The ‘R Changes: 2.9.1-2.10.0 Patched’ article from the 2009-2 issue.
The PCRE library has been updated to version 8.00.
R CMD INSTALL has new options –no-R, –no-libs, –no-data,
–no-help, –no-demo, –no-exec, and –no-inst to suppress
installation of the specified part of the package. These are
intended for special purposes (e.g. building a database of help
pages without fully installing all packages).
The documented line-length limit of 4095 bytes when reading from the
console now also applies also to parse(file="") (which previously
had a limit of around 1024 bytes).
A Bioconductor mirror can be set for use by setRepositories() via
the option "BioC_mirror", e.g. the European mirror can be selected
by options(BioC_mirror="http://bioconductor.
statistik.tu-dortmund.de")
Double-clicking in a tk_select.list() list box now selects the
item and closes the list box (as happens on the Windows
select.list() widget).
configure will be able to find a usable libtiff in some rare circumstances where it did not previously (where libtiff needed to be linked explicitly against -ljpeg).
Making refman.pdf works around a problem with the indexing with
hyperref 6.79d and later.
extended argument is deprecated in strsplit(), grep(),
grepl(), sub(), gsub(), regexpr() and gregexpr() (not just
the value extended = FALSE) and will be removed in R 2.11.0.trigamma(x) and other psigamma(x, n) calls are now accurate for
very large abs(x). (PR#14020)
[g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space
when used with a very long vector containing some non-ASCII strings.
The default method of weighted.mean(na.rm = TRUE) did not omit
weights for NA observations in 2.10.0. (PR#14032)
[g]regexpr(pattern, fixed = TRUE) returned match positions in
bytes (not characters) in an MBCS locale if pattern was a single
byte.
[g]sub(fixed = TRUE) with a single-byte pattern could conceivably
have matched part of a multibyte character in a non-UTF-8 MBCS.
findLineNum() and setBreakpoint() would sometimes fail if the
specified file was not in the current directory.
Package tcltk’s demo(tkdensity) was broken in 2.9.0 when demo()
was changed to set par(ask = TRUE).
gsub() with backrefs could fail on extremely long strings
(hundreds of thousands of characters) due to integer overflow in a
length calculation.
abline(*, untf=TRUE) now uses a better x-grid in log-scale, e.g.,
for plot(c(1,300), c(1,300), log="xy") ;
abline(4,1, untf=TRUE).
detach/unloadNamespace() arrange to flush the package’s lazyload
cache of R objects once the package/namespace is no longer needed.
There have been small fixes to the rendering of help, e.g.
\command is now rendered verbatim (so e.g. – is not interpreted,
PR#14045).
Also, there are many small changes to help files where the new converters were not rendering them in the same way as before.
available.packages() would fail when run on a repository with no
packages meeting the filtering conditions. (PR#14042)
rep(x, times, each = 2) gave invalid results when the times
argument is a vector longer than x. Reported by Bill Dunlap.
An error when unloadNamespace() attempted to run the .onUnload()
function gave an error in the reporting function and so was not
reported properly.
Text help rendering did not handle very long input lines properly.
promptMethods() generated signature documentation improperly.
pgamma(x, a, lower.tail=FALSE) and qgamma(..) are now
considerably more accurate in some regions for very small a.
qgamma() now correctly returns 0 instead of NaN in similar extreme
cases, and qgamma() no longer warns in the case of small a, see
(PR#12324).
unname() now also removes names from a zero length vector.
Printing results from ls.str() no longer evaluates unevaluated
calls.
complete.cases() failed on a 0-column data frame argument.
(Underlies PR#14066.)
It could return nonsensical results if no input determined the number of cases (seen in the no-segfault tests).
An error in nls() with a long formula could cause a segfault.
(PR#14059)
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 probablilities 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.
intToUtf8() could fail when asked to produce 10Mb or more strings,
something it was never intended to do: unfortunately Windows crashed
R (other OSes reported a lack of resources). (PR#14068)
chisq.test() could fail when given argument x or y which
deparsed to more than one line. (Reported by Laurent Gauthier.)
S4 methods are uncached whenever the name space containing them is
unloaded (by unloadNamespace() as well as by
detach(unload = TRUE)).
The internal record-keeping by dyn.load /dyn.unload was
incomplete, which could crash R if a DLL that registered .External
routines had earlier been unloaded.
bessel[JY](x, nu) with nu a negative integer (a singular case) is
now correct, analogously to besselI(), see PR#13556, below.
tools::file_path_as_absolute() doubled the file separator when
applied to a file such as /vmunix or (on Windows) d:/afile in a
directory for which getwd() would return a path with a trailing
separator (largely cosmetic, as reasonable file systems handle such
a path correctly). (Perhaps what was meant by PR#14078.)
unsplit(drop = TRUE) applied to a data frame failed to pass drop
to the computation of row names. (PR#14084)
The "difftime" method of mean() ignored its na.rm argument.
tcltk::tk_select.list() is now more likely to remove the widget
immediately after selection is complete.
