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Dear Emacs, please make this -*-Text-*- mode!
This file covers NEWS for R 2.x.y.
See 'NEWS' (or doc/html/NEWS.html or doc/NEWS.Rd) for
subsequent changes and NEWS.0 and NEWS.1 for earlier ones.
There is a change in format at 2.10.0: entries from
then on are generated from doc/NEWS.2.Rd.
CHANGES IN R VERSION 2.15.3:
NEW FEATURES:
• lgamma(x) for very small x (in the denormalized range) is no
longer Inf with a warning.
• image() now sorts an unsorted breaks vector, with a warning.
• The internal methods for tar() and untar() do a slightly more
general job for ‘ustar’-style handling of paths of more than 100
bytes.
• Packages compiler and parallel have been added to the reference
index (refman.pdf).
• untar(tar = "internal") has some support for pax headers as
produced by e.g. gnutar --posix (which seems prevalent on
OpenSUSE 12.2) or bsdtar --format pax, including long path and
link names.
• sQuote() and dQuote() now handle 0-length inputs. (Suggestion of
Ben Bolker.)
• summaryRprof() returns zero-row data frames rather than throw an
error if no events are recorded, for consistency.
• The included version of PCRE has been updated to 8.32.
• The tcltk namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child from package
parallel (as in e.g. mclapply()).
• parallel::makeCluster() recognizes the value random for the
environment variable R_PARALLEL_PORT: this chooses a random value
for the port and reduces the chance of conflicts when multiple
users start a cluster at the same time.
UTILITIES:
• The default for TAR on Windows for R CMD build has been changed
to be internal if no tar command is on the path.
This enables most packages to be built ‘out of the box’ without
Rtools: the main exceptions are those which need to be installed
to re-build vignettes and need Rtools for installation (usually
because they contain compiled code).
C-LEVEL FACILITIES:
• On a 64-bit Windows platform with enough RAM, R_alloc can now
allocate up to just under 32GB like other 64-bit platforms.
DEPRECATED AND DEFUNCT:
• Use of col2rgb(0) is deprecated (see the help page for its
limitations).
• The deprecated intensities component returned by hist() is no
longer recognized by the plot() method and will be removed in R
3.0.0.
• real(), as.real() and is.real() are now formally deprecated and
give a warning.
• This is formal notice that the non-API EISPACK entry points in R
will be removed shortly.
INSTALLATION:
• The configure tests for Objective C and Objective C++ now work on
Mac OS 10.8 with Xcode 4.5.2 (PR#15107).
• The cairo-based versions of X11() now work with current versions
of cairographics (e.g. 1.12.10). (PR#15168)
A workaround for earlier versions of R is to use X11.options(type
= "nbcairo").
• Configuration and R CMD javareconf now come up with a smaller set
of library paths for Java on Oracle-format JDK (including
OpenJDK). This helps avoid conflicts between libraries (such as
libjpeg) supplied in the JDK and system libraries. This can
always be overridden if needed: see the ‘R Installation and
Administration’ manual.
BUG FIXES:
• beta(a, b) could overflow to infinity in its calculations when
one of a and b was less than one. (PR#15075)
• lbeta(a, b) no longer gives NaN if a or b is very small (in the
denormalized range).
• bquote() is now able to substitute default arguments in
single-argument functions. (PR#15077)
• browseEnv(html = FALSE) would segfault if called from R (not
R.app) on a CRAN-style Mac OS X build of R.
• [[<- for lists (generic vectors) needed to increment NAMED count
when RHS is used more than once. (PR#15098)
• On Windows, warnings about opening a file or pipe with a
non-ASCII description were sometimes output in UTF-8 rather than
in the current locale's character set.
• The call() function did not duplicate its arguments. (PR#15115)
• TukeyHSD() could give NA results with some na.action methods such
as na.exclude(). (Hinted at on R-help by John Fox.)
• The deprecated svd(X, LINPACK = TRUE) could alter X in R
2.15.[12]. (Reported by Bill Dunlap.)
• Under Windows, file.link() and file.symlink() used the link name
twice, so would always fail. (Reported by Rui Barradas/Oliver
Soong).
• summaryRprof(memory = "both") mixed up the units of Vcells and
Ncells: it now works in bytes. (PR#15138)
• tools::Rd2HTML() would sometimes delete text. (PR#15134)
• plot() failed for "table" objects containing just one entry.
(PR#15118)
• embedFonts() needed to quote some filepaths. (PR#15149)
• parallel::mccollect() handled NULL returns incorrectly (removing
the element rather than setting it to NULL).
• The full reference index (fullrefman.pdf) was missing packages
compiler and parallel.
• The report for optim(method = "L-BFGS-B", control = list(trace =
1)) reported the last completed and not the current iteration,
unlike other methods and trace levels. (PR#15103)
• qt(1e-12, 1.2) no longer gives NaN.
• dt(1e160, 1.2, log=TRUE) no longer gives -Inf.
• On Windows the untar() function now quotes the directory name
when using an external tar utility, so R CMD check will handle
pathnames containing spaces.
• The version for Windows 8 and Windows Server 2012 is now
displayed by win.version(). (Reported by Gabor Grothendieck.)
• The custom Windows installer target myR in the installer Makefile
did not work in 2.15.2. (Reported by Erich Neuwirth.)
• aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), "A") no longer
segfaults.
• Expressions involving user defined operators were not always
deparsed faithfully. (PR#15179)
• The enc2utf8() function converted NA_character_ to "NA" in
non-UTF-8 locales. (PR#15201)
• The exclude argument to xtabs() was ignored for "factor"
arguments.
• On Windows, work around an event-timing problem when the RGui
console was closed from the ‘X’ control and the closure
cancelled. (This would on some 64-bit systems crash R, typically
those with a slow GPU relative to the CPU.)
• On unix Rscript will pass the r_arch setting it was compiled with
on to the R process so that the architecture of Rscript and that
of R will match unless overridden.
• On Windows, basename(), dirname() and file.choose() have more
support for long non-ASCII file names with 260 or more bytes when
expressed in UTF-8.
CHANGES IN R VERSION 2.15.2:
NEW FEATURES:
• The X11() window gains an icon: the latter may be especially
useful on Ubuntu's ‘Unity’ interface.
The WM_CLASS should be set in circumstances where the Window
Manager failed to make use of X11 resource settings.
(Contributed by Philip Johnson.)
• The "Date" and "POSIXt" methods for cut() will accept an unsorted
breaks argument (as the default method does, although this was
undocumented). (Wish of PR#14961.)
• Reference class methods (in the methods package) that use other
methods in an indirect way (e.g., by sapply()) must tell the code
analysis to include that method. They can now do so by invoking
$usingMethods().
• More Polish translations are available: for the RGui menus and
for several recommended packages.
• Multistratum MANOVA works. In fact, it seems to have done so for
years in spite of the help page claiming it did not.
• qqline() has new optional arguments distribution, probs and
qtype, following the example of lattice's panel.qqmathline().
• The handling of single quotes in the en@quot pseudo-language has
been slightly improved. Double quotes are no longer converted.
• New functions checkPoFiles() and checkPoFile() have been added to
the tools package to check for consistency of format strings in
translation files.
• model.matrix(~1, ...) now also contains the same rownames that
less trivial formulae produce. (Wish of PR#14992, changes the
output of several packages.)
• Misuse of rep() on undocumented types of objects (e.g. calls) is
now reported as an error.
• The included LAPACK has been updated to 3.4.1, with some patches
from the current SVN sources. (_Inter alia_, this resolves
PR#14692.)
• file.copy(recursive = TRUE) has some additional checks on user
error leading to attempted infinite recursion (and on some
platforms to crashing R).
• PCRE has been updated to version 8.31, a bug-fix release.
• The included version of liblzma has been updated to version
5.0.4, a minor bug-fix release.
• New function .bincode(), a ‘bare-bones’ version of
cut.default(labels = FALSE) for use in packages with image()
methods.
• The HTML manuals now use directional single quotes.
• maintainer() now converts embedded new lines to spaces. It no
longer gives a non-obvious error for non-installed packages.
• The X11() device has some protection against being used with
forked processes _via_ package parallel.
• Setting the environment variable R_OSX_VALGRIND (to any value)
allows R to be run under valgrind on Mac OS 10.6 and 10.7
(valgrind currently has very limited support for 10.8), provided
system() is not used (directly or indirectly). This should not
be needed for valgrind >= 3.8.1.
• The model.frame() method for "lm" uses xlevels: this is safer if
data was supplied or model = FALSE was used and the levels of
factors used in the fit had been re-ordered since fitting.
Similarly, model.frame(fm, data=<data>) copies across the
variables used for safe prediction from the fit.
• Functions such as parLapply() in package parallel can make use of
a default cluster if one is set. (Reported by Martin Morgan.)
• chol(pivot = TRUE, LINPACK = FALSE) is now available using LAPACK
3.2 subroutine DPSTRF.
• The functions .C(), .Call(), .External() and .Fortran() now check
that they are called with an unnamed first argument: the formal
arguments were changed from name= to .NAME= in R 2.13.0, but some
packages were still using the old name. This is currently a
warning, but will be an error in future.
• step() no longer tries to improve a model with AIC of -Inf (a
perfect fit).
• spline() and splinefun() gain a new method "hyman", an
implementation of Hyman's method of constructing monotonic
interpolation splines. (Based on contributions of Simon Wood and
Rob Hyndman.)
• On Windows, the C stack size has been increased to 64MB (it has
been 10MB since the days of 32MB RAM systems).
PERFORMANCE IMPROVEMENTS:
• array() is now implemented in C code (for speed) when data is
atomic or an unclassed list (so it is known that as.vector(data)
will have no class to be used by rep()).
• rep() is faster and uses less memory, substantially so in some
common cases (e.g. if times is of length one or length.out is
given, and each = 1).
• findInterval(), tabulate(), cut(), hist() and image.default() all
use .Call() and are more efficient.
• duplicated(), unique() and similar now support vectors of lengths
above 2^29 on 64-bit platforms.
• Omitting PACKAGE in .C() etc calls was supposed to make use of
the DLL from the namespace within which the enclosing function
was defined. It was less successful in doing so than it might
be, and gave no indication it had failed.
A new search strategy is very successful and gives a warning when
it fails. In most cases this is because the entry point is not
actually provided by that package (and so PACKAGE should be used
to indicate which package is intended) but in some the namespace
does not have a DLL specified by a useDynLib() directive so
PACKAGE is required.
UTILITIES:
• R CMD check now checks if a package can be loaded by
library(pkgname, lib.loc = "somewhere") without being on the
library search path (unless it is already installed in .Library,
when it always will be).
• R CMD check --as-cran notes ‘hidden’ files and directories (with
names starting with a dot) that are not needed for the operation
of R CMD INSTALL or R CMD build: such files should be excluded
from the published tarball.
• R CMD check (if checking subdirectories) checks that the R code
in any demos is ASCII and can be parsed, and warns if not.
• When R CMD Rd2pdf is used with inputenx.sty, it allows further
characters (mainly for Eastern European languages) by including
ix-utf8enc.dfu (if available). (Wish of PR#14989.)
• R CMD build now omits several types of hidden files/directories,
including inst/doc/.Rinstignore, vignettes/.Rinstignore,
(.Rinstignore should be at top level), .deps under src,
.Renviron, .Rprofile, .Rproj.user, .backups, .cvsignore,
.cproject, .directory, .dropbox, .exrc, .gdb.history,
.gitattributes, .gitignore, .gitmodules, .hgignore, .hgtags,
.htaccess, .latex2html-init, .project, .seed, .settings,
.tm_properties and various leftovers.
• R CMD check now checks for .C(), .Call(), .External() and
.Fortran() calls in other packages, and gives a warning on those
found from R itself (which are not part of the API and change
without notice: many will be changed for R 3.0.0).
C-LEVEL FACILITIES:
• The limit for R_alloc on 64-bit platforms has been raised to just
under 32GB (from just under 16GB).
• The misuse of .C("name", ..., PACKAGE = foo) where foo is an
arbitrary R object is now an error.
The misuse .C("name",..., PACKAGE = "") is now warned about in R
CMD check, and will be an error in future.
DEPRECATED AND DEFUNCT:
• Use of array() with a 0-length dim argument is deprecated with a
warning (and was contrary to the documentation).
• Use of tapply() with a 0-length INDEX list is deprecated with a
warning.
• Translation packages are deprecated.
• Calling rep() or rep.int() on a pairlist is deprecated and will
give a warning. In any case, rep() converted a pairlist to a
list so you may as well do that explicitly.
• Entry point rcont2 is no longer part of the API, and will move to
package stats in R 3.0.0.
• The ‘internal’ graphics device invoked by
.Call("R_GD_nullDevice", package = "grDevices") is about to be
removed: use pdf(file = NULL) instead.
• eigen(EISPACK = TRUE), chol(pivot = FALSE, LINPACK = TRUE),
chol2inv(LINPACK = TRUE), solve(LINPACK = TRUE) and svd(LINPACK =
TRUE) are deprecated and give a warning.
They were provided for compatibility with R 1.7.0 (Mar 2003)!
• The ‘internal function’ kappa.tri() has been renamed to
.kappa_tri() so it is not inadvertently called as a method for
class "tri".
