• The defaults for some of the options in ‘R CMD check’ (described in the ‘R Internals’ manual) have changed: the checks for unsafe and ‘.Internal()’ calls and for partial matching of arguments in R function calls are now done by default.

2.14.1 patched NEW FEATURES

• ‘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.)

• ‘NROW(x)’ and ‘NCOL(x)’ now work whenever ‘dim(x)’ looks appropriate, e.g., also for moregeneralized matrices.

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

2.14.1 patched BUG FIXES

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

• ‘R CMD check’ now warns (rather than notes) on undeclared use of other packages in examples and tests: increasingly people are using the metadata in the ‘DESCRIPTION’ file to compute information about packages, for example reverse dependencies.

2.14.1 patched BUG FIXES

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

• ‘R CMD check’ now warns (rather than notes) on undeclared use of other packages: increasingly people are using the metadata in the ‘DESCRIPTION’ file to compute information about packages, for example reverse dependencies.

• For consistency, circles with zero radius are omitted by ‘points’ and ‘grid.circle()’. Previously this was device-dependent, but they were usually invisible.

• ‘makePSOCKCluster()’ has a new option ‘useXDR = FALSE’ which can be used to avoid byte-shuffling for serialization when all the nodes are known to little-endian (or all big-endian).

• ‘makeForkCluster()’ and the multicore-based functions all use native byte order for serialization.

• The internal (un)serialization code is faster for long vectors, particularly with XDR on some platforms. (Based on a suggested patch by Michael Spiegel.)

• 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.

• 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.

2.14.1 patched NEW FEATURES

• 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.

• ‘merge()’ is no longer allowed to create a data frame with duplicate column names (which confused PR#14786).

2.14.1 patched 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’.

• PCRE has been upgraded to version 8.20 with 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’. (It is supported on most but not all platforms that run R.)

• 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.

• ‘serialize()’ has a new option ‘xdr = FALSE’ which will use the native byte-order for binary serializations. In scenarios where only little-endian machines are involved (these days, close to universal) and (un)serialization takes an appreciable amount of time this may speed up noticeably transferring data between systems.

CHANGES IN R-devel BUG FIXES

• The namespace import code was warning when identical S4 generic functions were imported more than once, but should not (reported by Brian Ripley, then Martin Morgan).

2.14.1 patched NEW FAEATURES

• 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’.

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

• ‘setGeneric()’ calls can be simplified when creating a new generic function by supplying the default method as the ‘def’ argument. See ‘?setGeneric’.

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.

• ‘R CMD check’ now gives a warning rather than a note if it finds inefficiently compressed datasets. With ‘bzip2’ and ‘xz’ compression having been available since R 2.10.0, it only exceptionally makes sense to not use them.

  The environment variable ‘_R_CHECK_COMPACT_DATA2_’ is no longer consulted: the check is always done if ‘_R_CHECK_COMPACT_DATA_’ has a true value (its default).

• ‘R CMD build’ has more options for ‘--compact-vignettes’: see ‘R CMD build --help’.

CHANGES IN R-devel BUG FIXES

• The ‘exportMethods’ directive now exports S4 generics as necessary, as the extensions manual said it does. The manual has also been updated to be a little more informative on this point.

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

• 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.

• The behaviour of ‘unlink(recursive = TRUE)’ for a symbolic link to a directory has changed: it now removes the link rather than the directory contents (as ‘rm -r’ does).

  On Windows it no longer follows reparse points (including junctions and symbolic links).

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ now gives a warning rather than a note if it finds inefficiently compressed datasets. With ‘bzip2’ and ‘xz’ compression having been available since R 2.10.0, it only exceptionally makes sense to not use them.

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’.

• 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.

• The namespace import code was warning when identical generic functions were imported more than once, but should not (reported by Martin Morgan).

• 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)

• The ‘traceback()’ function can now be called with an integer argument, to display a current stack trace. (Wish of PR#14770.)

• ‘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)

• 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.

• 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.

• The behaviour of ‘unlink(recursive = TRUE)’ for a symbolic link to a directory has changed: it now removes the link rather than the directory contents (as ‘rm -r’ does).

  On Windows it no longer follows reparse points (includiing junctions and symbolic links).