Adding/subtracting a "difftime" object to/from a "POSIXt" or
"Date" object works again (it was broken by the addition of
Ops.difftime).
Conversion to latex of an Rd file with no aliases failed.
wilcox.test(*, conf.int = TRUE) has
achieved.level corrected and, for exact = FALSE, now gives an
“estimate” which does not depend on the alternative used.
help.search() failed when the package argument was specified.
(PR#14113)
configure will be able to find a usable libtiff in some rare circumstances where it did not previously (where libtiff needed to be linked explicitly against -ljpeg).
cairo >= 1.2 is now required (1.2.0 was released in July 2006) for cairo-based graphics devices (which remain optional).
A suitable iconv() is now required: support for configure option
–without-iconv has been withdrawn (it was deprecated in R 2.5.0).
Perl is no longer “essential”. R can be built without it, but
scripts R CMD build, check, Rprof and Sd2d require it.
A system function is now essential (a working Sys.glob() has been
assumed since R 2.9.0 at least).
C99 support for MBCS is now required, and configure option
–disable-mbcs has been withdrawn.
Having a version of tar capable of automagically detecting
compressed archives is useful for utils::untar(), and so gtar (a
common name for GNU tar) is preferred to tar: set environment
variable TAR to specify a particular tar command.
extended argument is deprecated in strsplit(), grep(),
grepl(), sub(), gsub(), regexpr() and gregexpr() (not just
the value extended = FALSE) and will be removed in R 2.11.0.Package help is now converted from Rd by the R-based converters that were first introduced in 2.9.0. This means
- Packages that were installed by R-devel after 2009-08-09 should not be used with earlier versions of R, and most aspects of package help (including the runnable examples) will be missing if they are so used.
- Text, HTML and latex help and examples for packages installed
under the new system are converted on-demand from stored parsed Rd
files. (Conversions stored in packages installed under R < 2.10.0
are used if no parsed Rd files are found. It is recommended that
such packages be re-installed.)
HTML help is now generated dynamically using an HTTP server running in the R process and listening on the loopback interface.
- Those worried about security implications of such a server can
disable it by setting the environment variable R_DISABLE_HTTPD to
a non-empty value. This disables help.start() and HTML help (so
text help is shown instead).
- The Java/Javascript search engine has been replaced by an HTML
interface to help.search(). help.start() no longer has an
argument searchEngine as it is no longer needed.
- The HTML help can now locate cross-references of the form
\link[pkg]{foo} and \link[pkg:foo]{bar} where foo is an alias
in the package, rather than the documented (basename of a) filename
(since the documentation has been much ignored).
polygon(), pdf() and postscript() now have a parameter
fillOddEven (default FALSE), which controls the mode used for
polygon fills of self-intersecting shapes.
New debugonce() function; further,
getOption("deparse.max.lines") is now observed when debugging,
from a code suggestion by John Brzustowski. (PR#13647/8)
plot() methods for "stepfun" and hence "ecdf" no longer plot
points by default for n \(>=\) 1000.
{[g]sub(*, perl=TRUE)} now also supports '\E' in order to
*end* \U and \L case changes, thanks to a patch from Bill
Dunlap.
factor(), ‘levels<-‘(), etc, now ensure that the resulting
factor levels are unique (as was always the implied intention).
Factors with duplicated levels are still constructible by low-level
means, but are now declared illegal.
New print() (S3) method for class "function", also used for
auto-printing. Further, .Primitive functions now print and
auto-print identically. The new method is based on code suggestions
by Romain François.
The print() and toLatex() methods for class "sessionInfo" now
show the locale in a nicer format and have arguments to suppress
locale information.
In addition to previously only round(), there are other ‘Math’
group (S3) methods for "difftime", such as floor(), signif(),
abs(), etc.
For completeness, old.packages() and available.packages() allow
type to be specified (you could always specify available or
contriburl).
available.packages() by default only returns information on the
latest versions of packages whose version requirements are
satisified by the currently running R.
tools::write_PACKAGES() has a new argument latestOnly, which
defaults to TRUE when only the latest versions in the repository
will be listed in the index.
getOption() has a new argument default that is returned if the
specified option is not set. This simplifies querying a value and
checking whether it is NULL or not.
parse() now warns if the requested encoding is not supported.