• Functions sessionData() and browseAll() in package methods are on
a help page describing them as ‘deprecated’ and are now formally
deprecated.
PACKAGE INSTALLATION:
• For a Windows or Mac OS X binary package install,
install.packages() will check if a source package is available on
the same repositories, and report if it is a later version or
there is a source package but no binary package available.
This check can be suppressed: see the help page.
• install.packages(type = "both") has been enhanced. In
interactive use it will ask whether to choose the source version
of a package if the binary version is older and contains compiled
code, and also asks if source packages with no binary version
should be installed).
INSTALLATION:
• There is a new configure option --with-libtiff (mainly in case
the system installation needs to be avoided).
• LAPACK 3.4.1 does use some Fortran 90 features, so g77 no longer
suffices.
• If an external LAPACK is used, it must be version 3.2 or later.
BUG FIXES:
• On Windows, starting Rterm via R.exe caused Ctrl-C to misbehave.
(PR#14948)
• The tools::latexToUtf8() function missed conversions that were
contained within braces.
• Long timezone specifications (such as a file name preceded by :)
could crash as.POSIXlt. (PR#14945)
• R CMD build --resave-data could fail if there was no data
directory but there was an R/sysdata.rda file. (PR#14947)
• is.na() misbehaved on a 0-column data frame. (PR#14959)
• anova.lmlist() failed if test was supplied. (PR#14960)
It was unable to compute Cp tests for object of class "lm" (it
assumed class "glm").
• The formula method for sunflowerplot() now allows xlab and ylab
to be set. (Reported by Gerrit Eichner.)
• The "POSIXt" and "Date" methods for hist() could fail on Windows
where adjustments to the right-hand boundary crossed a DST
transition time.
• On Windows, the code in as.POSIXct() to handle incorrectly
specified isdst fields might have resulted in NA being returned.
• aov() and manova() gave spurious warning about singular error
model in the multiresponse case.
• In ns() and bs(), specifying knots = NULL is now equivalent to
omitting it, also when df is specified. (PR#14970)
• sprintf() did not accept numbered arguments ending in zero.
(PR#14975)
• rWishart() could overflow the C stack and maybe crash the R
process for dimensions of several hundreds or more. (Reported by
Michael Braun on R-sig-mac.)
• Base package vignettes (e.g. vignette("Sweave")) were not fully
installed in builds of R from the tarball.
• lchoose() and choose() could overflow the C stack and crash R.
• When given a 0-byte file and asked to keep source references,
parse() read input from stdin() instead.
• pdf(compress = TRUE) did not delete temporary files it created
until the end of the R session. (PR#14991)
• logLik() did not detect the error of applying it to a
multiple-response linear model. (PR#15000)
• file.copy(recursive = TRUE) did not always report FALSE for a
failure two or more directories deep.
• qgeom() could return -1 for extremely small q. (PR#14967)
• smooth.spline() used DUP = FALSE which allowed its compiled C
code to change the function: this was masked by the default
byte-compilation. (PR#14965)
• In Windows, the GUI preferences for foreground color were not
always respected. (Reported by Benjamin Wells.)
• On OS X, the Quartz versions of the bitmap devices did not
respect antialias = "none". (PR#15006)
• unique() and similar would infinite-loop if called on a vector of
length > 2^29 (but reported that the vector was too long for 2^30
or more).
• parallel::stopCluster() now works with MPI clusters without snow
being on the search path.
• terms.formula() could exhaust the stack, and the stack check did
not always catch this before the segfault. (PR#15013)
• sort.list(method = "radix") could give incorrect results on
certain compilers (seen with clang on Mac OS 10.7 and Xcode
4.4.1).
• backsolve(T, b) gave incorrect results when nrows(b) > ncols(T)
and b had more than one column.
It could segfault or give nonsense if k was specified as more
than ncols(T).
• smooth.spline() did not check that a specified numeric spar was
of length 1, and gave corrupt results if it was of length 0.
• Protection added to do_system. (PR#15025)
• Printing of vectors with names > 1000 characters now works
correctly rather than truncating. (PR#15028)
• qr() for a complex matrix did not pivot the column names.
• --with-blas='-framework vecLib' now also works on OS X 10.8.
• R CMD check no longer fails with an error if a DESCRIPTION file
incorrectly contains a blank line. (Reported by Bill Dunlap.)
• install.packages(type = "both") could call chooseCRANmirror()
twice.
• lm.wfit() could segfault in R 2.15.1 if all the weights were
zero. (PR#15044)
• A malformed package name could cause R CMD INSTALL to write
outside the target library.
• Some of the quality control functions (e.g. tools::checkFF())
were wrongly identifying the source of S4 methods in a package
and so not checking them.
• The default type of display by browseEnv() when using R.app on
Mac OS X has been incorrect for a long time.
• The implementation of importMethodsFrom in a NAMESPACE file could
be confused and fail to find generics when importing from
multiple packages (reported and fixed by Michael Lawrence).
• The detection of the C stack direction is better protected
against compiler optimization. (PR#15011)
• Long custom line types would sometimes segfault on the
cairographics-based devices. (PR#15055)
• tools::checkPoFile() unprotected too early in its C code and so
segfaulted from time to time.
• The Fortran code underlying nlminb() could infinite-loop if any
of the input functions returned NA or NaN. This is now an error
for the gradient or Hessian, and a warning for the function (with
the value replaced by Inf). (In part, PR#15052.)
• The code for creating coerce() methods could generate false notes
about ambiguous selection; the notes have been suppressed for
this function.
• arima.sim() could give too long an output in some corner cases
(in part, PR#15068).
• anova.glm() with test = "Rao" didn't work when models included an
offset. (Reported by Søren Feodor Nielsen.)
• as.data.frame.matrix() could return invalid data frame with no
row.names attribute for 0-row matrix. (Reported by Hervé Pagès.)
• Compilation with the vecLib or Accelerate frameworks on OS X
without using that also for LAPACK is more likely to be
successful.
CHANGES IN R VERSION 2.15.1:
NEW FEATURES:
• source() now uses withVisible() rather than
.Internal(eval.with.vis). This sometimes alters tracebacks
slightly.
• install.packages("pkg_version.tgz") on Mac OS X now has sanity
checks that this is actually a binary package (as people have
tried it with incorrectly named source packages).
• splineDesign() and spline.des() in package splines have a new
option sparse which can be used for efficient construction of a
sparse B-spline design matrix (_via_ Matrix).
• norm() now allows type = "2" (the ‘spectral’ or 2-norm) as well,
mainly for didactical completeness.
• pmin() and pmax()) now also work when one of the inputs is of
length zero and others are not, returning a zero-length vector,
analogously to, say, +.
• colorRamp() (and hence colorRampPalette()) now also works for the
boundary case of just one color when the ramp is flat.
• .C() gains some protection against the misuse of character vector
arguments. (An all too common error is to pass character(N),
which initializes the elements to "", and then attempt to edit
the strings in-place, sometimes forgetting to terminate them.)
• Calls to the new function globalVariables() in package utils
declare that functions and other objects in a package should be
treated as globally defined, so that CMD check will not note
them.
• print(packageDescription(*)) trims the Collate field by default.
• The included copy of zlib has been updated to version 1.2.7.
• A new option "show.error.locations" has been added. When set to
TRUE, error messages will contain the location of the most recent
call containing source reference information. (Other values are
supported as well; see ?options.)
• The NA warning messages from e.g. pchisq() now report the call to
the closure and not that of the .Internal.
• Added Polish translations by Łukasz Daniel.
PERFORMANCE IMPROVEMENTS:
• In package parallel, makeForkCluster() and the multicore-based
functions use native byte-order for serialization (deferred from
2.15.0).
• lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of
objects, mainly by using .Call() rather than .Fortran().
• .C() and .Fortran() do less copying: arguments which are raw,
logical, integer, real or complex vectors and are unnamed are not
copied before the call, and (named or not) are not copied after
the call. Lists are no longer copied (they are supposed to be
used read-only in the C code).
• tabulate() makes use of .C(DUP = FALSE) and hence does not copy
bin. (Suggested by Tim Hesterberg.) It also avoids making a
copy of a factor argument bin.
• Other functions (often or always) doing less copying include
cut(), dist(), the complex case of eigen(), hclust(), image(),
kmeans(), loess(), stl() and svd(LINPACK = TRUE).
• There is less copying when using primitive replacement functions
such as names(), attr() and attributes().
DEPRECATED AND DEFUNCT:
• The converters for use with .C() (see ?getCConverterDescriptions)
are deprecated: use the .Call() interface instead. There are no
known examples (they were never fully documented).
UTILITIES:
• For R CMD check, a few people have reported problems with
junctions on Windows (although they were tested on Windows 7, XP
and Server 2008 machines and it is unknown under what
circumstances the problems occur). Setting the environment
variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
~/.R/check.Renviron) will force copies to be used instead.
INSTALLATION:
• R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value
(as done by R CMD check --as-cran) now restricts the packages
available when lazy-loading as well as when test-loading (since
packages such as ETLUtils and agsemisc had top-level calls to
library() for undeclared packages).
This check is now also available on Windows.
C-LEVEL FACILITIES:
• C entry points mkChar and mkCharCE now check that the length of
the string they are passed does not exceed 2^31-1 bytes: they
used to overflow with unpredictable consequences.
• C entry points R_GetCurrentSrcref and R_GetSrcFilename have been
added to the API to allow debuggers access to the source
references on the stack.
WINDOWS-SPECIFIC CHANGES:
• Windows-specific changes will now be announced in this file
(NEWS). Changes up and including R 2.15.0 remain in the CHANGES
file.
• There are two new environment variables which control the
defaults for command-line options.
If R_WIN_INTERNET2 is set to a non-empty value, it is as if
--internet2 was used.
If R_MAX_MEM_SIZE is set, it gives the default memory limit if
--max-mem-size is not specified: invalid values being ignored.
BUG FIXES:
• lsfit() lost the names from the residuals.
• More cases in which merge() could create a data frame with
duplicate column names now give warnings. Cases where names
specified in by match multiple columns are errors.
• Nonsense uses such as seq(1:50, by = 5) (from package plotrix)
and seq.int(1:50, by = 5) are now errors.
• The residuals in the 5-number summary printed by summary() on an
"lm" object are now explicitly labelled as weighted residuals
when non-constant weights are present. (Wish of PR#14840.)
• tracemem() reported that all objects were copied by .C() or
.Fortran() whereas only some object types were ever copied.
It also reported and marked as copies _some_ transformations such
as rexp(n, x): it no longer does so.
• The plot() method for class "stepfun" only used the optional xval
argument to compute xlim and not the points at which to plot (as
documented). (PR#14864)
• Names containing characters which need to be escaped were not
deparsed properly. (PR#14846)
• Trying to update (recommended) packages in R_HOME/library without
write access is now dealt with more gracefully. Further, such
package updates may be skipped (with a warning), when a newer
installed version is already going to be used from .libPaths().
(PR#14866)
• hclust() is now fast again (as up to end of 2003), with a
different fix for the "median"/"centroid" problem. (PR#4195).
• get_all_vars() failed when the data came entirely from vectors in
the global environment. (PR#14847)
• R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as
done by the --as-cran option) could issue false errors if there
was an indirect dependency on a recommended package.
• formatC() uses the C entry point str_signif which could write
beyond the length allocated for the output string.
• Missing default argument added to implicit S4 generic for
backsolve(). (PR#14883)
• Some bugs have been fixed in handling load actions that could
fail to export assigned items or generate spurious warnings in
CMD check on loading.
• For tiff(type = "windows"), the numbering of per-page files
except the last was off by one.
• On Windows, loading package stats (which is done for a default
session) would switch line endings on stdout and stderr from CRLF
to LF. This affected Rterm and R CMD BATCH.
• On Windows, the compatibility function x11() had not kept up with
changes to windows(), and issued warnings about bad parameters.
(PR#14880)
• On Windows, the Sys.glob() function did not handle UNC paths as
it was designed to try to do. (PR#14884)
• In package parallel, clusterApply() and similar failed to handle
a (pretty pointless) length-1 argument. (PR#14898)
• Quartz Cocoa display reacted asynchronously to dev.flush() which
means that the redraw could be performed after the plot has been
already modified by subsequent code. The redraw is now done
synchronously in dev.flush() to allow animations without sleep
cycles.
• Source locations reported in traceback() were incorrect when
byte-compiled code was on the stack.
• plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early
for large x (e.g. 800).
• ?Arithmetic's “1 ^ y and y ^ 0 are 1, _always_” now also applies
for integer vectors y.
• X11-based pixmap devices like png(type = "Xlib") were trying to
set the cursor style, which triggered some warnings and hangs.
• Code executed by the built-in HTTP server no longer allows other
HTTP clients to re-enter R until the current worker evaluation
finishes, to prevent cascades.
• The plot() and Axis() methods for class "table" now respect
graphical parameters such as cex.axis. (Reported by Martin
Becker.)
• Under some circumstances package.skeleton() would give out
progress reports that could not be translated and so were
displayed by question marks. Now they are always in English.
(This was seen for CJK locales on Windows, but may have occurred
elsewhere.)
• The evaluator now keeps track of source references outside of
functions, e.g. when source() executes a script.
• The replacement method for window() now works correctly for
multiple time series of class "mts". (PR#14925)
• is.unsorted() gave incorrect results on non-atomic objects such
as data frames. (Reported by Matthew Dowle.)