CHANGES IN R-devel BUG FIXES

• The ‘exportMethods’ directive now exports generics as necessary, as the extensions manual said it does. The manual has also been updated to be a little more informative on this point.

• Reference methods can not safely use non-exported entries in the namespace. We now do not do so, and warn in the documentation.

2.14.1 patched BUG FIXES

• ‘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)

• The behaviour of ‘unlink(recursive = TRUE)’ for a symbolic link to a directory has changed: it now removes the link rather than the directory contents (as ‘rm -r’ does).

• New simple ‘fitted()’ method for ‘"kmeans"’ objects.

• new simple ‘fitted()’ method for ‘"kmeans"’ objects.

• There are new options for more rigorous testing by ‘R CMD check’ selected by environment variables - see the ‘Writing R Extensions’ manual.

• ‘R CMD check’ now gives a warning rather than a note if it finds inefficiently compressed datasets. With ‘bzip2’ and ‘xz’ compression having been available since R 2.10.0, it only expectionally makes sense to not use them.

• 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’ even if environment variable ‘R_GSCMD’ is set.

CHANGES IN R-devel INSTALLATION

• Building with a positive value of ‘--with-valgrind-instrumentation’ now also instruments logical, complex and raw vectors.

2.14.1 NEW FEATURES

• ‘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.

CHANGES IN R-devel NEW FEATURES

• The ‘"dendrogram"’ method of ‘str()’ now takes its default for ‘last.str’ from option ‘str.dendrogram.last’.

CHANGES IN R-devel 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.

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 internal ‘untar()’ (as used by default by ‘R CMD INSTALL’) now knows about some ‘pax’ headers which ‘bsdtar’ incorrectly includes in ‘tar’ files, and will skip them with a warning.

CHANGES IN R-devel 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.

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

• ‘bxp()’, the work horse of ‘boxplot()’, now uses a more sensible default ‘xlim’ in the case where ‘at’ is specified differently from ‘1:n’, see the discussion on R-devel, <URL: https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.

• Function ‘setClass()’ in package ‘methods’ now returns, invisibly, a generator function for the new class, slightly preferred to calling ‘new()’, as explained on the ‘setClass’ help page.

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

• There is a new option ‘install.packages(type = "both")’ which tries source packages if binary packages are not available, on those platforms where the latter is the default.

• The meaning of ‘install.packages(dependencies = TRUE)’ has changed: it now means to install the essential dependencies of the named packages plus the ‘Suggests’, but only the essential dependencies of dependencies. To get the previous behaviour, specify ‘dependencies’ as a character vector.

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ can optionally report timings on various parts of the check: this is controlled by environment variable ‘_R_CHECK_TIMINGS_’ documented in ‘Writing R Extensions’. Timings (in the style of ‘R CMD BATCH’ are given at the foot of the output file from running each test and the R code in each vignette.

CHANGES IN R-devel BUG FIXES

• The convention for ‘x %/% 0L’ for integer-mode ‘x’ has been changed from ‘0L’ to ‘NA_integer_’. (PR#14754)

• ‘R CMD check’ can optionally report timings on various parts of the check: this is controlled by environment variables documented in ‘Writing R Extensions’.

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

• 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)

• Function ‘setClass()’ now returns, invisibly, a generator function for the new class, slightly preferred to calling ‘new()’, as explained in the ‘?setClass’ documentation.

• ‘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)

• There is experimental support for _link-time optimization_ with ‘gcc’ 4.5.0 or later on platforms which support it.

2.14.0 patched BUG FIXES

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

• new function ‘paste0()’, an efficient version of ‘paste(*, sep="")’, to be used in many places for more concise (and slightly more efficient) code.

• ‘bxp()’, the work horse of ‘boxplot()’, now uses a more sensible default ‘xlim’ in the case where ‘at’ is specified differently from ‘1:n’, see the dialogue on R-devel, <URL: https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.

• ‘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.

• ‘attach()’ allows the default name for an attached file to be overridden.

2.14.0 patched BUG FIXES

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

• PCRE has been upgraded to version 8.20 with 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’. (It is supported on most but not all platforms that run R.)

• ‘summary()’ behaves slightly differently (or more precisely, its ‘print()’ method does). For numeric inputs, the number of NAs is printed as an integer and not a real. For dates and datetimes, the number of NAs is included in the printed output (the latter being the wish of PR#14720).