The "table" method of as.data.frame() gains a stringsAsFactors
argument to allow the classifying factors to be returned as
character vectors rather than the default factor type.
If model.frame.default() encounters a character variable where
xlev indicates a factor, it now converts the variable to a factor
(with a warning).
curve() now returns a list containing the points that were drawn.
spineplot() now accepts axes = FALSE, for consistency with other
functions called by plot.factor().
The Kendall and Spearman methods of cor.test() can optionally use
continuity correction when not computing exact p-values. (The
Kendall case is the wish of PR#13691.)
R now keeps track of line numbers during execution for code sourced
with options(keep.source = TRUE). The source reference is
displayed by debugging functions such as traceback(), browser(),
recover(), and dump.frames(), and is stored as an attribute on
each element returned by sys.calls(). [Experimental]
More functions now have an implicit (S4) generic definition.
quantile.default() now disallows factors (wish of PR#13631) and
its help documents what numeric-like properties its input need to
have to work correctly.
weighted.mean() is now generic and has "Date", "POSIXct" and
"POSIXlt" methods.
Naming subscripts (e.g. x[i=1, j=2]) in "data.frame" methods for
[ and [[ now gives a warning. (Names are ignored in the default
method, but could have odd semantics for other methods, and do for
the "data.frame" ones.)
as.data.frame() has an "aovproj" method. (Wish of PR#13505)
as.character(x) for numeric x no longer produces strings such as
"0.30", i.e., with trailing zeros. This change also renders levels
construction in factor() more consistent.
codocClasses(), which checks consistency of the documentation of
S4 class slots, now does so in considerably more cases. The
documentation of inherited slots (from superclasses) is now
optional. This affects R CMD check <pkg> when the package defines
S4 classes.
codoc() now also checks S4 methods for code/documentation
mismatches.
for(), while(), and repeat() loops now always return NULL as
their (invisible) value. This change was needed to address a
reference counting bug without creating performance penalties for
some common use cases.
The print() method for ls.str() results now obeys an optional
digits argument.
The method argument of glm() now allows user-contributed
methods.
More general reorder.default() replaces functionality of
reorder.factor() and reorder.character().
The function aspell() has been added to provide an interface to
the Aspell spell-checker.
Filters RdTextFilter() and SweaveTeXFilter() have been added to
the tools package to provide support for aspell() or other spell
checkers.
xtabs() with the new option sparse = TRUE now returns a sparse
Matrix, using package Matrix.
contr.sum() etc gain an argument sparse which allows sparse
matrices to be returned.
contrasts() also gains a sparse argument which it passes to the
actual contrast function if that has a formal argument sparse.
contrasts(f, .) <- val now also works when val is a sparse
Matrix. It is planned that model.matrix() will work with such
factors f in the future.
readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the
NEWS file. However, it is safer to use only ASCII code there
because not all editors recognize BOMs.
New utility function inheritedSlotNames() for S4 class
programming.
tabulate() now allows NAs to pass through (and be ignored).
If debug() is called on an S3 generic function then all methods
are debugged as well.
Outlier symbols drawn by boxplot() now obey the outlwd argument.
Reported by Jurgen Kluge.
svd(x) and eigen(x) now behave analogously to qr(x) in
accepting logical matrices x.
File NEWS is now in UTF-8, and has a BOM (often invisible) on the
first line, and Emacs local variables set for UTF-8 at the end.
RShowDoc("NEWS") should display this correctly, given suitable
fonts.
terms.formula(simplify = TRUE) now does not deparse the LHS and so
preserves non-standard responses such as ‘a: b‘ (requested by
Sundar Dorai-Raj).
New function news() for building and querying R or package news
information.
z^n for integer n and complex z is more accurate now if
\(|n| <= 65536\).
factor(NULL) now returns the same as factor(character(0))
instead of an error, and table(NULL) consequently does
analogously.
as.data.frame.vector() (and its copies) is slightly faster by
avoiding a copy if there are no names (following a suggestion of Tim
Hesterberg).
writeLines(), writeBin() and writeChar() have a new argument
useBytes. If false, character strings with marked encodings are
translated to the current locale (as before) but if true they are
written byte-by-byte.
iconv() has a new argument mark which can be used (by experts)
to suppress the declaration of encodings.
DESCRIPTION ‘LinkingTo’ specs are now recognized as installation
dependencies, and included in package management computations.
Standardized DESCRIPTION ‘License’ specs are now available for
package management computations.
"\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8
encoded string even in non-UTF-8 locales (this has been implemented
on Windows since R 2.7.0). The semantics have been changed slightly:
a string containing such escapes is always stored in UTF-8 (and
hence is suitable for portably including Unicode text in packages).
