Rnw’ (etc) files and the corresponding PDFs to ‘inst/doc’. Further files to be copied to ‘inst/doc’ can be specified _via_ the file ‘vignettes/.install_extras’.

• ‘R CMD Sweave’ now supports a ‘--driver’ option to select the Sweave driver: the default is equivalent to ‘--driver=RweaveLatex’.

• ‘R CMD Sweave’ and ‘R CMD Stangle’ support options ‘--encoding’ and ‘--options’.

• The ‘Rtangle()’ driver allows ‘output = "stdout"’ or ‘output = "stderr"’ to select the output or message connection. This is convenient for scripting using something like

  R CMD Stangle --options='output="stdout"' foo.Rnw > foo2.R

• There is a new option ‘pdf.compress’ controlling whether PDF figures are generated using Flate compression (they are by default).

• ‘R CMD Sweave’ now has a ‘--pdf’ option to produce a PDF version of the processed Sweave document.

• It is no longer allowed to have two vignettes with the same vignette basename (e.g. ‘vig.Rnw’ and ‘vig.Snw’). (Previously one vignette hid the other in the ‘vignette()’ function.)

CHANGES IN R-devel C-LEVEL FACILITIES

• Function ‘R_tmpnam2’ has been added to the API to allow a temporary filename to include a specified extension.

CHANGES IN R-devel PACKAGE INSTALLATION

• Package ‘DESCRIPTION’ file field ‘KeepSource’ forces the package to be installed with ‘keep.source = TRUE’ (or ‘FALSE’). (Suggestion of Greg Snow. Note that as all packages are lazy-loaded, this is now only relevant at installation.)

  There are corresponding options ‘--with-keep.source’ and ‘--without-keep.source’ for ‘R CMD INSTALL’.

• ‘R CMD INSTALL’ has a new option ‘--byte-compile’ to byte-compile the packages during installation (since all packages are now lazy-loaded). This can be controlled on a per-package basis by the optional field ‘ByteCompile’ in the ‘DESCRIPTION’ file.

• A package R code but without a ‘NAMESPACE’ file will have a default one created at ‘R CMD build’ or ‘R CMD INSTALL’ time, so all packages will be installed with namespaces. A consequence of this is that ‘.First.lib()’ functions need to be copied to ‘.onLoad()’ (usually) or ‘.onAttach()’. For the time being, if there is an auto-generated ‘NAMESPACE’ file and no ‘.onLoad()’ nor ‘.onAttach()’ function is found but ‘.First.lib()’ is, it will be run as the attach hook (unless the package is one of a list of known exceptions, when it will be run as the load hook).

• A warning is given if test-loading a package changes a locked binding in a package other than itself. It is likely that this will be disallowed in future releases. (There are _pro tem_ some exceptions to the warning.)

• A dependency on SVN revision is allowed for ‘R’, e.g. ‘R (>= r56550)’. This should be used in conjunction with a version number, e.g. ‘R (>= 2.14.0), R (>= r56550)’ to distinguish beteen R-patched and R-devel versions with the same SVN revision.

• ‘installed.packages()’ now hashes the names of its cache files to avoid very rare problems with excessively long path names. (PR#14669)

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ now gives an error if the R code in a vignette fails to run, unless this is caused by a missing package.

• ‘R CMD check’ now unpacks tarballs in the same way as ‘R CMD INSTALL’, including making use of the environment variable ‘R_INSTALL_TAR’ to override the default behaviour.

• ‘R CMD check’ performs additional code analysis of package startup functions, and notifies about incorrect argument lists and (incorrect) calls to functions which modify the search path or inappropriately generate messages.

• ‘R CMD check’ now also checks compiled code for symbols corresponding to functions which might terminate R or write to ‘stdout’/‘stderr’ instead of the console.

• ‘R CMD check’ now uses a ‘pdf()’ device when checking examples (rather than ‘postscript()’).

• ‘R CMD check’ now reports as a NOTE what look like methods documented with their full names even if there is a namespace and they are exported. In almost all cases they are intended to be used only as methods and should use the ‘\method’ markup. In the other rare cases the recommended form is to use a function such as ‘coefHclust’ which would not get confused with a method, document that and register it in the ‘NAMESPACE’ file by ‘s3method(coef, hclust, coefHclust)’.

• The default for the environment variable ‘_R_CHECK_COMPACT_DATA2_’ is now true: thus if using the newer forms of compression introduced in R 2.10.0 would be beneficial is now checked (by default).

• ‘R CMD Rd2dvi’ allows the use of LaTeX package ‘inputenx’ rather than ‘inputenc’: the value of the environment variable ‘RD2DVI_INPUTENC’ is used. (LaTeX package ‘inputenx’ is an optional install which provides greater coverage of the UTF-8 encoding.)

• ‘Rscript’ on a Unix-alike now accepts file names containing spaces (provided these are escaped or quoted in the shell).

• ‘R CMD build’ on a Unix-alike (only) now tries to preserve dates on files it copies from its input directory. (This was the undocumented behaviour prior to R 2.13.0.)

CHANGES IN R-devel DEPRECATED AND DEFUNCT

• ‘require()’ no longer has a ‘save’ argument.