• The value returned by tools::psnice() for invalid pid values was
not always NA as documented.
• Closing an X11() window while locator() was active could abort
the R process.
• getMethod(f, sig) produced an incorrect error message in some
cases when f was not a string).
• Using a string as a “call” in an error condition with
options(showErrorCalls=TRUE) could cause a segfault. (PR#14931)
• The string "infinity" allowed by C99 was not accepted as a
numerical string value by e.g. scan() and as.numeric().
(PR#14933)
• In legend(), setting some entries of lwd to NA was inconsistent
(depending on the graphics device) in whether it would suppress
those lines; now it consistently does so. (PR#14926)
• by() failed for a zero-row data frame. (Reported by Weiqiang
Qian.)
• The Yates' correction in chisq.test() could be bigger than the
terms it corrected, previously leading to an infinite test
statistic in some corner cases which are now reported as NaN.
• xgettext() and related functions sometimes returned items that
were not strings for translation. (PR#14935)
• plot(<lm>, which=5) now correctly labels the factor level
combinations for the special case where all h[i,i] are the same.
(PR#14837)
• Sys.glob() caused a segfault if the first element of path was
NA_character. (PR#14990)
CHANGES IN R VERSION 2.15.0:
SIGNIFICANT USER-VISIBLE CHANGES:
• 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 (just as rm -r does).
On Windows it no longer follows reparse points (including
junctions and symbolic links).
NEW FEATURES:
• Environment variable RD2DVI_INPUTENC has been renamed to
RD2PDF_INPUTENC.
• .Deprecated() becomes a bit more flexible, getting an old
argument.
• Even data-only packages without R code need a namespace and so
may need to be installed under R 2.14.0 or later.
• 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.
• system() and system2() when capturing output report a non-zero
status in the new "status" attribute.
• 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.
• 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).
• format() (and hence print()) on "bibentry" objects now uses
options("width") to set the output width.
• 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.)
• 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.
• The number of items retained with options(warn = 0) can be set by
options(nwarnings=).
• There is a new function assignInMyNamespace() which uses the
namespace of the function it is called from.
• attach() allows the default name for an attached file to be
overridden.
• 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>.
• New function paste0(), an efficient version of paste(*, sep=""),
to be used in many places for more concise (and slightly more
efficient) code.
• 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 "dendrogram" method of str() now takes its default for
last.str from option str.dendrogram.last.
• New simple fitted() method for "kmeans" objects.
• The traceback() function can now be called with an integer
argument, to display a current stack trace. (Wish of PR#14770.)
• setGeneric() calls can be simplified when creating a new generic
function by supplying the default method as the def argument.
See ?setGeneric.
• 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.
• The internal (un)serialization code is faster for long vectors,
particularly with XDR on some platforms. (Based on a suggested
patch by Michael Spiegel.)
• For consistency, circles with zero radius are omitted by points()
and grid.circle(). Previously this was device-dependent, but
they were usually invisible.
• NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate,
e.g., also for more generalized matrices.
• PCRE has been updated to version 8.30.
• The internal R_Srcref variable is now updated before the browser
stops on entering a function. (Suggestion of PR#14818.)
• There are ‘bare-bones’ functions .colSums(), .rowSums(),
.colMeans() and .rowMeans() for use in programming where ultimate
speed is required.
• The formerly internal function .package_dependencies() from
package tools for calculating (recursive) (reverse) dependencies
on package databases has been renamed to package_dependencies()
and is now exported.
• There is a new function optimHess() to compute the (approximate)
Hessian for an optim() solution if hessian = TRUE was forgotten.
• .filled.contour() is a ‘bare-bones’ function to add a
filled-contour rectangular plot to an already prepared plot
region.
• The stepping in debugging and single-step browsing modes has
changed slightly: now left braces at the start of the body are
stepped over for if statements as well as for for and while
statements. (Wish of PR#14814.)
• library() no longer warns about a conflict with a function from
package:base if the function has the same code as the base one
but with a different environment. (An example is Matrix::det().)
• When deparsing very large language objects, as.character() now
inserts newlines after each line of approximately 500 bytes,
rather than truncating to the first line.
• New function rWishart() generates Wishart-distributed random
matrices.
• Packages may now specify actions to be taken when the package is
loaded (setLoadActions()).
• options(max.print = Inf) and similar now give an error (instead
of warnings later).
• The "difftime" replacement method of units tries harder to
preserve other attributes of the argument. (Wish of PR#14839.)
• poly(raw = TRUE) no longer requires more unique points than the
degree. (Requested by John Fox.)
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 functions parLapplyLB() and
parSapplyLB().
• makePSOCKCluster() has a new option useXDR = FALSE which can be
used to avoid byte-shuffling for serialization when all the nodes
are known to be little-endian (or all big-endian).
PACKAGE INSTALLATION:
• Non-ASCII vignettes without a declared encoding are no longer
accepted.
• 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.
• 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_MAKE_DSYM, since R 2.12.0.]
• 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.)
• 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.
• R CMD INSTALL --merge-multiarch is now supported on OS X and
other Unix-alikes using multiple sub-architectures.
• R CMD INSTALL --libs-only now by default does a test load on
Unix-alikes as well as on Windows: suppress with --no-test-load.
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.
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).
• 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.
• 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
files from running each test and the R code in each vignette.
• 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 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.
• The defaults for some of the options in R CMD check (described in
the ‘R Internals’ manual) have changed: checks for unsafe and
.Internal() calls and for partial matching of arguments in R
function calls are now done by default.
• R CMD check has more comprehensive facilities for checking
compiled code and so gives fewer reports on entry points linked
into .so/.dll files from libraries (including C++ and Fortran
runtimes).
Checking compiled code is now done on FreeBSD (as well as the
existing supported platforms of Linux, Mac OS X, Solaris and
Windows).
• R CMD build has more options for --compact-vignettes: see R CMD
build --help.
• R CMD build has a new option --md5 to add an MD5 file (as done by
CRAN): this is used by R CMD INSTALL to check the integrity of
the distribution.
If this option is not specified, any existing (and probably
stale) MD5 file is removed.
DEPRECATED AND DEFUNCT:
• R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.
• Options such --max-nsize, --max-vsize and the function
mem.limits() are now defunct. (Options --min-nsize and
--min-vsize remain available.)
• 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 .readRDS() and .saveRDS() are now defunct.
• The off-line help() types "postscript" and "ps" are defunct.
• Sys.putenv(), replaced and deprecated in R 2.5.0, is finally
removed.
• 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().
• The ENCODING argument to .C() is deprecated. It was intended to
smooth the transition to multi-byte character strings, but can be
replaced by the use of iconv() in the rare cases where it is
still needed.
INSTALLATION:
• Building with a positive value of --with-valgrind-instrumentation
now also instruments logical, complex and raw vectors.
C-LEVEL FACILITIES:
• Passing R objects other than atomic vectors, functions, lists and
environments to .C() is now deprecated and will give a warning.
Most cases (especially NULL) are actually coding errors. NULL
will be disallowed in future.
.C() now passes a pairlist as a SEXP to the compiled code. This
is as was documented, but pairlists were in reality handled
differently as a legacy from the early days of R.
• call_R and call_S are deprecated. They still exist in the
headers and as entry points, but are no longer documented and
should not be used for new code.
BUG FIXES:
• str(x, width) now obeys its width argument also for function
headers and other objects x where deparse() is applied.
• The convention for x %/% 0L for integer-mode x has been changed
from 0L to NA_integer_. (PR#14754)
• The exportMethods directive in a NAMESPACE file 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.
It is now required that there is an S4 generic (imported or
created in the package) when methods are to be exported.
• Reference methods cannot safely use non-exported entries in the
namespace. We now do not do so, and warn in the documentation.
• 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).
• merge() is no longer allowed (in some ways) to create a data
frame with duplicate column names (which confused PR#14786).
• Fixes for rendering raster images on X11 and Windows devices when
the x-axis or y-axis scale is reversed.
• getAnywhere() found S3 methods as seen from the utils namespace
and not from the environment from which it was called.
• selectMethod(f, sig) would not return inherited group methods
when caching was off (as it is by default).
• dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827)
• Virtual classes (e.g., class unions) had a NULL prototype even if
that was not a legal subclass. See ?setClassUnion.
• The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been
changed to the more modern style rather than that used by f2c.
(Patch by Berwin Turlach.)
• isGeneric() produced an error for primitives that can not have
methods.
• .C() or .Fortran() had a lack-of-protection error if the
registration information resulted in an argument being coerced to
another type.
• boxplot(x=x, at=at) with non finite elements in x and non integer
at could not generate a warning but failed.
• heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors
in reversed order.
• predict(<ar>) was incorrect in the multivariate case, for p >= 2.
• print(x, max=m) is now consistent when x is a "Date"; also the
“reached ... max.print ..” messages are now consistently using
single brackets.
• Closed the <li> tag in pages generated by Rd2HTML(). (PR#14841)
• Axis tick marks could go out of range when a log scale was used.
(PR#14833)
• Signature objects in methods were not allocated as S4 objects
(caused a problem with trace() reported by Martin Morgan).
CHANGES IN R VERSION 2.14.2:
NEW FEATURES:
• The internal untar() (as used by default by R CMD INSTALL) now
knows about some pax headers which bsdtar (e.g., the default tar
for Mac OS >= 10.6) can incorrectly include in tar files, and
will skip them with a warning.
• PCRE has been upgraded to version 8.21: as well as bug fixes and
greater Perl compatibility, this adds a JIT pattern compiler,
about which PCRE's news says ‘large performance benefits can be
had in many situations’. This is supported on most but not all R
platforms.
• Function compactPDF() in package tools now takes the default for
argument gs_quality from environment variable GS_QUALITY: there
is a new value "none", the ultimate default, which prevents
GhostScript being used in preference to qpdf just because
environment variable R_GSCMD is set. If R_GSCMD is unset or set
to "", the function will try to find a suitable GhostScript
executable.
• The included version of zlib has been updated to 1.2.6.
• For consistency with the logLik() method, nobs() for "nls" files
now excludes observations with zero weight. (Reported by Berwin
Turlach.)
UTILITIES:
• R CMD check now reports by default on licenses not according to
the description in ‘Writing R Extensions’.
• R CMD check has a new option --as-cran to turn on most of the
customizations that CRAN uses for its incoming checks.
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.
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 an old computation to find
an S4 default method.
• readLines() could overflow a buffer if the last line of the file
was not terminated. (PR#14766)
• R CMD check could miss undocumented S4 objects in packages which
used S4 classes but did not Depends: methods in their DESCRIPTION
file.
• The HTML Help Search page had malformed links. (PR#14769)
• A couple of instances of lack of protection of SEXPs have been
squashed. (PR#14772, PR#14773)
• image(x, useRaster=TRUE) misbehaved on single-column x.
(PR#14774)
• Negative values for options("max.print") or the max argument to
print.default() caused crashes. Now the former are ignored and
the latter trigger an error. (PR#14779)
• The text of a function body containing more than 4096 bytes was
not properly saved by the parser when entered at the console.
• Forgetting the #endif tag in an Rd file could cause the parser to
go into a loop. (Reported by Hans-Jorg Bibiko.)
• str(*, ....., strict.width="cut") now also obeys list.len = n.
(Reported by Sören Vogel.)
• Printing of arrays did not have enough protection (C level),
e.g., in the context of capture.output(). (Reported by Hervé
Pagès and Martin Morgan.)
• pdf(file = NULL) would produce a spurious file named NA.
(PR#14808)
• list2env() did not check the type of its envir argument.
(PR#14807)
• svg() could segfault if called with a non-existent file path.
(PR#14790)
• make install can install to a path containing + characters.
(PR#14798)
• The edit() function did not respect the options("keep.source")
setting. (Reported by Cleridy Lennert.)
• predict.lm(*, type="terms", terms=*, se.fit=TRUE) did not work.
(PR#14817)
• There is a partial workaround for errors in the TRE
regular-expressions engine with named classes and repeat counts
of at least 2 in a MBCS locale (PR#14408): these are avoided when
TRE is in 8-bit mode (e.g. for useBytes = TRUE and when all the
data are ASCII).
• The C function R_ReplDLLdo1() did not call top-level handlers.
• The Quartz device was unable to detect window sessions on Mac OS
X 10.7 (Lion) and higher and thus it was not used as the default
device on the console. Since Lion any application can use window
sessions, so Quartz will now be the default device if the user's
window session is active and R is not run via ssh which is at
least close to the behavior in prior OS X versions.
• mclapply() would fail in code assembling the translated error
message if some (but not all) cores encountered an error.
• format.POSIXlt(x) raised an arithmetic exception when x was an
invalid object of class "POSIXlt" and parts were empty.
• installed.packages() has some more protection against package
installs going on in parallel.
• .Primitive() could be mis-used to call .Internal() entry points.
CHANGES IN R VERSION 2.14.1:
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.
• 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 unique 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).
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).
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).
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 ....
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 Jeffrey 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)
• srcfilecopy() has gained a new argument isFile and now records
the working directory, to allow debuggers to find the original
source file. (PR#14826)
• 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 VERSION 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).
• 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 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).
• 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.
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 accept 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 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’.
• 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.