  The ‘"data.frame"’ method is more consistent with the default method: in particular it now applies ‘zapsmall()’ to numeric/complex summaries.

CHANGES IN R-devel UTILITIES

• Where multiple sub-architectures are to be tested, ‘R CMD check’ now runs the examples and tests for all the sub-architectures even if one fails.

CHANGES IN R-devel DEPRECATED AND DEFUNCT

• Use of ‘library.dynam()’ without specifying all the first three arguments is now disallowed.

  Use of an argument ‘chname’ in ‘library.dynam()’ including the extension ‘.so’ or ‘.dll’ (which was never allowed according to the help page) is defunct. This also applies to ‘library.dynam.unload()’ and to ‘useDynLib’ directives in ‘NAMESPACE’ files.

• The internal functions (but still used by some packages) ‘.readRDS()’ and ‘.saveRDS()’ are now defunct.

2.14.0 patched NEW FEATURES

• 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’.

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

CHANGES IN R-devel PACKAGE parallel

• The ‘clusterExport()’ function now allows the specification of an environment from which to export.

CHANGES IN R-devel UTILITIES

• Where multiple sub-architectures are to be tested, ‘R CMD check’ now runs the examples and tests for all the sub-architectures even if the first one fails.

2.14.0 patched NEW FEATURES

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

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

2.14.0 patched BUG FIXES

• ‘read.dcf()’ removes trailing blanks: unfortunately this included on some platforms ‘\xa0’ (non-breaking space) which is the trailing byte of some UTF-8 characters. 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.)

• There is a new function ‘assignInMyNamespace()’ which uses the namespace of the function it is called from.

CHANGES IN R-devel PACKAGE parallel

• The ‘clusterExport()’ function now allows the 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 number of items retained with ‘options(warn = 0)’ can be set by ‘options(nwarnings=)’.

CHANGES IN R-devel PACKAGE parallel

• The ‘clusterExport’ function now allows specification of an environment from which to export.

CHANGES IN R-devel 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).

• ‘R CMD INSTALL’ will test loading under all installed sub-architectures even for packages without compiled code, unless the flag ‘--no-multiarch’ is used. (Pure R packages can do things which are architecture-dependent: in the case which prompted this, looking for an icon in a Windows R executable.)

2.14.0 patched 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).

2.14.0 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.)

• ‘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.)

• PCRE has been upgraded to version 8.20: 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’. (It is supported on most but not all platforms that run R.)

CHANGES IN R-devel PACKAGE parallel

• There are new load-balancing functions ‘parLapplyLB()’ and ‘parSapplyLB()’.

CHANGES IN R-devel PACKAGE INSTALLATION

• C/C++ code in packages is now compiled with ‘-NDEBUG’ to mitigate against the C/C++ function ‘assert’ being called in production use. Developers can turn this off during package development with ‘PKG_CPPFLAGS = -UNDEBUG’.

CHANGES IN R-devel DEPRECATED AND DEFUNCT

• Some functions/objects which have been defunct for five or more years have been removed completely. These include ‘.Alias()’, ‘La.chol()’, ‘La.chol2inv()’, ‘La.eigen()’, ‘Machine()’, ‘Platform()’, ‘Version’, ‘codes()’, ‘delay()’, ‘format.char()’, ‘getenv()’, ‘httpclient()’, ‘loadURL()’, ‘machine()’, ‘parse.dcf()’, ‘printNoClass()’, ‘provide()’, ‘read.table.url()’, ‘restart()’, ‘scan.url()’, ‘symbol.C()’, ‘symbol.For()’ and ‘unix()’.

CHANGES IN R-devel INSTALLATION

• Building wih a positive value of ‘--with-valgrind-instrumentation’ now also instruments logical, complex and raw vectors.

2.14.0 patched NEW FEATURES

• ‘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

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

• ‘summary()’ behaves slightly differently (or more precisely its ‘print()’ method does). For numeric inputs, the number of NAs is printed as an integer and not a real. For dates and datetimes, the number of NAs is included in the printed output (the latter being the wish of PR#14720).

  The ‘"data.frame"’ method is more consistent with the default method: in particular it now applies ‘zapsmall()’ to numeric/complex summaries.

• Building wih a positive value of ‘--with-valgrind-instrumentation’ now instruments logical, complex and raw vectors as well as the other atomic vector types.