• The ‘gamma’ argument to ‘hsv()’, ‘rainbow()’, and ‘rgb2hsv()’ has been removed.

• The ‘--no-docs’ option for ‘R CMD build --binary’ is defunct: use ‘--install-args’ instead.

• The option ‘--unsafe’ to ‘R CMD INSTALL’ is defunct: use the identical option ‘--no-lock’ instead.

• The entry point ‘pythag’ formerly in ‘Rmath.h’ is defunct: use instead the C99 function ‘hypot’.

• ‘R CMD build --binary’ is formally defunct: ‘R CMD INSTALL --build’ has long been the preferred alternative.

• ‘zip.file.extract()’ is now defunct: use ‘unzip()’ or ‘unz()’ instead.

• ‘R CMD Rd2dvi’ without the ‘--pdf’ option is now deprecated: only PDF output will be supported in future releases (since this allows the use of fonts only supported for PDF).

• A top-level ‘COPYING’ file in a package is now deprecated (file names ‘LICENSE’ or ‘LICENCE’ have long been preferred), and will not be installed as from R 2.15.0.

• Options such as ‘--max-nsize’ and the function ‘mem.limits()’ are now deprecated: these limits are nowadays almost never used, and are reported by ‘gc()’ when they are in use.

• Forms like ‘binomial(link = "link")’ for GLM families deprecated since R 2.4.0 are now defunct.

• The ‘declarativeOnly’ argument to ‘loadNamespace()’ (not relevant since R 2.13.0) has been removed.

• Use of ‘library.dynam()’ without specifying all the first three arguments is deprecated. (It is often called from a namespace, and the defaults are only appropriate to a package.)

CHANGES IN R-devel INSTALLATION

• The base and recommended packages are now byte-compiled (equivalent to ‘make bytecode’ in R 2.13.x).

• Configure option ‘--with-system-zlib’ now only makes use of the basic interface of ‘zlib’ and not the C function ‘gzseek’ which has shown erroneous behaviour in ‘zlib’ 1.2.4 and 1.2.5.

• The ‘zlib’ in the R sources is now version 1.2.5. (This is safe even on 32-bit Linux systems because only the basic interface is now used.)

• The ‘.afm’ files in package ‘grDevices’ are now installed as compressed files (as long done on Windows), saving ca 2MB on the installed size.

• The non-screen cairo-based devices are no longer in the X11 module and so can be installed without X11. (We have never seen a Unix-alike system with cairographics installed but not X11, but a user might select ‘--without-x’.)

• Configure will try to use ‘-fobjc-exceptions’ for the Objective-C compiler (if present) to ensure that even compilers that do not enable exceptions by default (such as vanilla gcc) can be used. (Objective-C is currently only used on Mac OS X.)

• The system call ‘times’ is required.

• The C99 functions ‘acosh’, ‘asinh’, ‘atanh’, ‘snprintf’ and ‘vsnprintf’ are now required.

• There is no longer support for making DVI manuals _via_ ‘make dvi’, ‘make install-dvi’ and similar. Only PDF manuals are supported (to allow the use of fonts which are only available for PDF.)

• The ‘configure’ arguments used during configuration of R are included as a comment in ‘Makeconf’ for informative purposes on Unix-alikes in a form suitable for shell execution. Note that those are merely command-line arguments, they do not include environment variables (one more reason to use configure variables instead) or site configuration settings.

• Framework installation now supports ‘DESTDIR’ (Mac OS X only).

CHANGES IN R-devel BUG FIXES

• The locale category ‘LC_MONETARY’ was only being set on startup on Windows: that is now done on Unix-alikes where supported.

• Reference class utilities will detect an attempt to modify methods or fields in a locked class definition (e.g., in a namespace) and generate an error.

• The formula methods for ‘lines()’, ‘points()’ and ‘text()’ now work even if package ‘stats’ is not on the search path.

• In principle, S4 classes from different packages could have the same name. This has not previously worked. Changes have now been installed that should allow such classes and permit methods to use them. New functions ‘className()’ and ‘multipleClasses()’ are related tools for programming.

• Work around an issue in Linux (a system ‘select’ call resetting ‘tv’) which prevented internet operations from timing out properly.

• Several stack trampling and overflow issues have been fixed in TRE, triggered by ‘agrep’ and friends with long patterns. (PR#14627.)

• (“design infelicity”) Field assignments in reference classes are now consistent with slots in S4 classes: the assigned value must come from the declared class (if any) for the field or from a subclass.

• The methods objects constructed for ‘"coerce"’ and ‘"coerce<-"’ were lacking some essential information in the ‘generic’, ‘defined’ and ‘target’ slots; ‘as()’ did not handle duplicate class definitions correctly.

• The parser no longer accepts the digit ‘8’ in an octal character code in a string, nor does it accept unterminated strings in a file. (Reported by Bill Dunlap.)

• The ‘print()’ method for class ‘"summary.aov"’ did not pass on argument ‘digits’ when ‘summary()’ was called on a single object, and hence used more digits than documented.

• X11 cairo back-end produced incorrect capture snapshot images on big-endian machines.