• 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.
*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).
• 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 environments 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.
This also applies to HTML searches, which now give results in all
of help pages, vignettes and demos.
• socketConnection() now has a timeout argument. It is now
documented that large values (package snow used a year) do not
work on some OSes.
• 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.
• 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.
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
screen 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
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).
• 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.
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.)
C-LEVEL FACILITIES:
• Function R_tmpnam2 has been added to the API to allow a temporary
filename to include a specified extension.
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 between
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).
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 checks line-endings of makefiles and
C/C++/Fortran sources in subdirectories of src as well as in src
itself.
• 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).
• Reference output for a vignette can be supplied when checking a
package by R CMD check: see ‘Writing R Extensions’.
• 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.)
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), and only R CMD Rd2pdf
will be available.
• 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.)
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 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).
• 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.
• Using a false value for the DESCRIPTION field LazyLoad is
deprecated.
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).
• Java detection (R CMD javareconf) works around bogus
java.library.path property in recent Oracle Java binaries.
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.
• 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)
• loess() is better protected against misuse, e.g. zero-length
span. (PR#14691)
• HoltWinters() checks that the optimization succeeded. (PR#14694)
• 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.
• 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.
• 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).
• 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.
• 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 and all
available input had been read.
• 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.
• A late change in R 2.13.2 broke \Sexpr expressions in Rd files.
• 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.
• qgamma() for small shape underflows to 0 rather than sometimes
giving NaN. (PR#8528, PR#14710)
• mapply() now gives an explicit error message (rather than an
obscure one) if inputs of zero and positive length are mixed.
• 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.
CHANGES IN R VERSION 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.
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’.
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.
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 NAs. (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)
• cbind() and rbind() could cause memory corruption when used on a
combination of raw and logical/integer vectors.
CHANGES IN R VERSION 2.13.1:
NEW FEATURES:
• iconv() no longer translates NA strings as "NA".
• 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)
• RShowDoc() can now display the licences shipped with R, e.g.
RShowDoc("GPL-3").
• New wrapper function showNonASCIIfile() in package tools.
• nobs() now has a "mle" method in package stats4.
• trace() now deals correctly with S4 reference classes and
corresponding reference methods (e.g., $trace()) have been added.
• xz has been updated to 5.0.3 (very minor bugfix release).
• tools::compactPDF() gets more compression (usually a little,
sometimes a lot) by using the compressed object streams of PDF
1.5.
• cairo_ps(onefile = TRUE) generates encapsulated EPS on platforms
with cairo >= 1.6.
• Binary reads (e.g. by readChar() and readBin()) are now supported
on clipboard connections. (Wish of PR#14593.)
• as.POSIXlt.factor() now passes ... to the character method
(suggestion of Joshua Ulrich). [Intended for R 2.13.0 but
accidentally removed before release.]
• vector() and its wrappers such as integer() and double() now warn
if called with a length argument of more than one element. This
helps track down user errors such as calling double(x) instead of
as.double(x).
INSTALLATION:
• Building the vignette PDFs in packages grid and utils is now part
of running make from an SVN checkout on a Unix-alike: a separate
make vignettes step is no longer required.
These vignettes are now made with keep.source = TRUE and hence
will be laid out differently.
• make install-strip failed under some configuration options.
• Packages can customize non-standard installation of compiled code
via a src/install.libs.R script. This allows packages that have
architecture-specific binaries (beyond the package's shared
objects/DLLs) to be installed in a multi-architecture setting.
SWEAVE & VIGNETTES:
• Sweave() and Stangle() gain an encoding argument to specify the
encoding of the vignette sources if the latter do not contain a
\usepackage[]{inputenc} statement specifying a single input
encoding.
• There is a new Sweave option figs.only = TRUE to run each figure
chunk only for each selected graphics device, and not first using
the default graphics device. This will become the default in R
2.14.0.
• Sweave custom graphics devices can have a custom function
foo.off() to shut them down.
• Warnings are issued when non-portable filenames are found for
graphics files (and chunks if split = TRUE). Portable names are
regarded as alphanumeric plus hyphen, underscore, plus and hash
(periods cause problems with recognizing file extensions).
• The Rtangle() driver has a new option show.line.nos which is by
default false; if true it annotates code chunks with a comment
giving the line number of the first line in the sources (the
behaviour of R >= 2.12.0).
• Package installation tangles the vignette sources: this step now
converts the vignette sources from the vignette/package encoding
to the current encoding, and records the encoding (if not ASCII)
in a comment line at the top of the installed .R file.
LICENCE:
• No parts of R are now licensed solely under GPL-2. The licences
for packages rpart and survival have been changed, which means
that the licence terms for R as distributed are GPL-2 | GPL-3.
DEPRECATED AND DEFUNCT:
• The internal functions .readRDS() and .saveRDS() are now
deprecated in favour of the public functions readRDS() and
saveRDS() introduced in R 2.13.0.
• Switching off lazy-loading of code _via_ the LazyLoad field of
the DESCRIPTION file is now deprecated. In future all packages
will be lazy-loaded.
• The off-line help() types "postscript" and "ps" are deprecated.
UTILITIES:
• R CMD check on a multi-architecture installation now skips the
user's .Renviron file for the architecture-specific tests (which
do read the architecture-specific Renviron.site files). This is
consistent with single-architecture checks, which use
--no-environ.
• R CMD build now looks for DESCRIPTION fields BuildResaveData and
BuildKeepEmpty for per-package overrides. See ‘Writing R
Extensions’.
BUG FIXES:
• plot.lm(which = 5) was intended to order factor levels in
increasing order of mean standardized residual. It ordered the
factor labels correctly, but could plot the wrong group of
residuals against the label. (PR#14545)
• mosaicplot() could clip the factor labels, and could overlap them
with the cells if a non-default value of cex.axis was used.
(Related to PR#14550.)
• dataframe[[row,col]] now dispatches on [[ methods for the
selected column. (Spotted by Bill Dunlap).
• sort.int() would strip the class of an object, but leave its
object bit set. (Reported by Bill Dunlap.)
• 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’)
• Complex arithmetic sometimes warned incorrectly about producing
NAs when there were NaNs in the input.
• seek(origin = "current") incorrectly reported it was not
implemented for a gzfile() connection.
• c(), unlist(), cbind() and rbind() could silently overflow the
maximum vector length and cause a segfault. (PR#14571)
• The fonts argument to X11(type = "Xlib") was being ignored.
• Reading (e.g. with readBin()) from a raw connection was not
advancing the pointer, so successive reads would read the same
value. (Spotted by Bill Dunlap.)
• Parsed text containing embedded newlines was printed incorrectly
by as.character.srcref(). (Reported by Hadley Wickham.)
• decompose() used with a series of a non-integer number of periods
returned a seasonal component shorter than the original series.
(Reported by Rob Hyndman.)
• fields = list() failed for setRefClass(). (Reported by Michael
Lawrence.)
• Reference classes could not redefine an inherited field which had
class "ANY". (Reported by Janko Thyson.)
• Methods that override previously loaded versions will now be
installed and called. (Reported by Iago Mosqueira.)
• addmargins() called numeric(apos) rather than
numeric(length(apos)).
• The HTML help search sometimes produced bad links. (PR#14608)
• Command completion will no longer be broken if tail.default() is
redefined by the user. (Problem reported by Henrik Bengtsson.)
• LaTeX rendering of markup in titles of help pages has been
improved; in particular, \eqn{} may be used there.
• isClass() used its own namespace as the default of the where
argument inadvertently.
• 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.)
• postscript() with an sRGB colormodel now uses sRGB for raster
images (in R 2.13.[01] it used uncalibrated RGB).
There is no longer an undocumented 21845-pixel limit on raster
images.
CHANGES IN R VERSION 2.13.0:
SIGNIFICANT USER-VISIBLE CHANGES:
• replicate() (by default) and vapply() (always) now return a
higher-dimensional array instead of a matrix in the case where
the inner function value is an array of dimension >= 2.
• Printing and formatting of floating point numbers is now using
the correct number of digits, where it previously rarely differed
by a few digits. (See “scientific” entry below.) This affects
_many_ *.Rout.save checks in packages.
NEW FEATURES:
• normalizePath() has been moved to the base package (from utils):
this is so it can be used by library() and friends.
It now does tilde expansion.
It gains new arguments winslash (to select the separator on
Windows) and mustWork to control the action if a canonical path
cannot be found.
• The previously barely documented limit of 256 bytes on a symbol
name has been raised to 10,000 bytes (a sanity check). Long
symbol names can sometimes occur when deparsing expressions (for
example, in model.frame).
• reformulate() gains a intercept argument.
• cmdscale(add = FALSE) now uses the more common definition that
there is a representation in n-1 or less dimensions, and only
dimensions corresponding to positive eigenvalues are used.
(Avoids confusion such as PR#14397.)
• Names used by c(), unlist(), cbind() and rbind() are marked with
an encoding when this can be ascertained.
• R colours are now defined to refer to the sRGB color space.
The PDF, PostScript, and Quartz graphics devices record this
fact. X11 (and cairo) and Windows just assume that your screen
conforms.
• system.file() gains a mustWork argument (suggestion of Bill
Dunlap).
• new.env(hash = TRUE) is now the default.
• list2env(envir = NULL) defaults to hashing (with a suitably sized
environment) for lists of more than 100 elements.
• text() gains a formula method.
• IQR() now has a type argument which is passed to quantile().
• as.vector(), as.double() etc duplicate less when they leave the
mode unchanged but remove attributes.
as.vector(mode = "any") no longer duplicates when it does not
remove attributes. This helps memory usage in matrix() and
array().
matrix() duplicates less if data is an atomic vector with
attributes such as names (but no class).
dim(x) <- NULL duplicates less if x has neither dimensions nor
names (since this operation removes names and dimnames).
• setRepositories() gains an addURLs argument.
• chisq.test() now also returns a stdres component, for
standardized residuals (which have unit variance, unlike the
Pearson residuals).
• write.table() and friends gain a fileEncoding argument, to
simplify writing files for use on other OSes (e.g. a spreadsheet
intended for Windows or Mac OS X Excel).
• Assignment expressions of the form foo::bar(x) <- y and
foo:::bar(x) <- y now work; the replacement functions used are
foo::`bar<-` and foo:::`bar<-`.
• Sys.getenv() gains a names argument so Sys.getenv(x, names =
FALSE) can replace the common idiom of as.vector(Sys.getenv()).
The default has been changed to not name a length-one result.
• Lazy loading of environments now preserves attributes and locked
status. (The locked status of bindings and active bindings are
still not preserved; this may be addressed in the future).
• options("install.lock") may be set to FALSE so that
install.packages() defaults to --no-lock installs, or (on
Windows) to TRUE so that binary installs implement locking.
• sort(partial = p) for large p now tries Shellsort if quicksort is
not appropriate and so works for non-numeric atomic vectors.
• sapply() gets a new option simplify = "array" which returns a
“higher rank” array instead of just a matrix when FUN() returns a
dim() length of two or more.
replicate() has this option set by default, and vapply() now
behaves that way internally.
• aperm() becomes S3 generic and gets a table method which
preserves the class.
• merge() and as.hclust() methods for objects of class "dendrogram"
are now provided.
• The character method of as.POSIXlt() now tries to find a format
that works for all non-NA inputs, not just the first one.
• str() now has a method for class "Date" analogous to that for
class "POSIXt".
• New function file.link() to create hard links on those file
systems (POSIX, NTFS but not FAT) that support them.
• New Summary() group method for class "ordered" implements min(),
max() and range() for ordered factors.
• mostattributes<-() now consults the "dim" attribute and not the
dim() function, making it more useful for objects (such as data
frames) from classes with methods for dim(). It also uses
attr<-() in preference to the generics name<-(), dim<-() and
dimnames<-(). (Related to PR#14469.)
• There is a new option "browserNLdisabled" to disable the use of
an empty (e.g. via the ‘Return’ key) as a synonym for c in
browser() or n under debug(). (Wish of PR#14472.)
• example() gains optional new arguments character.only and
give.lines enabling programmatic exploration.
• serialize() and unserialize() are no longer described as
‘experimental’. The interface is now regarded as stable,
although the serialization format may well change in future
releases. (serialize() has a new argument version which would
allow the current format to be written if that happens.)
New functions saveRDS() and readRDS() are public versions of the
‘internal’ functions .saveRDS() and .readRDS() made available for
general use. The dot-name versions remain available as several
package authors have made use of them, despite the documentation.
readRDS() no longer wraps non-file connections in a call to
gzcon(), for efficiency (see its documentation).
saveRDS() supports compress = "xz".
• Many functions when called with a not-open connection will now
ensure that the connection is left not-open in the event of
error. These include read.dcf(), dput(), dump(), load(),
parse(), readBin(), readChar(), readLines(), save(), writeBin(),
writeChar(), writeLines(), .readRDS(), .saveRDS() and
tools::parse_Rd(), as well as functions calling these.
• Public functions find.package() and path.package() replace the
internal dot-name versions.
• The default method for terms() now looks for a "terms" attribute
if it does not find a "terms" component, and so works for model
frames.
• httpd() handlers receive an additional argument containing the
full request headers as a raw vector (this can be used to parse
cookies, multi-part forms etc.). The recommended full signature
for handlers is therefore function(url, query, body, headers,
...).