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’ (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()’).

• ‘R CMD INSTALL’ has a new option ‘--dsym’ which on Mac OS X (Darwin) dumps the symbols alongside the ‘.so’ file: this is helpful when debugging with ‘valgrind’ (and especially when installing packages into ‘R.framework’). [This can also be enabled by setting the undocumented environment variable ‘PKG_NAKE_DSYM’, since R 2.12.0.]

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

• PCRE has been upgraded to version 8.20: 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’. (It is supported on most but not all CPUs that run R.)

• ‘legend()’ gains a ‘text.font’ argument. (Suggested by Tim Paine, PR#14719.)

• ‘nchar()’ and ‘nzchar()’ no longer accept factors (as integer vectors). (Wish of PR#6899.)

• ‘format()’ (and hence ‘print()’) on ‘"bibentry"’ objects now uses ‘options("width")’ to set the output width.

2.14.0 BUG FIXES

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

• ‘format()’ (and hence ‘print()’) on ‘"bibentry"’ objects now uses ‘options("width")’ to set the output width.

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

2.14.0 patched INSTALLATION

• ‘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.

• ‘format()’ (and hence ‘print()’) on ‘"bibentry"’ objects now uses ‘options("width")’ to set the output width.

2.14.0 patched BUG FIXES

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

• Non-ASCII vignettes without a declared encoding are no longer accepted.

• ‘pdf()’ accepts forms like ‘file = "|lpr"’ in the same way as ‘postscript()’.

• ‘pdf()’ accepts ‘file = NULL’. This means that the device does NOT create a PDF file (but it can still be queried, e.g., for font metric info).

• ‘pdf()’ now has an ‘offline’ argument. If that is set to ‘TRUE’ then the device does NOT create a PDF file (but it can still be queried, e.g., for font metric info).

CHANGES IN R-devel DEPRECATED AND DEFUNCT

• ‘Sys.putenv()’, replaced and deprecated in R 2.5.0, is finally removed.

• Some functions which have been defunct for five or more years have been removed completely. These include ‘.Alias()’, ‘La.chol()’, ‘La.chol2inv()’, ‘La.eigen()’, ‘Machine()’, ‘Platform()’, ‘Version’, ‘codes()’, ‘delay()’, ‘format.char()’, ‘getenv()’, ‘httpclient()’, ‘loadURL()’, ‘machine()’, ‘parse.dcf()’, ‘printNoClass()’, ‘provide()’, ‘read.table.url()’, ‘restart()’, ‘scan.url()’, ‘symbol.C()’, ‘symbol.For()’and ‘unix()’.

2.14.0 patched NEW FEATURES

• ‘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.

• 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 64-bit OS on those Linux distributions capable for supporting that concept.

CHANGES IN R-devel PACKAGE parallel

• There is a new function ‘mcmapply()’, a parallel version of ‘mapply()’, and a wrapper ‘mcMap()’, a parallel version of ‘Map()’.

• A default cluster can be registered by the new function ‘setDefaultCluster()’: this will be used by default in functions such as ‘parLapply()’.

• ‘clusterMap()’ has a new argument ‘.scheduling’ to allow the use of load-balancing.

• There are new load-balancing function ‘parLapplyLB()’ and ‘parSapplyLB()’.

CHANGES IN R-devel NEW FEATURES

• Package ‘parallel’ now allows a default cluster to be registered by ‘setDefaultCluster()’: this will be used by default in functions such as ‘parLapply()’.

  It has a new function ‘mcmapply()’, a parallel version of ‘mapply()’, and a wrapper ‘mcMap()’, a parallel version of ‘Map()’.

  ‘clusterMap()’ has a new argument ‘.scheduling’ to allow the use of load-balancing.

  There are new load-balancing versions ‘parLapplyLB’ and ‘parSapplyLB’.

CHANGES IN R-devel DEPRECATED AND DEFUNCT

• ‘Sys.putenv()’, deprecated in R 2.5.0, is finally removed.

• Some functions which have been defunct for 5 or more years have been removed completely.

CHANGES IN R-devel 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).

• ‘str(x, width)’ now obeys its ‘width’ argument also for function headers and other objects ‘x’ where ‘deparse()’ is applied.