2.14.0 SIGNIFICANT USER-VISIBLE CHANGES

• All packages must have a namespace, and one is created on installation if not supplied in the sources. This means that any package without a namespace must be re-installed under this version of R (but data-only packages without R code can still be used).

• The ‘yLineBias’ of the ‘X11()’ and ‘windows()’ families of devices has been changed from 0.1 to 0.2: this changes slightly the vertical positioning of text in the margins (including axis annotations). This is mainly for consistency with other devices such as ‘quartz()’ and ‘pdf()’. (Wish of PR#14538.)

  There is a new graphics parameter ‘"ylbias"’ which allows the y-line bias of the graphics device to be tweaked, including to reproduce output from earlier versions of R.

• Labeling of the p-values in various anova tables has been rationalized to be either ‘"Pr(>F)"’ or ‘"Pr(>Chi)"’ (i.e. the ‘"Pr(F)"’, ‘"Pr(Chi)"’ and ‘"P(>|Chi|)"’ variants have been eliminated). Code which extracts the p value _via_ indexing by name may need adjustment.

• ‘::’ can now be used for datasets made available for lazy-loading in packages with namespaces (which makes it consistent with its use for data-only packages without namespaces in earlier versions of R).

• There is a new package ‘parallel’.

  It incorporates (slightly revised) copies of packages ‘multicore’ and ‘snow’ (excluding MPI, PVM and NWS clusters). Code written to use those packages should work unchanged (apart from changing any references to their namespaces to a reference to ‘parallel’).

  It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both ‘mclapply’ and ‘snow’ clusters.

  (It is still incomplete/experimental.)

• Building PDF manuals (for R itself or packages, e.g. _via_ ‘R CMD check’) by default requires the LaTeX package ‘inconsolata’: see the section on ‘Making the manuals’ in the ‘R Installation and Administration Manual’.

• ‘axTicks(*, log=TRUE)’ has changed in some cases to satisfy the documented behavior and be consistent.

2.14.0 NEW FEATURES

• ‘txtProgressBar()’ can write to an open connection instead of the console.

• Non-portable package names ending in ‘.’ are no longer allowed. Nor are single-character package names (‘R’ was already disallowed).

• ‘regexpr()’ and ‘gregexpr()’ with ‘perl = TRUE’ allows Python-style named captures. (Wish and contribution of PR#14518.)

• The placement of ‘plotmath’ text in the margins of plots done by base graphics now makes the same vertical adjustment as ordinary text, so using ordinary and plotmath text on the same margin line will seem better aligned (but not exactly aligned, since ordinary text has descenders below the baseline and plotmath places them on the baseline). (Related to PR#14537.)

• ‘sunflowerplot()’ now has a formula interface. (Wish of PR#14541.)

• ‘iconv()’ has a new argument ‘toRaw’ to handle encodings such as ‘UTF-16’ with embedded nuls (as was possible before the ‘CHARSXP’ cache was introduced).

  It will also accept as input the type of list generated with ‘toRaw = TRUE’.

• Garbage-collecting an unused input text connection no longer gives a warning (since it ‘connects’ to nothing outside R).

• ‘read.table()’ and ‘scan()’ have gained a ‘text’ argument, to allow reading data from a (possibly literal) character string.

• ‘optim(*, method = .)’ now allows ‘method = "Brent"’ as an interface to ‘optimize()’, for use in cases such as ‘mle()’ where ‘optim()’ is used internally.

• ‘mosaicplot()’ gains a ‘border’ argument. (Wish of PR#14550.)

• ‘smooth.spline()’ gains a ‘tol’ argument which controls how different ‘x’ values need to be to be treated as distinct. The default has been changed to be more reliable for inputs whose range is small compared to their maximum absolute value. (Wish of PR#14452.)

• ‘gl()’ runs faster by avoiding calling ‘factor()’.

• The ‘print()’ method for ‘object.size()’ accepts ‘B’ as well as ‘b’ as an abbreviation for ‘bytes’.

• ‘unlink()’ gains a ‘force’ argument to work like ‘rm -f’ and if possible override restrictive permissions.

• ‘pbirthday()’ and ‘qbirthday()’ now use exact calculations for ‘coincident = 2’.

• ‘unzip()’ and ‘unz()’ connections have been updated with support for more recent Zip64 features (including large file sizes and ‘bzip2’ compression, but not UTF-8 file names).

  ‘unzip()’ has a new option to restore file times from those recorded (in an unknown timezone) in the zip file.

• ‘update.packages()’ now accepts a character vector of package names for the ‘oldPkgs’ argument. (Suggestion of Tal Galili.)

• The special reference class fields ‘.self’ and ‘.refClassDef’ are now read-only to prevent corrupting the object.

• ‘decompose()’ now returns the original series as part of its value, so it can be used (rather than reconstructed) when plotting. (Suggestion of Rob Hyndman.)

• Rao's efficient score test has been implemented for ‘glm’ objects. Specifically, the ‘add1’, ‘drop1’, and ‘anova’ methods now allow ‘test = "Rao"’.

• If a saved workspace (e.g. ‘.RData’) contains objects that cannot be loaded, R will now start with an warning message and an empty workspace, rather than failing to start.