• file.edit() gains a fileEncoding argument to specify the encoding
of the file(s).
• The format of the HTML package listings has changed. If there is
more than one library tree , a table of links to libraries is
provided at the top and bottom of the page. Where a library
contains more than 100 packages, an alphabetic index is given at
the top of the section for that library. (As a consequence,
package names are now sorted case-insensitively whatever the
locale.)
• isSeekable() now returns FALSE on connections which have
non-default encoding. Although documented to record if ‘in
principle’ the connection supports seeking, it seems safer to
report FALSE when it may not work.
• R CMD REMOVE and remove.packages() now remove file R.css when
removing all remaining packages in a library tree. (Related to
the wish of PR#14475: note that this file is no longer
installed.)
• unzip() now has a unzip argument like zip.file.extract(). This
allows an external unzip program to be used, which can be useful
to access features supported by Info-ZIP's unzip version 6 which
is now becoming more widely available.
• There is a simple zip() function, as wrapper for an external zip
command.
• bzfile() connections can now read from concatenated bzip2 files
(including files written with bzfile(open = "a")) and files
created by some other compressors (such as the example of
PR#14479).
• The primitive function c() is now of type BUILTIN.
• plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd
specification (allowing clipping to be turned off completely).
• nls(algorithm="port") now shares more code with nlminb(), and is
more consistent with the other nls() algorithms in its return
value.
• xz has been updated to 5.0.1 (very minor bugfix release).
• image() has gained a logical useRaster argument allowing it to
use a bitmap raster for plotting a regular grid instead of
polygons. This can be more efficient, but may not be supported by
all devices. The default is FALSE.
• list.files()/dir() gains a new argument include.dirs() to include
directories in the listing when recursive = TRUE.
• New function list.dirs() lists all directories, (even empty
ones).
• file.copy() now (by default) copies read/write/execute
permissions on files, moderated by the current setting of
Sys.umask().
• Sys.umask() now accepts mode = NA and returns the current umask
value (visibly) without changing it.
• There is a ! method for classes "octmode" and "hexmode": this
allows xor(a, b) to work if both a and b are from one of those
classes.
• as.raster() no longer fails for vectors or matrices containing
NAs.
• New hook "before.new.plot" allows functions to be run just before
advancing the frame in plot.new, which is potentially useful for
custom figure layout implementations.
• Package tools has a new function compactPDF() to try to reduce
the size of PDF files _via_ qpdf or gs.
• tar() has a new argument extra_flags.
• dotchart() accepts more general objects x such as 1D tables which
can be coerced by as.numeric() to a numeric vector, with a
warning since that might not be appropriate.
• The previously internal function create.post() is now exported
from utils, and the documentation for bug.report() and
help.request() now refer to that for create.post().
It has a new method = "mailto" on Unix-alikes similar to that on
Windows: it invokes a default mailer via open (Mac OS X) or
xdg-open or the default browser (elsewhere).
The default for ccaddress is now getOption("ccaddress") which is
by default unset: using the username as a mailing address
nowadays rarely works as expected.
• The default for options("mailer") is now "mailto" on all
platforms.
• unlink() now does tilde-expansion (like most other file
functions).
• file.rename() now allows vector arguments (of the same length).
• The "glm" method for logLik() now returns an "nobs" attribute
(which stats4::BIC() assumed it did).
The "nls" method for logLik() gave incorrect results for zero
weights.
• There is a new generic function nobs() in package stats, to
extract from model objects a suitable value for use in BIC
calculations. An S4 generic derived from it is defined in
package stats4.
• Code for S4 reference-class methods is now examined for possible
errors in non-local assignments.
• findClasses, getGeneric, findMethods and hasMethods are revised
to deal consistently with the package= argument and be consistent
with soft namespace policy for finding objects.
• tools::Rdiff() now has the option to return not only the status
but a character vector of observed differences (which are still
by default sent to stdout).
• The startup environment variables R_ENVIRON_USER, R_ENVIRON,
R_PROFILE_USER and R_PROFILE are now treated more consistently.
In all cases an empty value is considered to be set and will stop
the default being used, and for the last two tilde expansion is
performed on the file name. (Note that setting an empty value is
probably impossible on Windows.)
• Using R --no-environ CMD, R --no-site-file CMD or R
--no-init-file CMD sets environment variables so these settings
are passed on to child R processes, notably those run by INSTALL,
check and build. R --vanilla CMD sets these three options (but
not --no-restore).
• smooth.spline() is somewhat faster. With cv=NA it allows some
leverage computations to be skipped,
• 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.
• A new function grepRaw() has been introduced for finding subsets
of raw vectors. It supports both literal searches and regular
expressions.
• Package compiler is now provided as a standard package. See
?compiler::compile for information on how to use the compiler.
This package implements a byte code compiler for R: by default
the compiler is not used in this release. See the ‘R
Installation and Administration Manual’ for how to compile the
base and recommended packages.
• Providing an exportPattern directive in a NAMESPACE file now
causes classes to be exported according to the same pattern, for
example the default from package.skeleton() to specify all names
starting with a letter. An explicit directive to
exportClassPattern will still over-ride.
• 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.
• The new function removeSource() removes the internally stored
source from a function.
• "srcref" attributes now include two additional line number
values, recording the line numbers in the order they were parsed.
• New functions have been added for source reference access:
getSrcFilename(), getSrcDirectory(), getSrcLocation() and
getSrcref().
• Sys.chmod() has an extra argument use_umask which defaults to
true and restricts the file mode by the current setting of umask.
This means that all the R functions which manipulate
file/directory permissions by default respect umask, notably R
CMD INSTALL.
• tempfile() has an extra argument fileext to create a temporary
filename with a specified extension. (Suggestion and initial
implementation by Dirk Eddelbuettel.)
There are improvements in the way Sweave() and Stangle() handle
non-ASCII vignette sources, especially in a UTF-8 locale: see
‘Writing R Extensions’ which now has a subsection on this topic.
• factanal() now returns the rotation matrix if a rotation such as
"promax" is used, and hence factor correlations are displayed.
(Wish of PR#12754.)
• The gctorture2() function provides a more refined interface to
the GC torture process. Environment variables R_GCTORTURE,
R_GCTORTURE_WAIT, and R_GCTORTURE_INHIBIT_RELEASE can also be
used to control the GC torture process.
• file.copy(from, to) no longer regards it as an error to supply a
zero-length from: it now simply does nothing.
• rstandard.glm() gains a type argument which can be used to
request standardized Pearson residuals.
• A start on a Turkish translation, thanks to Murat Alkan.
• .libPaths() calls normalizePath(winslash = "/") on the paths:
this helps (usually) to present them in a user-friendly form and
should detect duplicate paths accessed via different symbolic
links.
• download.file() can be now used with external methods even if
there are spaces in the URL or the target filename.
• The first formal argument of .C(), .Fortran(), .Call() and
.External() is now referred to a .NAME rather than name: however
actual calls should have an unnamed first argument.
SWEAVE CHANGES:
• Sweave() has options to produce PNG and JPEG figures, and to use
a custom function to open a graphics device (see ?RweaveLatex).
(Based in part on the contribution of PR#14418.)
• The default for Sweave() is to produce only PDF figures (rather
than both EPS and PDF).
• Environment variable SWEAVE_OPTIONS can be used to supply
defaults for existing or new options to be applied after the
Sweave driver setup has been run.
• The Sweave manual is now included as a vignette in the utils
package.
• Sweave() handles keep.source=TRUE much better: it could duplicate
some lines and omit comments. (Reported by John Maindonald and
others.)
C-LEVEL FACILITIES:
• Because they use a C99 interface which a C++ compiler is not
required to support, Rvprintf and REvprintf are only defined by
R_ext/Print.h in C++ code if the macro R_USE_C99_IN_CXX is
defined when it is included.
• pythag duplicated the C99 function hypot. It is no longer
provided, but is used as a substitute for hypot in the very
unlikely event that the latter is not available.
• R_inspect(obj) and R_inspect3(obj, deep, pvec) are (hidden)
C-level entry points to the internal inspect function and can be
used for C-level debugging (e.g., in conjunction with the p
command in gdb).
• Compiling R with --enable-strict-barrier now also enables
additional checking for use of unprotected objects. In
combination with gctorture() or gctorture2() and a C-level
debugger this can be useful for tracking down memory protection
issues.
UTILITIES:
• R CMD Rdiff is now implemented in R on Unix-alikes (as it has
been on Windows since R 2.12.0).
• R CMD build no longer does any cleaning in the supplied package
directory: all the cleaning is done in the copy.
It has a new option --install-args to pass arguments to R CMD
INSTALL for --build (but not when installing to rebuild
vignettes).
There is new option, --resave-data, to call
tools::resaveRdaFiles() on the data directory, to compress
tabular files (.tab, .csv etc) and to convert .R files to .rda
files. The default, --resave-data=gzip, is to do so in a way
compatible even with years-old versions of R, but better
compression is given by --resave-data=best, requiring R >=
2.10.0.
It now adds a datalist file for data directories of more than
1Mb.
Patterns in .Rbuildignore are now also matched against all
directory names (including those of empty directories).
There is a new option, --compact-vignettes, to try reducing the
size of PDF files in the inst/doc directory. Currently this
tries qpdf: other options may be used in future.
When re-building vignettes and a inst/doc/Makefile file is found,
make clean is run if the makefile has a clean: target.
After re-building vignettes the default clean-up operation will
remove any directories (and not just files) created during the
process: e.g. one package created a .R_cache directory.
Empty directories are now removed unless the option
--keep-empty-dirs is given (and a few packages do deliberately
include empty directories).
If there is a field BuildVignettes in the package DESCRIPTION
file with a false value, re-building the vignettes is skipped.
• R CMD check now also checks for filenames that are
case-insensitive matches to Windows' reserved file names with
extensions, such as nul.Rd, as these have caused problems on some
Windows systems.
It checks for inefficiently saved data/*.rda and data/*.RData
files, and reports on those large than 100Kb. A more complete
check (including of the type of compression, but potentially much
slower) can be switched on by setting environment variable
_R_CHECK_COMPACT_DATA2_ to TRUE.
The types of files in the data directory are now checked, as
packages are _still_ misusing it for non-R data files.
It now extracts and runs the R code for each vignette in a
separate directory and R process: this is done in the package's
declared encoding. Rather than call tools::checkVignettes(), it
calls tools::buildVignettes() to see if the vignettes can be
re-built as they would be by R CMD build. Option --use-valgrind
now applies only to these runs, and not when running code to
rebuild the vignettes. This version does a much better job of
suppressing output from successful vignette tests.
The 00check.log file is a more complete record of what is output
to stdout: in particular contains more details of the tests.
It now checks all syntactically valid Rd usage entries, and warns
about assignments (unless these give the usage of replacement
functions).
.tar.xz compressed tarballs are now allowed, if tar supports them
(and setting environment variable TAR to internal ensures so on
all platforms).
• R CMD check now warns if it finds inst/doc/makefile, and R CMD
build renames such a file to inst/doc/Makefile.
INSTALLATION:
• Installing R no longer tries to find perl, and R CMD no longer
tries to substitute a full path for awk nor perl - this was a
legacy from the days when they were used by R itself. Because a
couple of packages do use awk, it is set as the make (rather than
environment) variable AWK.
• make check will now fail if there are differences from the
reference output when testing package examples and if environment
variable R_STRICT_PACKAGE_CHECK is set to a true value.
• The C99 double complex type is now required.
The C99 complex trigonometric functions (such as csin) are not
currently required (FreeBSD lacks most of them): substitutes are
used if they are missing.
• The C99 system call va_copy is now required.
• If environment variable R_LD_LIBRARY_PATH is set during
configuration (for example in config.site) it is used unchanged
in file etc/ldpaths rather than being appended to.
• configure looks for support for OpenMP and if found compiles R
with appropriate flags and also makes them available for use in
packages: see ‘Writing R Extensions’.
This is currently experimental, and is only used in R with a
single thread for colSums() and colMeans(). Expect it to be more
widely used in later versions of R.
This can be disabled by the --disable-openmp flag.
PACKAGE INSTALLATION:
• R CMD INSTALL --clean now removes copies of a src directory which
are created when multiple sub-architectures are in use.
(Following a comment from Berwin Turlach.)
• File R.css is now installed on a per-package basis (in the
package's html directory) rather than in each library tree, and
this is used for all the HTML pages in the package. This helps
when installing packages with static HTML pages for use on a
webserver. It will also allow future versions of R to use
different stylesheets for the packages they install.
• A top-level file .Rinstignore in the package sources can list (in
the same way as .Rbuildignore) files under inst that should not
be installed. (Why should there be any such files? Because all
the files needed to re-build vignettes need to be under inst/doc,
but they may not need to be installed.)
• R CMD INSTALL has a new option --compact-docs to compact any PDFs
under the inst/doc directory. Currently this uses qpdf, which
must be installed (see ‘Writing R Extensions’).
• There is a new option --lock which can be used to cancel the
effect of --no-lock or --pkglock earlier on the command line.
• Option --pkglock can now be used with more than one package, and
is now the default if only one package is specified.
• Argument lock of install.packages() can now be use for Mac binary
installs as well as for Windows ones. The value "pkglock" is now
accepted, as well as TRUE and FALSE (the default).