2.14.0 patched NEW FEATURES

• ‘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).

2.14.0 NEW FEATURES

• 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’.

• 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 64-bit OS on those Linux distributions capable for supporting that concept.

CHANGES IN R-devel NEW FEATURES

• ‘kronecker()’ now has an S4 generic in package ‘methods’ on which packages can set methods. It will be invoked by ‘X %x% Y’ if either ‘X’ or ‘Y’ is an S4 object.

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

CHANGES IN R-devel NEW FEATURES

• ‘system()’ and ‘system2()’ when capturing output report a non-zero status in the new ‘"status"’ attribute.

• ‘assignInNamespace()’ has further restrictions on use apart from at top-level, as its help page has warned. Expect it to be disabled from programmatic use in the future.

CHANGES IN R-devel 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).

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ now gives a warning rather than a note if it finds inefficiently compressed datasets. With ‘bzip2’ and ‘xz’ compression having been available since R 2.10.0, there is no excuse for not using them.

CHANGES IN R-devel BUG FIXES

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

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.

2.14.0 DEPRECATED AND DEFUNCT

• 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).

• ‘assignInNamepspace()’ has further restrictions on use apart from at top-level, as its help page has warned. Expect it to be disabled from programmatic use in the future.

CHANGES IN R-devel PACKAGE INSTALLATION

• Package start-up code attempting to change locked bindings in standard packages is now a error, not a warning.

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ now gives a warning rather than a note if it finds inefficiently compressed datasets. With bzip2 and xz compression having been available since 2.10.0, there is no excuse for not using them.

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

CHANGES IN R-devel 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).

• ‘R CMD check’ now gives a warning rather than a note if it finds inefficiently compressed datasets. With bzip2 and xz compression having been available since 2.10.0, there is no excuse for not using them.

CHANGES IN R-devel PACKAGE INSTALLATION

• Package start-up code attempting to change locked bindings in standard packages is now a error, not a warning.

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

• 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.

• Package ‘parallel’ now allows a default cluster to be registered by ‘setDefaultCluster()’: this will be used by default in functions such as ‘parLapply()’.

  It has a new function ‘mcmapply()’, a parallel version of ‘mapply()’, and a wrapper ‘mcMap()’, a parallel version of ‘Map()’.

  ‘clusterMap()’ has a new argument ‘.scheduling’ to allow the use of load-balancing.

  There are new load-balancing versions ‘parLapplyLB’ and ‘parSapplyLB’.

CHANGES IN R-devel 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.

2.14.0 SIGNIFICANT USER-VISIBLE CHANGES

• 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)

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

CHANGES IN R-devel BUG FIXES

• ‘str(x, width)’ now “obeys” its ‘width’ argument also for function headers and other objects ‘x’ where ‘deparse()’ is applied.

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 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.

• Code in packages is now compiled with ‘-NDEBUG’ to mitigate against ‘assert’ being called in production use. Developers can turn this off during package development with ‘PKG_CPPFLAGS = -UNDEBUG’.

2.14.0 NEW FEATURES

• ‘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.

• Package ‘parallel’ now allows a default cluster to be registered by ‘setDefaultCluster()’: this will be used by default in functions such as ‘parLapply()’.

2.14.0 SIGNIFICANT USER-VISIBLE CHANGES

• 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’).

• 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.

• 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 INSTALLATION

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

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

• ‘str(x, width)’ now “obeys” its ‘width’ argument also for function headers and other objects ‘x’, where ‘deparse()’ is applied.

CHANGES IN R-devel NEW FEATURES

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

2.14.0 BUG FIXES

• ‘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)’.

• Even data-only packages without R code need a namespace and so may need to be installed under R 2.14.0 or later.

2.14.0 DEPRECATED AND DEFUNCT

• 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()’.

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

2.14.0 BUG FIXES

• Raster drawing on Windows Metafile (or copying a scene that includes a raster 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).

2.14.0 BUG FIXES

• Raster drawing on Windows Metafile (or copying a scene that includes a raster from another device to a Metafile) now does not crash. (Reported by Stefan Gelissen.)

• ‘.Deprecated()’ becomes a bit more flexible, getting an ‘old’ argument.

2.14.0 DEPRECATED AND DEFUNCT

• 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.

• 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’ (it often gave nonsensical results).