• ‘strptime()’ now accepts times such as ‘24:00’ for midnight at the end of the day, for although these are disallowed by POSIX 1003.1-2008, ISO 8601:2004 allows them.

• Assignment of ‘names()’ to S4 objects now checks for a corresponding ‘"names"’ slot, and generates a warning or an error if that slot is not defined. See the section on slots in ‘?Classes’.

• The default methods for ‘is.finite()’, ‘is.infinite()’ and ‘is.nan()’ now signal an error if their argument is not an atomic vector.

• The formula method for ‘plot()’ no longer places package ‘stats’ on the search path (it loads the namespace instead).

• There now is a genuine ‘"function"’ method for ‘plot()’ rather than the generic dispatching internally to ‘graphics::plot.function()’. It is now exported, so can be called directly as ‘plot.function()’.

• The one-sided ‘ks.test()’ allows ‘exact = TRUE’ to be specified in the presence of ties (but the approximate calculation remains the default: the ‘exact’ computation makes assumptions known to be invalid in the presence of ties).

• The behaviour of ‘curve(add = FALSE)’ has changed: it now no longer takes the default x limits from the previous plot (if any): rather they default to ‘c(0, 1)’ just as the ‘"function"’ method for ‘plot()’. To get the previous behaviour use ‘curve(add = NA)’, which also takes the default for log-scaling of the x-axis from the previous plot.

• Both ‘curve()’ and the ‘plot()’ method for functions have a new argument ‘xname’ to facilitate plots such as ‘sin(t)’ _vs_ ‘t’.

• The ‘local’ argument to ‘source()’ can specify an environment as well as ‘TRUE’ (‘parent.env()’) and ‘FALSE’ (‘.GlobalEnv’). It gives better error messages for other values, such as ‘NA’.

• ‘vcov()’ gains methods for classes ‘"summary.lm"’ and ‘"summary.glm"’.

• The ‘plot()’ method for class ‘"profile.nls"’ gains ‘ylab’ and ‘lty’ arguments, and passes ‘...’ on to ‘plot.default’.

• Character-string arguments such as the ‘mode’ argument of ‘vector()’, ‘as.vector()’ and ‘is.vector()’ and the ‘description’ argument of ‘file()’ are required to be of length exactly one, rather than any further elements being silently discarded. This helps catch incorrect usage in programming.

• The ‘length’ argument of ‘vector()’ and its wrappers such as ‘numeric()’ is required to be of length exactly one (other values are now an error rather than giving a warning as previously).

• ‘vector(len)’ and ‘length(x) <- len’ no longer acccept ‘TRUE’/‘FALSE’ for ‘len’ (not that they were ever documented to, but there was special-casing in the C code).

• There is a new function ‘Sys.setFileTime()’ to set the time of a file (including a directory). See its help for exactly which times it sets on various OSes.

• The file times reported by ‘file.info()’ are reported to sub-second resolution on systems which support it. (Currently the POSIX 2008 and FreeBSD/Darwin/NetBSD methods are detected.)

• New function ‘getCall(m)’ as an abstraction for ‘m$call’, enabling ‘update()’'s default method to apply more universally. (NB: this can be masked by existing functions in packages.)

• ‘Sys.info()’ gains a ‘euser’ component to report the ‘effective’ user on OSes which have that concept.

• The result returned by ‘try()’ now contains the original error condition object as the ‘"condition"’ attribute.

• All packages with R code are lazy-loaded irrespective of the ‘LazyLoad’ field in the ‘DESCRIPTION’ file. A warning is given if the ‘LazyLoad’ field is overridden.

• ‘Rd’ markup has a new ‘\figure’ tag so that figures can be included in help pages when converted to HTML or LaTeX. There are examples on the help pages for ‘par()’ and ‘points()’.

• The built-in httpd server now allows access to files in the session temporary directory ‘tempdir()’, addressed as the ‘/session’ directory on the httpd server.

• Development versions of R are no longer referred to by the number under which they might be released, e.g. in the startup banner, ‘R --version’ and ‘sessionUtils()’. The correct way to refer to a development version of R is ‘R-devel’, preferably with the date and SVN version number. E.g. ‘R-devel (2011-07-04 r56266)’

• There is a new function ‘texi2pdf()’ in package ‘tools’, currently a convenience wrapper for ‘texi2dvi(pdf = TRUE)’.

• There are two new options for typesetting PDF manuals from Rd files. These are ‘beramono’ and ‘inconsolata’, and used the named font for mononspaced output. They are intended to be used in combination with ‘times’, and ‘times,inconsolata,hyper’ is now the default for the reference manual and package manuals. If you do not have that font installed, you can set ‘R_RD4PF’ to one of the other options: see the ‘R Installation and Administration Manual’.

• Automatic printing for reference classes is now done by the ‘$show()’ method. A method is defined for class ‘envRefClass’ and may be overriden for user classes (see the ‘?ReferenceClasses’ example). S4 ‘show()’ methods should no longer be needed for reference classes.

• ‘tools::Rdiff’ (by default) and ‘R CMD Rdiff’ now ignore differences in pointer values when comparing printed environments, compiled byte code, etc.