New as.raw() method for "tclObj" objects (wish of PR#13578).
Rd.sty now makes a better job of setting email addresses,
including using a monospaced font.
textConnection() gains an encoding argument to determine how
input strings with marked encodings will be handled.
R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi –pdf.
R CMD check now checks links where a package is specified
(\link[pkg]{file} or \link[pkg:file]{topic}), if the package is
available. It notes if the package is not available, as in many
cases this is an error in the link.
identical() gains three logical arguments, which allow for even
more differentiation, notably -0 and 0.
legend() now can specify the border color of filled boxes,
thanks to a patch from Frederic Schutz.
Indexing with a vector index to [[]] has now been extended to all
recursive types.
Pairlists may now be assigned as elements of lists. (Lists could
always be created with pairlist elements, but [[<- didn’t support
assigning them.)
The parser now supports C-preprocessor-like #line directives, so
error messages and source references may refer to the original file
rather than an intermediate one.
New functions findLineNum() and setBreakpoint() work with the
source references to find the location of source lines and set
breakpoints (using trace()) at those lines.
Namespace importing is more careful about warning on masked generics, thanks to a patch by Yohan Chalabi.
detach() now has an argument character.only with the same
meaning as for library() or require().
available.packages() gains a filters argument for specifying the
filtering operations performed on the packages found in the
repositories. A new built-in license/FOSS filter only retains
packages for which installation can proceed solely based on packages
which can be verified as Free or Open Source Software (FOSS)
employing the available license specifications.
In registering an S3 class by a call to setOldClass(), the data
part (e.g., the object type) required for the class can be included
as one of the superclasses in the Classes argument.
The argument f to showMethods() can be an expression evaluating
to a generic function, allowing methods to be shown for non-exported
generics and other nonstandard cases.
sprintf() now supports %o for octal conversions.
New function Sys.readlink() for information about symbolic links,
including if a file is a symbolic link.
Package tools has new functions checkRdaFiles() and
resaveRdaFiles() to report on the format of .rda/.RData data
files, and to re-save them in a different compressed format,
including choosing the most compact format available.
A new INSTALL option, –resave-data, makes use of this.
File ~/.R/config is used in preference to ~/.Rconfig, and these
are now documented in ‘R Installation and Administration’.
Logic operations with complex numbers now work, as they were always documented to, and as in S.
arrows() and segments() allow one of x1 or y1 to be omitted
to simplify the specification of vertical or horizontal lines
(suggestion of Tim Hesterberg).
approxfun() is faster by avoiding repeated NA checks (diagnosis
and patch by Karline Soetaert & Thomas Petzoldt).
There are the beginnings of a Nynorsk translation by Karl Ove Hufthammer.
stripchart() allows par bg to be passed in for the background
colour for pch = 21 (wish of PR#13984).
New generic function .DollarNames() to enable class authors to
customize completion after the $ extractor.
load(), save(), dput() and dump() now open a not-yet-open
connection in the appropriate mode (as other functions using
connections directly already did).
A different regular expression engine is used for basic and extended regexps and is also for approximate matching. This is based on the TRE library of Ville Laurikari, a modifed copy of which is included in the R sources.
This is often faster, especially in a MBCS locale.
Some known differences are that it is less tolerant of invalid
inputs in MBCS locales, and in its interpretation of undefined
(extended) regexps such as "^*". Also, the interpretation of
ranges such as [W-z] in caseless matching is no longer to map the
range to lower case.
This engine may in future be used in ‘literal’ mode for
fixed = TRUE, and there is a compile-time option in
src/main/grep.c to do so.
The use of repeated boundary regexps in gsub() and gregexpr() as
warned about in the help page does not work in this engine (it did
in the previous one since 2005).
Extended (and basic) regexps now support same set of options as for
fixed = TRUE and perl = TRUE, including useBytes and support
for UTF-8-encoded strings in non-UTF-8 locales.
agrep() now has full support for MBCS locales with a modest speed
penalty. This enables help.search() to use approximate matching
character-wise rather than byte-wise.
[g]sub use a single-pass algorithm instead of matching twice and
so is usually faster.
The perl = TRUE versions now work correctly in a non-UTF-8 MBCS
locale, by translating the inputs to UTF-8.
useBytes = TRUE now inhibits the translation of inputs with marked
encodings.
strsplit() gains a useBytes argument.
The algorithm used by strsplit() has been reordered to batch by
elements of split: this can be much faster for fixed = FALSE (as
multiple compilation of regexps is avoided).
The help pages, including ?regexp, have been updated and should be
consulted for details of the new implementations.