2.14.0 BUG FIXES

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

• The internal functions ‘.readRDS()’ and ‘.saveRDS()’ are now defunct.

• The off-line ‘help()’ types ‘"postscript"’ and ‘"ps"’ are defunct.

2.14.0 BUG FIXES

• ‘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.

• 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.)

• Use of ‘library.dynam()’ without specifying all the first three arguments is now disallowed.

  Use of ‘chname’ in ‘library.dynam()’ with the extension ‘.so’ or ‘.dll’ (which was never allowed according to the help page) is defunct. This also applies to ‘library.dynam.unload()’ and to ‘useDynLib’ directives in ‘NAMESPACE’ files.

2.14.0 DEPRECATED AND DEFUNCT

• ‘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)

• 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)

CHANGES IN R-devel 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.

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 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.

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.

• Environment variable ‘RD2DVI_INPUTENC’ has been renamed to ‘RD2PDF_INPUTENC’.

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.)

• ‘R CMD Rd2dvi’ is now defunct: use ‘R CMD Rd2pdf’.

• Options such as ‘--max-nsize’ and the function ‘mem.limits()’ are now defunct.

• Use of ‘library.dynam()’ without specifying all the first three arguments is now disallowed.

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

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

CHANGES IN R-devel NEW FEATURES

• ‘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.

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

CHANGES IN R-devel BUG FIXES

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

• ‘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"’.

• ‘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.)

• 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).

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

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

CHANGES IN R-devel PACKAGE INSTALLATION

• 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).

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ now gives an NOTE about S3 methods with their full name in the usage even if they are exported from a namespace: 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)’.

• ‘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’ 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)’.

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

2.13.2 NEW FEATURES

• PCRE has been updated to version 8.13, a bug-fix release with updated Unicode tables (version 6.0.0). An additional patch (r611 from PCRE 8.20-to-be) has been added to fix a collation symbol recognition issue.

• 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.

CHANGES IN R-devel UTILITIES

• ‘R CMD check’ now gives an NOTE about S3 methods with their full name in the usage even if they are exported from a namespace: 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 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.)

• ‘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’.

• 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.

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

CHANGES IN R-devel GRAPHICS DEVICES

• 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).

• 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.

CHANGES IN R-devel SWEAVE & VIGNETTES

• 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 PACKAGE INSTALLATION

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

• ‘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.

CHANGES IN R-devel PACKAGE INSTALLATION

• 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 one of a list of known exceptions, when it will be run as the load hook).

• 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’.

CHANGES IN R-devel PACKAGE INSTALLATION

• ‘installed.packages()’ now hashes the names of its cache files to avoid very rare problems with excessively long path names. (PR#14699)

2.13.2 BUG FIXES

• ‘cbind()’ and ‘rbind()’ could cause memory corruption when used on a combination of raw and logical/integer vectors.

• ‘mem.limits()’ now reports values larger than the maximum integer (previously documented to be reported as ‘NA’), and allows larger values to be set, including ‘Inf’ to remove the limit.

• The ‘print()’ methods for classes ‘"Date"’, ‘"POSIXct"’ and ‘"POSIXlt"’ respect the option ‘"max.print"’ and so are much faster for very long datetime vectors. (Suggestion of Yohan Chalabi.)

• ‘untar2()’ now works around errors generated with ‘tar’ files that use more than the standard 6 digits for the checksum. (PR#14654)

• ‘install.packages()’ with ‘Ncpus > 1’ guards against simultaneous installation of indirect dependencies as well as direct ones.

• Sweave now knows about a few more Windows' encodings (including ‘cp1250’ and ‘cp1257’) and some ‘inputenx’ encodings such as ‘koi8-r’.

• ‘postscript(colormodel = "rgb-nogray")’ no longer sets the sRGB colorspace for each colour and so some viewers may render its files much faster than the default ‘colormodel ="rgb"’.

• The default for ‘pdf(maxRasters=)’ has been increased from 64 to 1000.

• ‘readBin()’ now warns if ‘signed = FALSE’ is used inappropriately (rather than being silently ignored).

  It enforces the documented limit of 2^31-1 bytes in a single call.

• PCRE has been updated to version 8.13, a bug-fix release with updated Unicode tables (version 6.0.0). An additional patch (r611 from PCRE 8.20-to-be) has been added to fix a collation symbol recognition issue.