• The ‘"source"’ attribute on functions created with ‘keep.source=TRUE’ has been replaced with a ‘"srcref"’ attribute. The ‘"srcref"’ attribute references an in-memory copy of the source file using the ‘"srcfilecopy"’ class or the new ‘"srcfilealias"’ class.

• New items User Manuals and Technical Papers have been added to the HTML help main page. These link to vignettes in the base and recommended packages and to a collection of papers about R issues, respectively.

• Documentation and messages have been standardized to use “namespace” rather than “name space”.

• ‘setGeneric()’ now looks in the default packages for a non-generic version of a function if called from a package with a namespace. (It always did for packages without a namespace.)

• Setting the environment variable ‘_R_WARN_ON_LOCKED_BINDINGS_’ will give a warning if an attempt is made to change a locked binding.

• ‘\SweaveInput’ is now supported when generating concordances in ‘Sweave()’.

• ‘findLineNum()’ and ‘setBreakpoint()’ now allow the environment to be specified indirectly; the latter gains a ‘clear’ argument to allow it to call ‘untrace()’.

• The body of a closure can be one of further types of R objects, including enviroments and external pointers.

• The ‘Rd2HTML()’ function in package ‘tools’ now has a ‘stylesheet’ argument, allowing pages to be displayed in alternate formats.

• New function ‘requireNamespace()’ analogous to ‘require()’, returning a logical value after attempting to load a namespace.

• There is a new type of RNG, ‘"L'Ecuyer-CMRG"’, implementing L'Ecuyer (1999)'s ‘combined multiple-recursive generator’ ‘MRG32k3a’. See the comments on ‘?RNG’.

• ‘help.search()’ and ‘??’ can now display vignettes and demos as well as help pages. The new option ‘"help.search.types"’ controls the types of documentation and the order of their display.

• ‘socketConnection()’ now has a ‘timeout’ argument.

• The initialization of the random-number generator now uses the process ID as well as the current time, just in case two R processes are launched very rapidly on a machine with low-resolution wall clock (some have a resolution of a second; modern systems have microsecond-level resolution).

• New function ‘pskill()’ in the ‘tools’ package to send a terminate signal to one or more processes, plus constants such as ‘SIGTERM’ to provide a portable way to refer to signals (since the numeric values are OS-dependent).

• New function ‘psnice()’ in the ‘tools’ package to return or change the ‘niceness’ of a process. (Refers to the ‘priority class’ on Windows.)

• ‘list.dirs()’ gains a ‘recursive’ argument.

• An ‘Authors@R’ field in a package ‘DESCRIPTION’ file can now be used to generate ‘Author’ and ‘Maintainer’ fields if needed, and to auto-generate package citations.

• New utility ‘getElement()’ for accessing either a list component or a slot in an S4 object.

• ‘stars()’ gains a ‘col.lines’ argument, thanks to Dustin Sallings. (Wish of PR#14657.)

• New function ‘regmatches()’ for extracting or replacing matched or non-matched substrings from match data obtained by ‘regexpr()’, ‘gregexpr()’ and ‘regexec()’.

• ‘help(package = "pkg_name", help_type = "HTML")’ now gives HTML help on the package rather than text help. (This gives direct access to the HTML version of the package manual shown _via_ ‘help.start()’'s ‘Packages’ menu.)

• ‘agrep()’ gains a ‘fixed’ argument to optionally allow approximate regular expression matching, and a ‘costs’ argument to specify possibly different integer match costs for insertions, deletions and substitutions.

• ‘read.dcf()’ and ‘write.dcf()’ gain a ‘keep.white’ argument to indicate fields where whitespace should be kept as is.

• ‘available.packages()’ now works around servers that fail to return an error code when ‘PACKAGES.gz’ does not exist. (Patch submitted by Seth Schommer.)

• ‘readBin()’ can now read more than 2^31 - 1 bytes in a single call (the previously documented limitation).

• New function ‘regexec()’ for finding the positions of matches as well as all substrings corresponding to parenthesized subexpressions of the given regular expression.

• New function ‘adist()’ in package ‘utils’ for computing ‘edit’ (generalized Levenshtein) distances between strings.

• Class ‘"raster"’ gains an ‘is.na’ method to avoid confusion from the misuse of the matrix method (such as PR#14618).

• The ‘identical()’ function gains an ‘ignore.bytecode’ argument to control comparison of compiled functions.

• ‘pmin’ and ‘pmax’ now warn if an argument is partially recycled (wish of PR#14638).

• The default for ‘image(useRaster=)’ is now taken from option ‘"preferRaster"’: for the small print see ‘?image’.

• ‘str()’ now displays reference class objects and their fields, rather than treating them as classical S4 classes.

• New function ‘aregexec()’ in package ‘utils’ for finding the positions of approximate string matches as well as all substrings corresponding to parenthesized subexpressions of the given regular expression.

• ‘download.file()’ has an ‘extra’ argument to pass additional command-line options to the non-default methods using command-line utilities.

  ‘cacheOK = FALSE’ is now supported for ‘method = "curl"’.