• There is a new option --no-clean-on-error for R CMD INSTALL to
retain a partially installed package for forensic analysis.
• Packages with names ending in . are not portable since Windows
does not work correctly with such directory names. This is now
warned about in R CMD check, and will not be allowed in R 2.14.x.
• The vignette indices are more comprehensive (in the style of
browseVignetttes()).
DEPRECATED & DEFUNCT:
• require(save = TRUE) is defunct, and use of the save argument is
deprecated.
• R CMD check --no-latex is defunct: use --no-manual instead.
• R CMD Sd2Rd is defunct.
• The gamma argument to hsv(), rainbow(), and rgb2hsv() is
deprecated and no longer has any effect.
• The previous options for R CMD build --binary (--auto-zip,
--use-zip-data and --no-docs) are deprecated (or defunct): use
the new option --install-args instead.
• When a character value is used for the EXPR argument in switch(),
only a single unnamed alternative value is now allowed.
• The wrapper utils::link.html.help() is no longer available.
• Zip-ing data sets in packages (and hence R CMD INSTALL options
--use-zip-data and --auto-zip, as well as the ZipData: yes field
in a DESCRIPTION file) is defunct.
Installed packages with zip-ed data sets can still be used, but a
warning that they should be re-installed will be given.
• The ‘experimental’ alternative specification of a namespace via
.Export() etc is now defunct.
• The option --unsafe to R CMD INSTALL is deprecated: use the
identical option --no-lock instead.
• The entry point pythag in Rmath.h is deprecated in favour of the
C99 function hypot. A wrapper for hypot is provided for R 2.13.x
only.
• Direct access to the "source" attribute of functions is
deprecated; use deparse(fn, control="useSource") to access it,
and removeSource(fn) to remove it.
• R CMD build --binary is now formally deprecated: R CMD INSTALL
--build has long been the preferred alternative.
• Single-character package names are deprecated (and R is already
disallowed to avoid confusion in Depends: fields).
BUG FIXES:
• drop.terms and the [ method for class "terms" no longer add back
an intercept. (Reported by Niels Hansen.)
• aggregate preserves the class of a column (e.g. a date) under
some circumstances where it discarded the class previously.
• p.adjust() now always returns a vector result, as documented. In
previous versions it copied attributes (such as dimensions) from
the p argument: now it only copies names.
• On PDF and PostScript devices, a line width of zero was recorded
verbatim and this caused problems for some viewers (a very thin
line combined with a non-solid line dash pattern could also cause
a problem). On these devices, the line width is now limited at
0.01 and for very thin lines with complex dash patterns the
device may force the line dash pattern to be solid. (Reported by
Jari Oksanen.)
• The str() method for class "POSIXt" now gives sensible output for
0-length input.
• The one- and two-argument complex maths functions failed to warn
if NAs were generated (as their numeric analogues do).
• Added .requireCachedGenerics to the dont.mind list for library()
to avoid warnings about duplicates.
• $<-.data.frame messed with the class attribute, breaking any S4
subclass. The S4 data.frame class now has its own $<- method,
and turns dispatch on for this primitive.
• Map() did not look up a character argument f in the correct
frame, thanks to lazy evaluation. (PR#14495)
• file.copy() did not tilde-expand from and to when to was a
directory. (PR#14507)
• It was possible (but very rare) for the loading test in R CMD
INSTALL to crash a child R process and so leave around a lock
directory and a partially installed package. That test is now
done in a separate process.
• plot(<formula>, data=<matrix>,..) now works in more cases;
similarly for points(), lines() and text().
• edit.default() contained a manual dispatch for matrices (the
"matrix" class didn't really exist when it was written). This
caused an infinite recursion in the no-GUI case and has now been
removed.
• data.frame(check.rows = TRUE) sometimes worked when it should
have detected an error. (PR#14530)
• scan(sep= , strip.white=TRUE) sometimes stripped trailing spaces
from within quoted strings. (The real bug in PR#14522.)
• The rank-correlation methods for cor() and cov() with use =
"complete.obs" computed the ranks before removing missing values,
whereas the documentation implied incomplete cases were removed
first. (PR#14488)
They also failed for 1-row matrices.
• The perpendicular adjustment used in placing text and expressions
in the margins of plots was not scaled by par("mex"). (Part of
PR#14532.)
• Quartz Cocoa device now catches any Cocoa exceptions that occur
during the creation of the device window to prevent crashes. It
also imposes a limit of 144 ft^2 on the area used by a window to
catch user errors (unit misinterpretation) early.
• The browser (invoked by debug(), browser() or otherwise) would
display attributes such as "wholeSrcref" that were intended for
internal use only.
• R's internal filename completion now properly handles filenames
with spaces in them even when the readline library is used. This
resolves PR#14452 provided the internal filename completion is
used (e.g., by setting rc.settings(files = TRUE)).
• Inside uniroot(f, ...), -Inf function values are now replaced by
a maximally *negative* value.
• rowsum() could silently over/underflow on integer inputs
(reported by Bill Dunlap).
• as.matrix() did not handle "dist" objects with zero rows.
CHANGES IN R VERSION 2.12.2 patched:
NEW FEATURES:
• max() and min() work harder to ensure that NA has precedence over
NaN, so e.g. min(NaN, NA) is NA. (This was not previously
documented except for within a single numeric vector, where
compiler optimizations often defeated the code.)
BUG FIXES:
• A change to the C function R_tryEval had broken error messages in
S4 method selection; the error message is now printed.
• PDF output with a non-RGB color model used RGB for the line
stroke color. (PR#14511)
• stats4::BIC() assumed without checking that an object of class
"logLik" has an "nobs" attribute: glm() fits did not and so BIC()
failed for them.
• In some circumstances a one-sided mantelhaen.test() reported the
p-value for the wrong tail. (PR#14514)
• Passing the invalid value lty = NULL to axis() sent an invalid
value to the graphics device, and might cause the device to
segfault.
• Sweave() with concordance=TRUE could lead to invalid PDF files;
Sweave.sty has been updated to avoid this.
• Non-ASCII characters in the titles of help pages were not
rendered properly in some locales, and could cause errors or
warnings.
• checkRd() gave a spurious error if the \href macro was used.
CHANGES IN R VERSION 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).
• There is a workaround for crashes seen with several packages on
systems using zlib 1.2.5: see the INSTALLATION section.
NEW FEATURES:
• PCRE has been updated to 8.12 (two bug-fix releases since 8.10).
• rep(), seq(), seq.int() and seq_len() report more often when the
first element is taken of an argument of incorrect length.
• The Cocoa back-end for the quartz() graphics device on Mac OS X
provides a way to disable event loop processing temporarily
(useful, e.g., for forked instances of R).
• kernel()'s default for m was not appropriate if coef was a set of
coefficients. (Reported by Pierre Chausse.)
• bug.report() has been updated for the current R bug tracker,
which does not accept emailed submissions.
• R CMD check now checks for the correct use of $(LAPACK_LIBS) (as
well as $(BLAS_LIBS)), since several CRAN recent submissions have
ignored ‘Writing R Extensions’.
INSTALLATION:
• The zlib sources in the distribution are now built with all
symbols remapped: this is intended to avoid problems seen with
packages such as XML and rggobi which link to zlib.so.1 on
systems using zlib 1.2.5.
• The default for FFLAGS and FCFLAGS with gfortran on x86_64 Linux
has been changed back to -g -O2: however, setting -g -O may still
be needed for gfortran 4.3.x.
PACKAGE INSTALLATION:
• A LazyDataCompression field in the DESCRIPTION file will be used
to set the value for the --data-compress option of R CMD INSTALL.
• Files R/sysdata.rda of more than 1Mb are now stored in the
lazyload database using xz compression: this for example halves
the installed size of package Imap.
• R CMD INSTALL now ensures that directories installed from inst
have search permission for everyone.
It no longer installs files inst/doc/Rplots.ps and
inst/doc/Rplots.pdf. These are almost certainly left-overs from
Sweave runs, and are often large.
DEPRECATED & DEFUNCT:
• The ‘experimental’ alternative specification of a namespace via
.Export() etc is now deprecated.
• zip.file.extract() is now deprecated.
• Zip-ing data sets in packages (and hence R CMD INSTALL
--use-zip-data and the ZipData: yes field in a DESCRIPTION file)
is deprecated: using efficiently compressed .rda images and
lazy-loading of data has superseded it.
BUG FIXES:
• identical() could in rare cases generate a warning about
non-pairlist attributes on CHARSXPs. As these are used for
internal purposes, the attribute check should be skipped.
(Reported by Niels Richard Hansen).
• If the filename extension (usually .Rnw) was not included in a
call to Sweave(), source references would not work properly and
the keep.source option failed. (PR#14459)
• format.data.frame() now keeps zero character column names.
• pretty(x) no longer raises an error when x contains solely
non-finite values. (PR#14468)
• The plot.TukeyHSD() function now uses a line width of 0.5 for its
reference lines rather than lwd = 0 (which caused problems for
some PDF and PostScript viewers).
• The big.mark argument to prettyNum(), format(), etc. was inserted
reversed if it was more than one character long.
• R CMD check failed to check the filenames under man for Windows'
reserved names.
• The "Date" and "POSIXt" methods for seq() could overshoot when to
was supplied and by was specified in months or years.
• The internal method of untar() now restores hard links as file
copies rather than symbolic links (which did not work for
cross-directory links).
• unzip() did not handle zip files which contained filepaths with
two or more leading directories which were not in the zipfile and
did not already exist. (It is unclear if such zipfiles are valid
and the third-party C code used did not support them, but
PR#14462 created one.)
• combn(n, m) now behaves more regularly for the border case m = 0.
(PR#14473)
• The rendering of numbers in plotmath expressions (e.g.
expression(10^2)) used the current settings for conversion to
strings rather than setting the defaults, and so could be
affected by what has been done before. (PR#14477)
• The methods of napredict() and naresid() for na.action =
na.exclude fits did not work correctly in the very rare event
that every case had been omitted in the fit. (Reported by Simon
Wood.)
• weighted.residuals(drop0=TRUE) returned a vector when the
residuals were a matrix (e.g. those of class "mlm"). (Reported
by Bill Dunlap.)
• Package HTML index files <pkg>/html/00Index.html were generated
with a stylesheet reference that was not correct for static
browsing in libraries.
• ccf(na.action = na.pass) was not implemented.
• The parser accepted some incorrect numeric constants, e.g. 20x2.
(Reported by Olaf Mersmann.)
• format(*, zero.print) did not always replace the full zero parts.
• Fixes for subsetting or subassignment of "raster" objects when
not both i and j are specified.
• R CMD INSTALL was not always respecting the ZipData: yes field of
a DESCRIPTION file (although this is frequently incorrectly
specified for packages with no data or which specify lazy-loading
of data).
R CMD INSTALL --use-zip-data was incorrectly implemented as
--use-zipdata since R 2.9.0.
• source(file, echo=TRUE) could fail if the file contained #line
directives. It now recovers more gracefully, but may still
display the wrong line if the directive gives incorrect
information.
• atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms
without C99 complex support.
• library() failed to cache S4 metadata (unlike loadNamespace())
causing failures in S4-using packages without a namespace (e.g.
those using reference classes).
• The function qlogis(lp, log.p=TRUE) no longer prematurely
overflows to Inf when exp(lp) is close to 1.
• Updating S4 methods for a group generic function requires
resetting the methods tables for the members of the group (patch
contributed by Martin Morgan).
• In some circumstances (including for package XML), R CMD INSTALL
installed version-control directories from source packages.
• Added PROTECT calls to some constructed expressions used in C
level eval calls.
• utils:::create.post() (used by bug.report() and help.request())
failed to quote arguments to the mailer, and so often failed.
• bug.report() was naive about how to extract maintainer email
addresses from package descriptions, so would often try mailing
to incorrect addresses.
• debugger() could fail to read the environment of a call to a
function with a ... argument. (Reported by Charlie Roosen.)
• prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work
correctly.
CHANGES IN R VERSION 2.12.1:
NEW FEATURES:
• The DVI/PDF reference manual now includes the help pages for all
the standard packages: splines, stats4 and tcltk were previously
omitted (intentionally).
• <URL: http://www.rforge.net> has been added to the default set of
repositories known to setRepositories().
• xz-utils has been updated to version 5.0.0.
• reshape() now makes use of sep when forming names during
reshaping to wide format. (PR#14435)
• legend() allows the length of lines to be set by the end user
_via_ the new argument seg.len.
• New S4 reference class utility methods copy(), field(),
getRefClass() and getClass() have been added to package methods.
• When a character value is used for the EXPR argument in switch(),
a warning is given if more than one unnamed alternative value is
given. This will become an error in R 2.13.0.
• StructTS(type = "BSM") now allows series with just two seasons.
(Reported by Birgit Erni.)
INSTALLATION:
• The PDF reference manual is now built as PDF version 1.5 with
object compression, which on platforms for which this is not the
default (notably MiKTeX) halves its size.
• Variable FCLIBS can be set during configuration, for any
additional library flags needed when linking a shared object with
the Fortran 9x compiler. (Needed with Solaris Studio 12.2.)
BUG FIXES:
• seq.int() no longer sometimes evaluates arguments twice.