2.13.1 patched INSTALLATION

• It is possible to build in ‘src/extra/xdr’ on more platforms. (Needed since glibc 2.14 hides its RPC implementation.)

• ‘configure’ will find the Sun TI-RPC implementation of xdr (in ‘libtirpc’) provided its header files are in the search path: see the ‘R Installation and Administration Manual’.

2.13.1 patched PACKAGE INSTALLATION

• Using a broad ‘exportPattern’ directive in a ‘NAMESPACE’ file is no longer allowed to export internal objects such as ‘.onLoad’ and ‘.__S3MethodsTable__.’ .

  These are also excluded from imports, along with ‘.First.lib’.

2.13.1 patched BUG FIXES

• ‘fisher.test()’ had a buglet: If arguments were factors with unused levels, levels were dropped and you would get an error saying that there should be at least two levels, inconsistently with pre-tabulated data. (Reported by Michael Fay).

• ‘package.skeleton()’ will no longer dump S4 objects supplied directly rather than in a code file. These cannot be restored correctly from the dumped version.

• Build-time expressions in help files did not have access to functions in the package being built (with ‘R CMD build’).

• Because ‘quote()’ did not mark its result as being in use, modification of the result could in some circumstances modify the original call.

• Plotting ‘pch = '.'’ now guarantees at least a one-pixel dot if ‘cex > 0’.

• The very-rarely-used command-line option ‘--max-vsize’ was incorrectly interpreted as a number of Vcells and not in bytes as documented. (Spotted by Christophe Rhodes.)

• The HTML generated by ‘Rd2HTML()’ comes closer to being standards compliant.

• ‘filter(x, recursive = TRUE)’ gave incorrect results on a series containing ‘NA’s. (Spotted by Bill Dunlap.)

• Profiling ‘stats::mle()’ fits with a ‘fixed’ parameter was not supported. (PR#14646)

• ‘retracemem()’ was still using positional matching. (PR#14650)

• The ‘quantile’ method for ‘"ecdf"’ objects now works and is documented.

• ‘xtabs(~ .., ..., sparse=TRUE)’ now also works together with an ‘exclude = ..’ specification.

• ‘decompose()’ computed an incorrect seasonal component for time series with odd frequencies.

• The ‘pdf()’ device only includes the definition of the sRGB colorspace in the output file for the ‘"rgb"’ colormodel (and not for ‘"gray"’ nor ‘"cmyk"’): this saves ca 9KB in the output file.

• ‘.hasSlot()’ wrongly gave ‘FALSE’ in some cases.

• ‘Sweave()’ with ‘keep.source=TRUE’ could generate spurious ‘NA’ lines when a chunk reference appeared last in a code chunk.

• ‘\Sexpr[results=rd]’ in an ‘.Rd’ file now first tries ‘parse_Rd(fragment=FALSE)’ to allow Rd section-level macros to be inserted.

• The ‘print()’ method for class ‘"summary.aov"’ did not pass on arguments such as ‘signif.stars’ when ‘summary()’ was called on a single object. (PR#14684)

• In rare cases ‘ks.test()’ could return a p-value very slightly less than 0 by rounding error. (PR#14671)

2.13.2 NEW FEATURES

• ‘mem.limits()’ now reports values larger than the maximum integer (previously documented to be reported as ‘NA’), and allows larger values to be set, including ‘Inf’ to remove the limit.

• The ‘print()’ methods for classes ‘"Date"’, ‘"POSIXct"’ and ‘"POSIXlt"’ respect the option ‘"max.print"’ and so are much faster for very long datetime vectors. (Suggestion of Yohan Chalabi.)

• ‘untar2()’ now works around errors generated with ‘tar’ files that use more than the standard 6 digits for the checksum. (PR#14654)

• ‘install.packages()’ with ‘Ncpus > 1’ guards against simultaneous installation of indirect dependencies as well as direct ones.

• Sweave now knows about a few more Windows' encodings (including ‘cp1250’ and ‘cp1257’) and some ‘inputenx’ encodings such as ‘koi8-r’.

• ‘postscript(colormodel = "rgb-nogray")’ no longer sets the sRGB colorspace for each colour and so some viewers may render its files much faster than the default ‘colormodel ="rgb"’.