• ‘interaction.plot(*, type = .)’ now also allows type ‘"o"’ or ‘"c"’.

• ‘axTicks(*, log=TRUE)’ did sometimes give more values than the ticks in the corresponding ‘graphics::axis()’. By default, it now makes use of the new (‘graphics’-package independent) ‘axisTicks()’ which can make use of a new utility ‘.axisPars()’. Further, it now returns a decreasing sequence (as for ‘log=FALSE’) when ‘usr’ is decreasing.

2.14.0 GRAPHICS DEVICES

• The ‘pdf()’ device makes use of Flate compression: this is controlled by the new logical argument ‘compress’, and is enabled by default.

• Devices ‘svg()’, ‘cairo_pdf()’ and ‘cairo_ps()’ gain a ‘family’ argument.

  On a Unix-alike ‘X11()’ gains a ‘family’ argument. This is one of the ‘x11.options()’ and so can be passed as an argument to the ‘bmp()’, ‘jpeg()’, ‘png()’ and ‘tiff()’ devices.

  Analogous changes have been made on Windows, so all built-in R graphics devices now have a ‘family’ argument except ‘pictex()’ (which has no means to change fonts).

• The ‘bmp()’, ‘jpeg()’, ‘png()’ and ‘tiff()’ devices now make use of the ‘antialias’ argument for ‘type = "quartz"’.

• There are several new built-in font mappings for ‘X11(type = "Xlib")’: see the help on ‘X11Fonts()’.

• There is a new type ‘X11(type = "dbcairo")’ which updates the screeen less frequently: see its help page.

• The ‘X11()’ device now makes use of cursors to distinguish its states. The normal cursor is an arrow (rather than a crosshair); the crosshair is used when the locator is in use, and a watch cursor is shown when plotting computations are being done. (These are the standard names for X11 cursors: how they are actually displayed depends on the window manager.)

• New functions ‘dev.hold()’ and ‘dev.flush()’ for use with graphics devices with buffering. These are used for most of the high-level graphics functions such as ‘boxplot()’, so that the plot is only displayed when the page is complete.

  Currently implemented for ‘windows(buffered = TRUE)’, ‘quartz()’ and the cairographics-based ‘X11()’ types with buffering (which are the default on-screen devices).

• New function ‘dev.capture()’ for capture of bitmap snapshots of image-based devices (a superset of the functionality provided by ‘grid.cap()’ in ‘grid’).

• The default ‘colormodel’ for ‘pdf()’ and ‘postscript()’ is now called ‘"srgb"’ to more accurately describe it. (Instead of ‘"rgb"’, and in the case of ‘postscript()’ it no longer switches to and from the gray colorspace, by default.)

  The‘colormodel’ for ‘postscript()’ which does use both gray and sRGB colorspace is now called ‘"srgb+gray"’.

  Plots which are known to use only black/white/transparent can advantageously use ‘colormodel = "gray"’ (just as before, but there is now slightly more advantage in doing so).

• ‘postscript()’ with values ‘colormodel = "rgb"’ and ‘colormodel = "rgb-nogray"’ give the behaviour prior to R 2.13.0 of uncalibrated RGB, which under some circumstances can be rendered much faster by a viewer.

  ‘pdf(colormodel = "rgb")’ gives the behaviour prior to R 2.13.0 of uncalibrated RGB, which under some circumstances can be rendered faster by a viewer, and the files will be smaller (by about 9KB if compression is not used).

• The ‘postscript()’ device only includes the definition of the sRGB colorspace in the output file for the colormodels which use it.

• The ‘postscript()’ and ‘pdf()’ devices now output greyscale raster images (and not RGB) when ‘colormodel = "gray"’.

• ‘postscript(colormodel = "gray")’ now accepts non-grey colours and uses their luminance (as ‘pdf()’ long has).

• ‘colormodel = "grey"’ is allowed as an alternative name for ‘postscript()’ and ‘pdf()’.

• ‘pdf()’ in the default sRGB colorspace outputs many fewer changes of colorspace, which may speed up rendering in some viewing applications.

• There is a new function ‘dev.capabilities()’ to query the capabilities of the current device. The initial set of capabilities are support for semi-transparent colours, rendering and capturing raster images, the locator and for interactive events.

• For ‘pdf()’, ‘maxRasters’ is increased as needed so the argument is no longer used.

2.14.0 SWEAVE & VIGNETTES

• Options ‘keep.source = TRUE, figs.only = FALSE’ are now the default.

• The way the type of user-defined options is determined has changed. Previously they were all regarded as logical: now the type is determined by the value given at first use.

• The allowed values of logical options are now precisely those allowed for character inputs to ‘as.logical()’: this means that ‘t’ and ‘f’ are no longer allowed (although ‘T’ and ‘F’ still are).

• The preferred location for vignette sources is now the directory ‘vignettes’ and not ‘inst/doc’: ‘R CMD build’ will now re-build vignettes in directory ‘vignettes’ and copy the ‘.Rnw’ (etc) files and the corresponding PDFs to ‘inst/doc’. Further files to be copied to ‘inst/doc’ can be specified _via_ the file ‘vignettes/.install_extras’.