(PR#14388)
• The data.frame method of format() failed if a column name was
longer than 256 bytes (the maximum length allowed for an R name).
• predict(<lm object>, type ="terms", ...) failed if both terms and
interval were specified. (Reported by Bill Dunlap.)
Also, if se.fit = TRUE the standard errors were reported for all
terms, not just those selected by a non-null terms.
• The TRE regular expressions engine could terminate R rather than
give an error when given certain invalid regular expressions.
(PR#14398)
• cmdscale(eig = TRUE) was documented to return n-1 eigenvalues but
in fact only returned k. It now returns all n eigenvalues.
cmdscale(add = TRUE) failed to centre the return configuration
and sometimes lost the labels on the points. Its return value
was described wrongly (it is always a list and contains component
ac).
• promptClass() in package methods now works for reference classes
and gives a suitably specialized skeleton of documentation.
Also, callSuper() now works via the methods() invocation as well
as for initially specified methods.
• download.file() could leave the destination file open if the URL
was not able to be opened. (PR#14414)
• Assignment of an environment to functions or as an attribute to
other objects now works for S4 subclasses of "environment".
• Use of [[<- for S4 subclasses of "environment" generated an
infinite recursion from the method. The method has been replaced
by internal code.
• In a reference class S4 method, callSuper() now works in
initialize() methods when there is no explicit superclass method.
• ! dropped attributes such as names and dimensions from a
length-zero argument. (PR#14424)
• When list2env() created an environment it was missing a PROTECT
call and so was vulnerable to garbage collection.
• Sweave() with keep.source=TRUE dropped comments at the start and
end of code chunks. It could also fail when \SweaveInput was
combined with named chunks.
• The Fortran code used by nls(algorithm = "port") could
infinite-loop when compiled with high optimization on a modern
version of gcc, and SAFE_FFLAGS is now used to make this less
likely. (PR#14427, seen with 32-bit Windows using gcc 4.5.0 used
from R 2.12.0.)
• sapply() with default simplify = TRUE and mapply() with default
SIMPLIFY = TRUE wrongly simplified language-like results, as,
e.g., in mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j)).
• Backreferences to undefined patterns in [g]sub(pcre = TRUE) could
cause a segfault. (PR#14431)
• The format() (and hence the print()) method for class "Date"
rounded fractional dates towards zero: it now always rounds them
down.
• Reference S4 class creation could generate ambiguous inheritance
patterns under very special circumstances.
• [[<- turned S4 subclasses of "environment" into plain
environments.
• Long titles for help pages were truncated in package indices and
a few other places.
• Additional utilities now work correctly with S4 subclasses of
"environment" (rm, locking tools and active bindings).
• spec.ar() now also work for the "ols" method. (Reported by
Hans-Ruedi Kuensch.)
• The initialization of objects from S4 subclasses of "environment"
now allocates a new environment object.
• R CMD check has more protection against (probably erroneous)
example or test output which is invalid in the current locale.
• qr.X() with column names and pivoting now also pivots the column
names. (PR#14438)
• unit.pmax() and unit.pmin() in package grid gave incorrect
results when all inputs were of length 1. (PR#14443)
• The parser for NAMESPACE files ignored misspelled directives,
rather than signalling an error. For 2.12.x a warning will be
issued, but this will be correctly reported as an error in later
releases. (Reported by Charles Berry.)
• Fix for subsetting of "raster" objects when only one of i or j is
specified.
• grid.raster() in package grid did not accept "nativeRaster"
objects (like rasterImage() does).
• Rendering raster images in PDF output was resetting the clipping
region.
• Rendering of raster images on cairo X11 device was wrong,
particularly when a small image was being scaled up using
interpolation.
With cairo < 1.6, will be better than before, though still a
little clunky. With cairo >= 1.6, should be sweet as.
• Several bugs fixed in read.DIF(): single column inputs caused
errors, cells marked as "character" could be converted to other
types, and (in Windows) copying from the clipboard failed.
CHANGES IN R VERSION 2.12.0:
NEW FEATURES:
• Reading a package's CITATION file now defaults to ASCII rather
than Latin-1: a package with a non-ASCII CITATION file should
declare an encoding in its DESCRIPTION file and use that encoding
for the CITATION file.
• difftime() now defaults to the "tzone" attribute of "POSIXlt"
objects rather than to the current timezone as set by the default
for the tz argument. (Wish of PR#14182.)
• pretty() is now generic, with new methods for "Date" and "POSIXt"
classes (based on code contributed by Felix Andrews).
• unique() and match() are now faster on character vectors where
all elements are in the global CHARSXP cache and have unmarked
encoding (ASCII). Thanks to Matthew Dowle for suggesting
improvements to the way the hash code is generated in unique.c.
• The enquote() utility, in use internally, is exported now.
• .C() and .Fortran() now map non-zero return values (other than
NA_LOGICAL) for logical vectors to TRUE: it has been an implicit
assumption that they are treated as true.
• The print() methods for "glm" and "lm" objects now insert
linebreaks in long calls in the same way that the print() methods
for "summary.[g]lm" objects have long done. This does change the
layout of the examples for a number of packages, e.g. MASS.
(PR#14250)
• constrOptim() can now be used with method "SANN". (PR#14245)
It gains an argument hessian to be passed to optim(), which
allows all the ... arguments to be intended for f() and grad().
(PR#14071)
• curve() now allows expr to be an object of mode "expression" as
well as "call" and "function".
• The "POSIX[cl]t" methods for Axis() have been replaced by a
single method for "POSIXt".
There are no longer separate plot() methods for "POSIX[cl]t" and
"Date": the default method has been able to handle those classes
for a long time. This _inter alia_ allows a single date-time
object to be supplied, the wish of PR#14016.
The methods had a different default ("") for xlab.
• Classes "POSIXct", "POSIXlt" and "difftime" have generators
.POSIXct(), .POSIXlt() and .difftime(). Package authors are
advised to make use of them (they are available from R 2.11.0) to
proof against planned future changes to the classes.
The ordering of the classes has been changed, so "POSIXt" is now
the second class. See the document ‘Updating packages for
changes in R 2.12.x’ on <URL: http://developer.r-project.org> for
the consequences for a handful of CRAN packages.
• The "POSIXct" method of as.Date() allows a timezone to be
specified (but still defaults to UTC).
• New list2env() utility function as an inverse of
as.list(<environment>) and for fast multi-assign() to existing
environment. as.environment() is now generic and uses list2env()
as list method.
• There are several small changes to output which ‘zap’ small
numbers, e.g. in printing quantiles of residuals in summaries
from "lm" and "glm" fits, and in test statistics in
print.anova().
• Special names such as "dim", "names", etc, are now allowed as
slot names of S4 classes, with "class" the only remaining
exception.
• File .Renviron can have architecture-specific versions such as
.Renviron.i386 on systems with sub-architectures.
• installed.packages() has a new argument subarch to filter on
sub-architecture.
• The summary() method for packageStatus() now has a separate
print() method.
• The default summary() method returns an object inheriting from
class "summaryDefault" which has a separate print() method that
calls zapsmall() for numeric/complex values.
• The startup message now includes the platform and if used,
sub-architecture: this is useful where different
(sub-)architectures run on the same OS.
• The getGraphicsEvent() mechanism now allows multiple windows to
return graphics events, through the new functions
setGraphicsEventHandlers(), setGraphicsEventEnv(), and
getGraphicsEventEnv(). (Currently implemented in the windows()
and X11() devices.)
• tools::texi2dvi() gains an index argument, mainly for use by R
CMD Rd2pdf.
It avoids the use of texindy by texinfo's texi2dvi >= 1.157,
since that does not emulate 'makeindex' well enough to avoid
problems with special characters (such as (, {, !) in indices.
• The ability of readLines() and scan() to re-encode inputs to
marked UTF-8 strings on Windows since R 2.7.0 is extended to
non-UTF-8 locales on other OSes.
• scan() gains a fileEncoding argument to match read.table().
• points() and lines() gain "table" methods to match plot(). (Wish
of PR#10472.)
• Sys.chmod() allows argument mode to be a vector, recycled along
paths.
• There are |, & and xor() methods for classes "octmode" and
"hexmode", which work bitwise.
• Environment variables R_DVIPSCMD, R_LATEXCMD, R_MAKEINDEXCMD,
R_PDFLATEXCMD are no longer used nor set in an R session. (With
the move to tools::texi2dvi(), the conventional environment
variables LATEX, MAKEINDEX and PDFLATEX will be used.
options("dvipscmd") defaults to the value of DVIPS, then to
"dvips".)
• New function isatty() to see if terminal connections are
redirected.
• summaryRprof() returns the sampling interval in component
sample.interval and only returns in by.self data for functions
with non-zero self times.
• print(x) and str(x) now indicate if an empty list x is named.
• install.packages() and remove.packages() with lib unspecified and
multiple libraries in .libPaths() inform the user of the library
location used with a message rather than a warning.
• There is limited support for multiple compressed streams on a
file: all of [bgx]zfile() allow streams to be appended to an
existing file, but bzfile() reads only the first stream.
• Function person() in package utils now uses a given/family scheme
in preference to first/middle/last, is vectorized to handle an
arbitrary number of persons, and gains a role argument to specify
person roles using a controlled vocabulary (the MARC relator
terms).
• Package utils adds a new "bibentry" class for representing and
manipulating bibliographic information in enhanced BibTeX style,
unifying and enhancing the previously existing mechanisms.
• A bibstyle() function has been added to the tools package with
default JSS style for rendering "bibentry" objects, and a
mechanism for registering other rendering styles.
• Several aspects of the display of text help are now customizable
using the new Rd2txt_options() function.
options("help_text_width") is no longer used.
• Added \href tag to the Rd format, to allow hyperlinks to URLs
without displaying the full URL.
• Added \newcommand and \renewcommand tags to the Rd format, to
allow user-defined macros.
• New toRd() generic in the tools package to convert objects to
fragments of Rd code, and added "fragment" argument to Rd2txt(),
Rd2HTML(), and Rd2latex() to support it.
• Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree (‘root directory’ in MiKTeX parlance).
• S3 generic functions now use correct S4 inheritance when
dispatching on an S4 object. See ?Methods, section on “Methods
for S3 Generic Functions” for recommendations and details.
• format.pval() gains a ... argument to pass arguments such as
nsmall to format(). (Wish of PR#9574)
• legend() supports title.adj. (Wish of PR#13415)
• Added support for subsetting "raster" objects, plus assigning to
a subset, conversion to a matrix (of colour strings), and
comparisons (== and !=).
• Added a new parseLatex() function (and related functions
deparseLatex() and latexToUtf8()) to support conversion of
bibliographic entries for display in R.
• Text rendering of \itemize in help uses a Unicode bullet in UTF-8
and most single-byte Windows locales.
• Added support for polygons with holes to the graphics engine.
This is implemented for the pdf(), postscript(),
x11(type="cairo"), windows(), and quartz() devices (and
associated raster formats), but not for x11(type="Xlib") or
xfig() or pictex(). The user-level interface is the polypath()
function in graphics and grid.path() in grid.
• File NEWS is now generated at installation with a slightly
different format: it will be in UTF-8 on platforms using UTF-8,
and otherwise in ASCII. There is also a PDF version, NEWS.pdf,
installed at the top-level of the R distribution.
• kmeans(x, 1) now works. Further, kmeans now returns between and
total sum of squares.
• arrayInd() and which() gain an argument useNames. For arrayInd,
the default is now false, for speed reasons.
• As is done for closures, the default print method for the formula
class now displays the associated environment if it is not the
global environment.
• A new facility has been added for inserting code into a package
without re-installing it, to facilitate testing changes which can
be selectively added and backed out. See ?insertSource.
• New function readRenviron to (re-)read files in the format of
~/.Renviron and Renviron.site.
• require() will now return FALSE (and not fail) if loading the
package or one of its dependencies fails.
• aperm() now allows argument perm to be a character vector when
the array has named dimnames (as the results of table() calls
do). Similarly, array() allows MARGIN to be a character vector.
(Based on suggestions of Michael Lachmann.)
• Package utils now exports and documents functions
aspell_package_Rd_files() and aspell_package_vignettes() for
spell checking package Rd files and vignettes using Aspell,
Ispell or Hunspell.
• Package news can now be given in Rd format, and news() prefers
these inst/NEWS.Rd files to old-style plain text NEWS or
inst/NEWS files.
• New simple function packageVersion().
• The PCRE library has been updated to version 8.10.
• The standard Unix-alike terminal interface declares its name to
readline as 'R', so that can be used for conditional sections in
~/.inputrc files.
• ‘Writing R Extensions’ now stresses that the standard sections in
.Rd files (other than \alias, \keyword and \note) are intended to
be unique, and the conversion tools now drop duplicates with a
warning.
The .Rd conversion tools also warn about an unrecognized type in
a \docType section.
• ecdf() objects now have a quantile() method.
• format() methods for date-time objects now attempt to make use of
a "tzone" attribute with "%Z" and "%z" formats, but it is not
always possible. (Wish of PR#14358.)
• tools::texi2dvi(file, clean = TRUE) now works in more cases (e.g.
where emulation is used and when file is not in the current
directory).
• New function droplevels() to remove unused factor levels.
• system(command, intern = TRUE) now gives an error on a Unix-alike
(as well as on Windows) if command cannot be run. It reports a
non-success exit status from running command as a warning.