• The default for ‘pdf(maxRasters=)’ has been increased from 64 to 1000.

• ‘readBin()’ now warns if ‘signed = FALSE’ is used inappropriately (rather than being silently ignored).

  It enforces the documented limit of 2^31-1 bytes in a single call.

• PCRE has been updated to version 8.13, a bug-fix release with updated Unicode tables (version 6.0.0). An additional patch (r611 from PCRE 8.20-to-be) has been added to fix a collation symbol recognition issue.

2.13.2 INSTALLATION

• It is possible to build in ‘src/extra/xdr’ on more platforms. (Needed since glibc 2.14 hides its RPC implementation.)

• ‘configure’ will find the Sun TI-RPC implementation of xdr (in ‘libtirpc’) provided its header files are in the search path: see the ‘R Installation and Administration Manual’.

2.13.2 PACKAGE INSTALLATION

• Using a broad ‘exportPattern’ directive in a ‘NAMESPACE’ file is no longer allowed to export internal objects such as ‘.onLoad’ and ‘.__S3MethodsTable__.’ .

  These are also excluded from imports, along with ‘.First.lib’.

2.13.2 BUG FIXES

• ‘fisher.test()’ had a buglet: If arguments were factors with unused levels, levels were dropped and you would get an error saying that there should be at least two levels, inconsistently with pre-tabulated data. (Reported by Michael Fay).

• ‘package.skeleton()’ will no longer dump S4 objects supplied directly rather than in a code file. These cannot be restored correctly from the dumped version.

• Build-time expressions in help files did not have access to functions in the package being built (with ‘R CMD build’).

• Because ‘quote()’ did not mark its result as being in use, modification of the result could in some circumstances modify the original call.

• Plotting ‘pch = '.'’ now guarantees at least a one-pixel dot if ‘cex > 0’.

• The very-rarely-used command-line option ‘--max-vsize’ was incorrectly interpreted as a number of Vcells and not in bytes as documented. (Spotted by Christophe Rhodes.)

• The HTML generated by ‘Rd2HTML()’ comes closer to being standards compliant.

• ‘filter(x, recursive = TRUE)’ gave incorrect results on a series containing ‘NA’s. (Spotted by Bill Dunlap.)

• Profiling ‘stats::mle()’ fits with a ‘fixed’ parameter was not supported. (PR#14646)

• ‘retracemem()’ was still using positional matching. (PR#14650)

• The ‘quantile’ method for ‘"ecdf"’ objects now works and is documented.

• ‘xtabs(~ .., ..., sparse=TRUE)’ now also works together with an ‘exclude = ..’ specification.

• ‘decompose()’ computed an incorrect seasonal component for time series with odd frequencies.

• The ‘pdf()’ device only includes the definition of the sRGB colorspace in the output file for the ‘"rgb"’ colormodel (and not for ‘"gray"’ nor ‘"cmyk"’): this saves ca 9KB in the output file.

• ‘.hasSlot()’ wrongly gave ‘FALSE’ in some cases.

• ‘Sweave()’ with ‘keep.source=TRUE’ could generate spurious ‘NA’ lines when a chunk reference appeared last in a code chunk.

• ‘\Sexpr[results=rd]’ in an ‘.Rd’ file now first tries ‘parse_Rd(fragment=FALSE)’ to allow Rd section-level macros to be inserted.

• The ‘print()’ method for class ‘"summary.aov"’ did not pass on arguments such as ‘signif.stars’ when ‘summary()’ was called on a single object. (PR#14684)

• In rare cases ‘ks.test()’ could return a p-value very slightly less than 0 by rounding error. (PR#14671)

• If ‘trunc()’ was called on a ‘"POSIXlt"’ vector and the result was subsetted, all but the first element was converted to ‘NA’. (PR#14679)

• ‘install.packages()’ puts its cache files in subdirectories to avoid very rare problems with excessively long path names. (PR#14699)

CHANGES IN R-devel BUG FIXES

• 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.

2.13.1 patched BUG FIXES

• The ‘print()’ method for class ‘"summary.aov"’ did not pass on arguments such as ‘signif.stars’ when ‘summary()’ was called on a single object. (PR#14684)

• In rare cases ‘ks.test()’ could return a p-value very slightly less than 0 by rounding error. (PR#14671)