Rd file changesA new dynamic HTML help system is used by default, and may be
controlled using tools::startDynamicHelp(). With this enabled,
HTML help pages will be generated on request, resolving links by
searching through the current .libPaths(). The user may set
options("help.ports") to control which IP port is used by the
server.
help.start() no longer sets options(htmlhelp = TRUE) (it used to
on Unix but not on Windows). Nor does it on Unix reset the
"browser" option if given an argument of that name.
Arguments update and remote are now available on all platforms:
the default is update = FALSE since the http server will update
the package index at first use.
help() has a new argument help_type (with default set by the
option of that name) to supersede offline, htmlhelp and
chmhelp (although for now they still work if help_type is
unset). There is a new type, "PDF" to allow offline PDF (rather
than PostScript).
A function offline_help_helper() will be used if this exists in
the workspace or further down the search path, otherwise the
function of that name in the ‘utils’ name space is used.
Plain text help is now used as the fallback for HTML help (as it always was for Compiled HTML help on Windows).
It is possible to ask for static HTML pages to be prebuilt via the
configure option –enable-prebuilt-html. This may be useful for
those who wish to make HTML help available outside R, e.g. on a
local web site.
An experimental tag \Sexpr has been added to Rd files, to
evaluate expressions at build, install, or render time. Currently
install time and render time evaluation are supported.
Tags \if, \ifelse and \out have been added to allow
format-specific (or more general, using \Sexpr) conditional text
in man pages.
The parse_Rd() parser has been made more tolerant of coding errors
in Rd files: now all syntax errors are reported as warnings, and
an attempt is made to continue parsing.
parse_Rd() now has an argument fragment (default FALSE) to
accept small fragments of Rd files (so that \Sexpr can output Rd
code which is then parsed).
parse_Rd() now always converts its input to UTF-8. The Rd2*
rendering functions have a new parameter, outputEncoding, which
controls how their output is encoded.
parse_Rd() no longer includes the newline as part of a "%"-style
comment.
There have been various bug fixes and code reorganization in the Rd renderers Rd2HTML, Rd2latex, Rd2txt, and Rd2ex.
All example files are now created with either ASCII or UTF-8 encoding, and the encoding is only marked in the file if there is any non-UTF-8 code (previously it was marked if the help file had non-ASCII contents, possibly in other sections).
print.Rd() now adds necessary escape characters so that printing
and re-parsing an Rd object should produce an equivalent object.
parse_Rd() was incorrectly handling multiple backslashes in R code
strings, converting 4n+3 backslashes to 2n+1 instead of 2n+2.
parse_Rd() now recognizes the tag within a quoted string in R-like
text.
parse_Rd() now treats the argument of as LaTeX-like, rather than
verbatim.
New function untar() to list or unpack tar archives, possibly
compressed. This uses either an external tar command or an
internal implementation.
New function tar() to create (possibly compressed) tar archives.
New functions memCompress() and memDecompress() for in-memory
compression and decompression.
bzfile() has a compress argument to select the amount of effort
put into compression when writing.
New function xzfile() for use with xz-compressed files. (This can
also read files compressed by some versions of ‘lzma’.)
gzfile() looks at the file header and so can now also read
bzip2-ed files and xz-compressed files.
There are the new options of save(compress = "bzip2") and "xz"
to use bzip2 or xz compression (which will be slower, but can give
substantially smaller files). Argument compression_level gives finer
control over the space/time tradeoffs.
load() can read such saves (but only as from this version of R).
R CMD INSTALL/check and writePACKAGES (tools) accept a wider
range of compressed tar archives. Precisely how wide depends on the
capabilities of the host system’s tar command: they almost always
include .tar.bz2 archives, and with modern versions of tar other
forms of compression such as lzma and xz, and arbitrary extensions.
R CMD INSTALL has a new option –data-compress to control the
compression used when lazy-loading data. New possibilities are
–data-compress=bzip2 which will give ca 15% better compression at
the expense of slower installation times, and –data-compress=xz,
often giving even better compression on large datasets at the
expense of much longer installation times. (The latter is used for
the recommended packages: it is particularly effective for
survival.)
file() for open = "", "r" or "rt" will automagically detect
compressed files (from gzip, bzip2 or xz). This means that
compressed files can be specified by file name (rather than via a
gzfile() connection) to read.table(), readlines(), scan()
and so on.
data() can handle compressed text files with extensions
.{txt,tab,csv}.{gz,bz2,xz} .
png(type="cairo1") is defunct: the value is no longer recognized.
tools::Rd_parse() is defunct (as this version of R uses only Rd
version 2).
Use of ~/.Rconf (which was deprecated in favour of ~/.Rconfig
in 2004) has finally been removed.