• ‘R CMD Sweave’ now supports a ‘--driver’ option to select the Sweave driver: the default is equivalent to ‘--driver=RweaveLatex’.

• ‘R CMD Sweave’ and ‘R CMD Stangle’ support options ‘--encoding’ and ‘--options’.

• The ‘Rtangle()’ driver allows ‘output = "stdout"’ or ‘output = "stderr"’ to select the output or message connection. This is convenient for scripting using something like

  R CMD Stangle --options='output="stdout"' foo.Rnw > foo2.R

• There is a new option ‘pdf.compress’ controlling whether PDF figures are generated using Flate compression (they are by default).

• ‘R CMD Sweave’ now has a ‘--pdf’ option to produce a PDF version of the processed Sweave document.

• It is no longer allowed to have two vignettes with the same vignette basename (e.g. ‘vig.Rnw’ and ‘vig.Snw’). (Previously one vignette hid the other in the ‘vignette()’ function.)

2.14.0 C-LEVEL FACILITIES

• Function ‘R_tmpnam2’ has been added to the API to allow a temporary filename to include a specified extension.

2.14.0 PACKAGE INSTALLATION

• Package ‘DESCRIPTION’ file field ‘KeepSource’ forces the package to be installed with ‘keep.source = TRUE’ (or ‘FALSE’). (Suggestion of Greg Snow. Note that as all packages are lazy-loaded, this is now only relevant at installation.)

  There are corresponding options ‘--with-keep.source’ and ‘--without-keep.source’ for ‘R CMD INSTALL’.

• ‘R CMD INSTALL’ has a new option ‘--byte-compile’ to byte-compile the packages during installation (since all packages are now lazy-loaded). This can be controlled on a per-package basis by the optional field ‘ByteCompile’ in the ‘DESCRIPTION’ file.

• A package R code but without a ‘NAMESPACE’ file will have a default one created at ‘R CMD build’ or ‘R CMD INSTALL’ time, so all packages will be installed with namespaces. A consequence of this is that ‘.First.lib()’ functions need to be copied to ‘.onLoad()’ (usually) or ‘.onAttach()’. For the time being, if there is an auto-generated ‘NAMESPACE’ file and no ‘.onLoad()’ nor ‘.onAttach()’ function is found but ‘.First.lib()’ is, it will be run as the attach hook (unless the package is one of a list of known exceptions, when it will be run as the load hook).

• A warning is given if test-loading a package changes a locked binding in a package other than itself. It is likely that this will be disallowed in future releases. (There are _pro tem_ some exceptions to the warning.)

• A dependency on SVN revision is allowed for ‘R’, e.g. ‘R (>= r56550)’. This should be used in conjunction with a version number, e.g. ‘R (>= 2.14.0), R (>= r56550)’ to distinguish beteen R-patched and R-devel versions with the same SVN revision.

• ‘installed.packages()’ now hashes the names of its cache files to avoid very rare problems with excessively long path names. (PR#14669)

• A top-level ‘COPYING’ file in a package is no longer installed (file names ‘LICENSE’ or ‘LICENCE’ having long been preferred).

2.14.0 UTILITIES

• ‘R CMD check’ now gives an error if the R code in a vignette fails to run, unless this is caused by a missing package.

• ‘R CMD check’ now unpacks tarballs in the same way as ‘R CMD INSTALL’, including making use of the environment variable ‘R_INSTALL_TAR’ to override the default behaviour.

• ‘R CMD check’ performs additional code analysis of package startup functions, and notifies about incorrect argument lists and (incorrect) calls to functions which modify the search path or inappropriately generate messages.

• ‘R CMD check’ now also checks compiled code for symbols corresponding to functions which might terminate R or write to ‘stdout’/‘stderr’ instead of the console.

• ‘R CMD check’ now uses a ‘pdf()’ device when checking examples (rather than ‘postscript()’).

• ‘R CMD check’ now reports as a NOTE what look like methods documented with their full names even if there is a namespace and they are exported. In almost all cases they are intended to be used only as methods and should use the ‘\method’ markup. In the other rare cases the recommended form is to use a function such as ‘coefHclust’ which would not get confused with a method, document that and register it in the ‘NAMESPACE’ file by ‘s3method(coef, hclust, coefHclust)’.

• The default for the environment variable ‘_R_CHECK_COMPACT_DATA2_’ is now true: thus if using the newer forms of compression introduced in R 2.10.0 would be beneficial is now checked (by default).

• ‘R CMD Rd2dvi’ allows the use of LaTeX package ‘inputenx’ rather than ‘inputenc’: the value of the environment variable ‘RD2DVI_INPUTENC’ is used. (LaTeX package ‘inputenx’ is an optional install which provides greater coverage of the UTF-8 encoding.)

• ‘Rscript’ on a Unix-alike now accepts file names containing spaces (provided these are escaped or quoted in the shell).

• ‘R CMD build’ on a Unix-alike (only) now tries to preserve dates on files it copies from its input directory. (This was the undocumented behaviour prior to R 2.13.0.)

2.14.0 DEPRECATED AND DEFUNCT

• ‘require()’ no longer has a ‘save’ argument.