Bundles of packages are deprecated. See ‘Writing R Extensions’ for the steps needed to unbundle a bundle.
help() arguments offline, htmlhelp and chmhelp are
deprecated in favour of help_type.
clearNames() (stats) is deprecated for unname().
Basic regular expressions (extended = FALSE) are deprecated in
strsplit, grep and friends. There is a precise POSIX standard for
them, but it is not what recent RE engines implement, and it seems
that in almost all cases package authors intended fixed = TRUE
when using extended = FALSE.
methods::trySilent() is deprecated for try(*, silent=TRUE) or -
more efficiently and flexibly - something like
tryCatch(*, error = function(e) e).
index.search() is deprecated: there are no longer directories of
types other than ‘help’.
There is some makefile support for adding/updating translations in
packages: see po/README and ‘Writing R Extensions’.
There is support for the use of ‘dngettext’ for C-level translations in packages: see ‘Writing R Extensions’.
trigamma(x) and other psigamma(x, n) calls are now accurate for
very large abs(x). (PR#14020)
[g]sub() could use excessive stack space when used with a very
long vector of non-ASCII data.
The default method of weighted.mean(na.rm = TRUE) did not omit
weights for NA observations in 2.10.0. (PR#14032)
Assigning an extra 0-length column to a data frame by
DF[, "foo"] <- value now works in most cases (by filling with
NAs) or fails. (It used to give a corrupt data frame.)
validObject() avoids an error during evaluation in the case of
various incorrect slot definitions.
n:m now returns a result of type "integer" in a few more
boundary cases.
The zap.ind argument to printCoefmat() did not usually work as
other code attempted to ensure that non-zero values had a non-zero
representation.
printCoefmat() formatted groups of columns together, not just the
cs.ind group but also the zap.ind group and a residual group. It
now formats all columns except the cs.ind group separately (and zaps
the zap.ind group column-by-column). The main effect will be see
in the output from print.anova, as this grouped SS-like columns in
the zap.ind group.
R_ReplDLLinit() initializes the top-level jump so that some
embedded applications on Windows no longer crash on error.
identical() failed to take the encoding of character strings into
account, so identical byte patterns are not necessarily identical
strings, and similarly Latin-1 and UTF-8 versions of the same string
differ in byte pattern.
methods(f) used to warn unnecessarily for an S4 generic f which
had been created based on an existing S3 generic.
The check for consistent ordering of superclasses was not ignoring all conditional relations (the symptom was usually spurious warnings for classes extending "array").
Trying to assign into a raw vector with an index vector containing
NAs could cause a segfault. Reported by Hervé Pagès.
Rscript could segfault if (by user error) its filename argument was missing. Reported by Martin Morgan.
getAnywhere() (and functions that use it, including argument
completion in the console) did not handle special built-in
functions. Reported by Romain François.
order() was missing a PROTECT() call and so could segfault when
called on character data under certain (rare) circumstances
involving marked non-native encodings.
prettyNum(z, drop0trailing=TRUE) did not work correctly when z was
a complex vector. Consequently, str(z, ...) also did not.
(PR#13985)
make distclean removed too many files in etc/ if
builddir = srcdir.
R CMD replaced TEXINPUTS rather than appending to it (as
documented and intended).
help.start() no longer fails on unix when "browser" is a
function.
pbeta(x, *, log.p = TRUE) is sometimes more accurate, e.g., for
very small x.
Unserializing a pre-2.8 workspace containing pure ASCII character objects with a LATIN1 or UTF-8 encoding would corrupt the CHARSXP cache.
Sys.setlocale() to change the LC_COLLATE setting is more likely to
change the collation provided by ICU.Names of datasets could clash with temporary filenames used when running examples, causing errors.
as.complex() sometimes warned about NAs on coercions and
sometimes not (when the C function asComplex was used, e.g. on list
elements). (PR#13942)
cat() on an unopened connection could close it twice, and file()
connections segfaulted on some systems.
Printing a list could segfault if the elements are nested too deeply.
install.packages(NULL) now lists packages only once even if they
occur in more than one repository (as the latest compatible version
of those available will always be downloaded).
approxfun() and approx() now accept a rule of length two, for
easy specification of different interpolation rules on left and
right.
They no longer segfault for invalid zero-length specification of
yleft, yright, or f.
seq_along(x) is now equivalent to seq_len(length(x)) even where
length() has an S3/S4 method; previously it (intentionally) always
used the default method for length().
PCRE has been updated to version 7.9 (for bug fixes).
agrep() uses 64-bit ints where available on 32-bit platforms and
so may do a better job with complex matches. (E.g. PR#13789, which
failed only on 32-bit systems.)