• The ‘gamma’ argument to ‘hsv()’, ‘rainbow()’, and ‘rgb2hsv()’ has been removed.

• The ‘--no-docs’ option for ‘R CMD build --binary’ is defunct: use ‘--install-args’ instead.

• The option ‘--unsafe’ to ‘R CMD INSTALL’ is defunct: use the identical option ‘--no-lock’ instead.

• The entry point ‘pythag’ formerly in ‘Rmath.h’ is defunct: use instead the C99 function ‘hypot’.

• ‘R CMD build --binary’ is formally defunct: ‘R CMD INSTALL --build’ has long been the preferred alternative.

• ‘zip.file.extract()’ is now defunct: use ‘unzip()’ or ‘unz()’ instead.

• ‘R CMD Rd2dvi’ without the ‘--pdf’ option is now deprecated: only PDF output will be supported in future releases (since this allows the use of fonts only supported for PDF).

• Options such as ‘--max-nsize’ and the function ‘mem.limits()’ are now deprecated: these limits are nowadays almost never used, and are reported by ‘gc()’ when they are in use.

• Forms like ‘binomial(link = "link")’ for GLM families deprecated since R 2.4.0 are now defunct.

• The ‘declarativeOnly’ argument to ‘loadNamespace()’ (not relevant since R 2.13.0) has been removed.

• Use of ‘library.dynam()’ without specifying all the first three arguments is deprecated. (It is often called from a namespace, and the defaults are only appropriate to a package.)

2.14.0 INSTALLATION

• The base and recommended packages are now byte-compiled (equivalent to ‘make bytecode’ in R 2.13.x).

• Configure option ‘--with-system-zlib’ now only makes use of the basic interface of ‘zlib’ and not the C function ‘gzseek’ which has shown erroneous behaviour in ‘zlib’ 1.2.4 and 1.2.5.

• The ‘zlib’ in the R sources is now version 1.2.5. (This is safe even on 32-bit Linux systems because only the basic interface is now used.)

• The ‘.afm’ files in package ‘grDevices’ are now installed as compressed files (as long done on Windows), saving ca 2MB on the installed size.

• The non-screen cairo-based devices are no longer in the X11 module and so can be installed without X11. (We have never seen a Unix-alike system with cairographics installed but not X11, but a user might select ‘--without-x’.)

• Configure will try to use ‘-fobjc-exceptions’ for the Objective-C compiler (if present) to ensure that even compilers that do not enable exceptions by default (such as vanilla gcc) can be used. (Objective-C is currently only used on Mac OS X.)

• The system call ‘times’ is required.

• The C99 functions ‘acosh’, ‘asinh’, ‘atanh’, ‘snprintf’ and ‘vsnprintf’ are now required.

• There is no longer support for making DVI manuals _via_ ‘make dvi’, ‘make install-dvi’ and similar. Only PDF manuals are supported (to allow the use of fonts which are only available for PDF.)

• The ‘configure’ arguments used during configuration of R are included as a comment in ‘Makeconf’ for informative purposes on Unix-alikes in a form suitable for shell execution. Note that those are merely command-line arguments, they do not include environment variables (one more reason to use configure variables instead) or site configuration settings.

• Framework installation now supports ‘DESTDIR’ (Mac OS X only).

2.14.0 BUG FIXES

• The locale category ‘LC_MONETARY’ was only being set on startup on Windows: that is now done on Unix-alikes where supported.

• Reference class utilities will detect an attempt to modify methods or fields in a locked class definition (e.g., in a namespace) and generate an error.

• The formula methods for ‘lines()’, ‘points()’ and ‘text()’ now work even if package ‘stats’ is not on the search path.

• In principle, S4 classes from different packages could have the same name. This has not previously worked. Changes have now been installed that should allow such classes and permit methods to use them. New functions ‘className()’ and ‘multipleClasses()’ are related tools for programming.

• Work around an issue in Linux (a system ‘select’ call resetting ‘tv’) which prevented internet operations from timing out properly.

• Several stack trampling and overflow issues have been fixed in TRE, triggered by ‘agrep’ and friends with long patterns. (PR#14627.)

• (“design infelicity”) Field assignments in reference classes are now consistent with slots in S4 classes: the assigned value must come from the declared class (if any) for the field or from a subclass.

• The methods objects constructed for ‘"coerce"’ and ‘"coerce<-"’ were lacking some essential information in the ‘generic’, ‘defined’ and ‘target’ slots; ‘as()’ did not handle duplicate class definitions correctly.

• The parser no longer accepts the digit ‘8’ in an octal character code in a string, nor does it accept unterminated strings in a file. (Reported by Bill Dunlap.)

• The ‘print()’ method for class ‘"summary.aov"’ did not pass on argument ‘digits’ when ‘summary()’ was called on a single object, and hence used more digits than documented.

• X11 cairo back-end produced incorrect capture snapshot images on big-endian machines.

• ‘loglin()’ gave a spurious error when argument ‘margin’ consists of a single element of length one. (PR#14690)

• ‘loess()’ is better protected against misuse, e.g. zero-length ‘span’. (PR#14691)