R CMD Rd2txt is deprecated, and will be removed in 2.10.0. (It is
just a wrapper for R CMD Rdconv -t txt.)
tools::Rd_parse() is deprecated and will be removed in 2.10.0
(which will use only Rd version 2).
parse_Rd() still did not handle source reference encodings
properly.
The C utility function PrintValue no longer attempts to print attributes for CHARSXPs as those attributes are used internally for the CHARSXP cache. This fixes a segfault when calling it on a CHARSXP from C code.
PDF graphics output was producing two instances of anything drawn with the symbol font face. (Report from Baptiste Auguié.)
length(x) <- newval and grep() could cause memory corruption.
(PR#13837)
If model.matrix() was given too large a model, it could crash R.
(PR#13838, fix found by Olaf Mersmann.)
gzcon() (used by load()) would re-open an open connection,
leaking a file descriptor each time. (PR#13841)
The checks for inconsistent inheritance reported by setClass() now
detect inconsistent superclasses and give better warning messages.
print.anova() failed to recognize the column labelled P(>|Chi|)
from a Poisson/binomial GLM anova as a p-value column in order to
format it appropriately (and as a consequence it gave no
significance stars).
A missing PROTECT caused rare segfaults during calls to load().
(PR#13880, fix found by Bill Dunlap.)
gsub() in a non-UTF-8 locale with a marked UTF-8 input could in
rare circumstances overrun a buffer and so segfault.
R CMD Rdconv –version was not working correctly.
Missing PROTECTs in nlm() caused "random" errors. (PR#13381 by
Adam D.I. Kramer, analysis and suggested fix by Bill Dunlap.)
Some extreme cases of pbeta(log.p = TRUE) are more accurate
(finite values < -700 rather than -Inf). (PR#13786)
pbeta() now reports on more cases where the asymptotic expansions
lose accuracy (the underlying TOMS708 C code was ignoring some of
these, including the PR#13786 example).
new.env(hash = TRUE, size = NA) now works the way it has been
documented to for a long time.
tcltk::tk_choose.files(multi = TRUE) produces better-formatted
output with filenames containing spaces. (PR#13875)
R CMD check –use-valgrind did not run valgrind on the package
tests.
The tclvalue() and the print() and as.xxx methods for class
"tclObj" crashed R with an invalid object – seen with an object
saved from an earlier session.
R CMD BATCH garbled options -d <debugger> (useful for
valgrind, although –debugger=valgrind always worked)
INSTALL with LazyData and Encoding declared in DESCRIPTION might
have left options("encoding") set for the rest of the package
installation.
New function anyDuplicated(x) returns 0 (= FALSE) or the index
of the first duplicated entry of x.
matplot(), matlines() and matpoints() now also obey a lend
argument, determining line end styles. (Wish of PR#13619).
bw.SJ(), bw.bcv() and bw.ucv() now gain an optional tol
argument allowing more accurate estimates.
new.packages() no longer regards packages with the same name as a
member of an installed bundle as ‘new’ (this is now consistent with
the dependency checks in install.packages()).
It no longer reports on partially installed bundles (since members can be updated individually if a bundle is unbundled).
old.packages() and hence updates.packages() will look for
updates to members of package bundles before updates to the whole
bundle: this allow bundles to be split and installations updated.
nlminb() gives better non-convergence messages in some cases.
S3 method dispatch will support S4 class inheritance for S3 methods,
for primitives and via UseMethod(), if the argument
S3methods=TRUE is given to setClass(). S4 method dispatch will
use S3 per-object inheritance if S3Class() is set on the object.
See ?Methods and the paper referenced there.
R CMD INSTALL is more tolerant of (malformed) packages with a
‘man’ directory but no validly named .Rd files.
R CMD check now reports where options are used that cause some of
the checks to be skipped.
RSiteSearch has been updated to be consistent with the new layout
of the search site itself, which now includes separate options for
vignettes, views, and r-sig-mixed-models, as well as changed names
for r-help. (Contributed by Jonathan Baron.)
That R CMD check makes use of a
<pkg>/tests/Examples/<pkg>-Ex.Rout.save file as a reference result
is now documented in ‘Writing R Extensions’.
print.atomic() (defunct since 1.9.0) has been removed since it
caused confusion for an S4 class union "atomic".
png(type="cairo1") is deprecated – it was only needed for
platforms with 1.0 \(<=\) cairo \(<\) 1.2.
The ... argument was not handled properly when ... was found in
the enclosure of the current function, rather than in the function
header itself. (This caused integrate() to fail in certain cases.)
interaction() now ensures that the levels of the result are
unique.
packageDescription() and hence sessionInfo() now report the
correct package version also for a non-attached loaded namespace of
a version different from the default lib.loc.
smoothScatter() now also works when e.g. xlim[2] < xlim[1].
parse_Rd() would mishandle braces when they occurred at the start
of a line within an R string in an Rd file (reported by Alex
Couture-Beil) or when they occurred in an R comment (reported by
Mark Bravington).
readNEWS() missed version numbers with more than one digit.
building R –without-x no longer fails (PR#13665)
printCoefmat(cbind(0,1)) now works too (PR#13677)
bw.SJ(c(1:99, 1e6)) now works too.
Rd2txt() could not handle empty descriptions of items in an Rd
file (reported by Mark Bravington), and did not wrap long lists of
arguments if they were given in a single item.
stars() would do a partial plot when called with plot = FALSE;
it now consistently returns the locations of the stars.
Rd2latex() could not handle empty sections.
old.packages() and hence update.packages() would fail on a
repository which contained only one package but with multiple
versions of that package.
as.character.Rd() added extra braces when displaying two-argument
macros. (Report and fix by Manuel Eugster.)
unsplit() was misbehaving in the case of single-column data
frames. (Reported by Will Gray.)
as(I(1), "vector") and similar coercions from objects of
"unregistered" S3 classes now work.
srcref records produced by parse() and parse_Rd() did not record
the encoding of the source file. (Reported by Romain François.)
The X11 version of View() was misbehaving in MBCS locales, and
PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama.
R CMD check looked at the environment variable PDFLATEX, but as
from R 2.8.1 R CMD Rd2dvi used R_PDFLATEXCMD in preference, and
that was set by R CMD (and not PDFLATEX). Now R CMD check
looks at R_PDFLATEXCMD.
The new (in 2.9.0) stringsAsFactors argument to expand.grid()
was not working: it now does work but has default TRUE for
backwards compatibility.
tcrossprod(<1d-array>, <matrix>) now does work when the arguments
are of compatible dimensions.
qbinom() now is accurate also in (large size, small prob) cases.
(PR#13711)
The calculation of the Spearman p-value in cor.test() is slightly
more accurate in some cases. (PR#13574)
The digamma(), trigamma() and psigamma() functions could be
inaccurate for values of x around 1e-15 due to cancellation.
(PR#13714).
median.default() was altered in 2.8.1 to use sum() rather than
mean(), although it was still documented to use mean(). This
caused problems for POSIXt objects, for which mean() but not
sum() makes sense, so the change has been reverted.
Assigning an extra 0-length column to a data frame by
DF$foo <- value gave a corrupt data frame rather than failing.
(PR#13724) This also happened for DF[["foo"]] <- value.
R CMD INSTALL no longer gives a spurious warning about old R
versions ignoring multiple dependencies, if the conditions are known
to be satisfied.
The test for setting dim() allowed a value with two or more NAs
to be set on a 0-length object. (PR#13729) Also, it allowed an even
number of negative values.
xtfrm(), rank(), sort() and order() did not always make use
of custom comparison methods specific to the class of elements being
sorted.
Increase NAMED value on seq value in for() loop so loop code
cannot modify seq value.
Prevent rectangles of size < 0.5 pixel from disappearing in Quartz when using rastered backend. (PR#13744)
Printing _NA_complex_ had a low-level thinko; patch thanks to Bill
Dunlap.
CP1257 encoding for postscript/PDF has been corrected. (PR#13736)
aov() with an error term was evaluating the ... arguments in
2.9.0 whilst checking their names, so could fail by evaluating them
in the wrong place. (PR#13733)
The print() method for arima() failed if all coefs were fixed.
R CMD INSTALL –no-latex was not implemented in 2.9.0 (only).
Added a needed PROTECT call in RunFinalizers to handle cases where
the routine is called recursively from a GC in a finalizer.
Constructing error messages about unused arguments in calls to closures no longer evaluates the arguments.
qr(x, LAPACK=TRUE) did not coerce integer x to numeric.
qr.coef() misbehaved in the LAPACK case with a matrix RHS, so that
solve(qr(x, LAPACK=TRUE)) gave wrong results. (Found by Avraham
Adler, PR#13762 by Ravi Varadhan.)
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
team, "The R Journal: R Changes: 2.9.1-2.10.0 Patched", The R Journal, 2009
BibTeX citation
@article{RJ-2009-2-r-changes,
author = {team, The R Core},
title = {The R Journal: R Changes: 2.9.1-2.10.0 Patched},
journal = {The R Journal},
year = {2009},
note = {https://journal.r-project.org/news/RJ-2009-2-r-changes},
volume = {1},
issue = {2},
issn = {2073-4859},
pages = {68-79}
}