On a Unix-alike an attempt is made to return the actual exit
status of the command in system(intern = FALSE): previously this
had been system-dependent but on POSIX-compliant systems the
value return was 256 times the status.
• system() has a new argument ignore.stdout which can be used to
(portably) ignore standard output.
• system(intern = TRUE) and pipe() connections are guaranteed to be
available on all builds of R.
• Sys.which() has been altered to return "" if the command is not
found (even on Solaris).
• A facility for defining reference-based S4 classes (in the OOP
style of Java, C++, etc.) has been added experimentally to
package methods; see ?ReferenceClasses.
• The predict method for "loess" fits gains an na.action argument
which defaults to na.pass rather than the previous default of
na.omit.
Predictions from "loess" fits are now named from the row names of
newdata.
• Parsing errors detected during Sweave() processing will now be
reported referencing their original location in the source file.
• New adjustcolor() utility, e.g., for simple translucent color
schemes.
• qr() now has a trivial lm method with a simple (fast) validity
check.
• An experimental new programming model has been added to package
methods for reference (OOP-style) classes and methods. See
?ReferenceClasses.
• bzip2 has been updated to version 1.0.6 (bug-fix release).
--with-system-bzlib now requires at least version 1.0.6.
• R now provides jss.cls and jss.bst (the class and bib style file
for the Journal of Statistical Software) as well as RJournal.bib
and Rnews.bib, and R CMD ensures that the .bst and .bib files are
found by BibTeX.
• Functions using the TAR environment variable no longer quote the
value when making system calls. This allows values such as tar
--force-local, but does require additional quotes in, e.g., TAR =
"'/path with spaces/mytar'".
DEPRECATED & DEFUNCT:
• Supplying the parser with a character string containing both
octal/hex and Unicode escapes is now an error.
• File extension .C for C++ code files in packages is now defunct.
• R CMD check no longer supports configuration files containing
Perl configuration variables: use the environment variables
documented in ‘R Internals’ instead.
• The save argument of require() now defaults to FALSE and save =
TRUE is now deprecated. (This facility is very rarely actually
used, and was superseded by the Depends field of the DESCRIPTION
file long ago.)
• R CMD check --no-latex is deprecated in favour of --no-manual.
• R CMD Sd2Rd is formally deprecated and will be removed in R
2.13.0.
PACKAGE INSTALLATION:
• install.packages() has a new argument libs_only to optionally
pass --libs-only to R CMD INSTALL and works analogously for
Windows binary installs (to add support for 64- or 32-bit
Windows).
• When sub-architectures are in use, the installed architectures
are recorded in the Archs field of the DESCRIPTION file. There
is a new default filter, "subarch", in available.packages() to
make use of this.
Code is compiled in a copy of the src directory when a package is
installed for more than one sub-architecture: this avoid problems
with cleaning the sources between building sub-architectures.
• R CMD INSTALL --libs-only no longer overrides the setting of
locking, so a previous version of the package will be restored
unless --no-lock is specified.
UTILITIES:
• R CMD Rprof|build|check are now based on R rather than Perl
scripts. The only remaining Perl scripts are the deprecated R
CMD Sd2Rd and install-info.pl (used only if install-info is not
found) as well as some maintainer-mode-only scripts.
*NB:* because these have been completely rewritten, users should
not expect undocumented details of previous implementations to
have been duplicated.
R CMD no longer manipulates the environment variables PERL5LIB
and PERLLIB.
• R CMD check has a new argument --extra-arch to confine tests to
those needed to check an additional sub-architecture.
Its check for “Subdirectory 'inst' contains no files” is more
thorough: it looks for files, and warns if there are only empty
directories.
Environment variables such as R_LIBS and those used for
customization can be set for the duration of checking _via_ a
file ~/.R/check.Renviron (in the format used by .Renviron, and
with sub-architecture specific versions such as
~/.R/check.Renviron.i386 taking precedence).
There are new options --multiarch to check the package under all
of the installed sub-architectures and --no-multiarch to confine
checking to the sub-architecture under which check is invoked.
If neither option is supplied, a test is done of installed
sub-architectures and all those which can be run on the current
OS are used.
Unless multiple sub-architectures are selected, the install done
by check for testing purposes is only of the current
sub-architecture (_via_ R CMD INSTALL --no-multiarch).
It will skip the check for non-ascii characters in code or data
if the environment variables _R_CHECK_ASCII_CODE_ or
_R_CHECK_ASCII_DATA_ are respectively set to FALSE. (Suggestion
of Vince Carey.)
• R CMD build no longer creates an INDEX file (R CMD INSTALL does
so), and --force removes (rather than overwrites) an existing
INDEX file.
It supports a file ~/.R/build.Renviron analogously to check.
It now runs build-time \Sexpr expressions in help files.
• R CMD Rd2dvi makes use of tools::texi2dvi() to process the
package manual. It is now implemented entirely in R (rather than
partially as a shell script).
• R CMD Rprof now uses utils::summaryRprof() rather than Perl. It
has new arguments to select one of the tables and to limit the
number of entries printed.
• R CMD Sweave now runs R with --vanilla so the environment setting
of R_LIBS will always be used.
C-LEVEL FACILITIES:
• lang5() and lang6() (in addition to pre-existing lang[1-4]())
convenience functions for easier construction of eval() calls.
If you have your own definition, do wrap it inside #ifndef lang5
.... #endif to keep it working with old and new R.
• Header R.h now includes only the C headers it itself needs, hence
no longer includes errno.h. (This helps avoid problems when it
is included from C++ source files.)
• Headers Rinternals.h and R_ext/Print.h include the C++ versions
of stdio.h and stdarg.h respectively if included from a C++
source file.
INSTALLATION:
• A C99 compiler is now required, and more C99 language features
will be used in the R sources.
• Tcl/Tk >= 8.4 is now required (increased from 8.3).
• System functions access, chdir and getcwd are now essential to
configure R. (In practice they have been required for some
time.)
• make check compares the output of the examples from several of
the base packages to reference output rather than the previous
output (if any). Expect some differences due to differences in
floating-point computations between platforms.
• File NEWS is no longer in the sources, but generated as part of
the installation. The primary source for changes is now
doc/NEWS.Rd.
• The popen system call is now required to build R. This ensures
the availability of system(intern = TRUE), pipe() connections and
printing from postscript().
• The pkg-config file libR.pc now also works when R is installed
using a sub-architecture.
• R has always required a BLAS that conforms to IE60559 arithmetic,
but after discovery of more real-world problems caused by a BLAS
that did not, this is tested more thoroughly in this version.
BUG FIXES:
• Calls to selectMethod() by default no longer cache inherited
methods. This could previously corrupt methods used by as().
• The densities of non-central chi-squared are now more accurate in
some cases in the extreme tails, e.g. dchisq(2000, 2, 1000), as a
series expansion was truncated too early. (PR#14105)
• pt() is more accurate in the left tail for ncp large, e.g.
pt(-1000, 3, 200). (PR#14069)
• The default C function (R_binary) for binary ops now sets the S4
bit in the result if either argument is an S4 object. (PR#13209)
• source(echo=TRUE) failed to echo comments that followed the last
statement in a file.
• S4 classes that contained one of "matrix", "array" or "ts" and
also another class now accept superclass objects in new(). Also
fixes failure to call validObject() for these classes.
• Conditional inheritance defined by argument test in
methods::setIs() will no longer be used in S4 method selection
(caching these methods could give incorrect results). See
?setIs.
• The signature of an implicit generic is now used by setGeneric()
when that does not use a definition nor explicitly set a
signature.
• A bug in callNextMethod() for some examples with "..." in the
arguments has been fixed. See file
src/library/methods/tests/nextWithDots.R in the sources.
• match(x, table) (and hence %in%) now treat "POSIXlt" consistently
with, e.g., "POSIXct".
• Built-in code dealing with environments (get(), assign(),
parent.env(), is.environment() and others) now behave
consistently to recognize S4 subclasses; is.name() also
recognizes subclasses.
• The abs.tol control parameter to nlminb() now defaults to 0.0 to
avoid false declarations of convergence in objective functions
that may go negative.
• The standard Unix-alike termination dialog to ask whether to save
the workspace takes a EOF response as n to avoid problems with a
damaged terminal connection. (PR#14332)
• Added warn.unused argument to hist.default() to allow suppression
of spurious warnings about graphical parameters used with
plot=FALSE. (PR#14341)
• predict.lm(), summary.lm(), and indeed lm() itself had issues
with residual DF in zero-weighted cases (the latter two only in
connection with empty models). (Thanks to Bill Dunlap for
spotting the predict() case.)
• aperm() treated resize = NA as resize = TRUE.
• constrOptim() now has an improved convergence criterion, notably
for cases where the minimum was (very close to) zero; further,
other tweaks inspired from code proposals by Ravi Varadhan.
• Rendering of S3 and S4 methods in man pages has been corrected
and made consistent across output formats.
• Simple markup is now allowed in \title sections in .Rd files.
• The behaviour of as.logical() on factors (to use the levels) was
lost in R 2.6.0 and has been restored.
• prompt() did not backquote some default arguments in the \usage
section. (Reported by Claudia Beleites.)
• writeBin() disallows attempts to write 2GB or more in a single
call. (PR#14362)
• new() and getClass() will now work if Class is a subclass of
"classRepresentation" and should also be faster in typical calls.
• The summary() method for data frames makes a better job of names
containing characters invalid in the current locale.
• [[ sub-assignment for factors could create an invalid factor
(reported by Bill Dunlap).
• Negate(f) would not evaluate argument f until first use of
returned function (reported by Olaf Mersmann).
• quietly=FALSE is now also an optional argument of library(), and
consequently, quietly is now propagated also for loading
dependent packages, e.g., in require(*, quietly=TRUE).
• If the loop variable in a for loop was deleted, it would be
recreated as a global variable. (Reported by Radford Neal; the
fix includes his optimizations as well.)
• Task callbacks could report the wrong expression when the task
involved parsing new code. (PR#14368)
• getNamespaceVersion() failed; this was an accidental change in
2.11.0. (PR#14374)
• identical() returned FALSE for external pointer objects even when
the pointer addresses were the same.
• L$a@x[] <- val did not duplicate in a case it should have.
• tempfile() now always gives a random file name (even if the
directory is specified) when called directly after startup and
before the R RNG had been used. (PR#14381)
• quantile(type=6) behaved inconsistently. (PR#14383)
• backSpline(.) behaved incorrectly when the knot sequence was
decreasing. (PR#14386)
• The reference BLAS included in R was assuming that 0*x and x*0
were always zero (whereas they could be NA or NaN in IEC 60559
arithmetic). This was seen in results from tcrossprod, and for
example that log(0) %*% 0 gave 0.
• The calculation of whether text was completely outside the device
region (in which case, you draw nothing) was wrong for screen
devices (which have [0, 0] at top-left). The symptom was (long)
text disappearing when resizing a screen window (to make it
smaller). (PR#14391)
• model.frame(drop.unused.levels = TRUE) did not take into account
NA values of factors when deciding to drop levels. (PR#14393)
• library.dynam.unload required an absolute path for libpath.
(PR#14385)
Both library() and loadNamespace() now record absolute paths for
use by searchpaths() and getNamespaceInfo(ns, "path").
• The self-starting model NLSstClosestX failed if some deviation
was exactly zero. (PR#14384)
• X11(type = "cairo") (and other devices such as png using
cairographics) and which use Pango font selection now work around
a bug in Pango when very small fonts (those with sizes between 0
and 1 in Pango's internal units) are requested. (PR#14369)
• Added workaround for the font problem with X11(type = "cairo")
and similar on Mac OS X whereby italic and bold styles were
interchanged. (PR#13463 amongst many other reports.)
• source(chdir = TRUE) failed to reset the working directory if it
could not be determined - that is now an error.
• Fix for crash of example(rasterImage) on x11(type="Xlib").
• Force Quartz to bring the on-screen display up-to-date
immediately before the snapshot is taken by grid.cap() in the
Cocoa implementation. (PR#14260)
• model.frame had an unstated 500 byte limit on variable names.
(Example reported by Terry Therneau.)
• The 256-byte limit on names is now documented.
• Subassignment by [, [[ or $ on an expression object with value
NULL coerced the object to a list.
CHANGES IN R VERSION 2.11.1 patched:
NEW FEATURES:
• install.packages() has a new optional argument INSTALL_opts which
can be used to pass options to R CMD INSTALL for source-package
installs.
• R CMD check now runs the package-specific tests with LANGUAGE=en
to facilitate comparison to .Rout.save files.
• sessionInfo() gives more detailed platform information, including
32/64-bit and the sub-architecture if one is used.
DEPRECATED & DEFUNCT:
• The use of Perl configuration variables for R CMD check (as
previously documented in ‘Writing R Extensions’) is deprecated
and will be removed in R 2.12.0. Use the environment variables
documented in ‘R Internals’ instead.
BUG FIXES:
• R CMD Rd2dvi failed if run from a path containing space(s). This
also affected R CMD check, which calls Rd2dvi.
• stripchart() could fail with an empty factor level. (PR#14317)
• Text help rendering of \tabular{} has been improved: under some
circumstances leading blank columns were not rendered.
• strsplit(x, fixed=TRUE) marked UTF-8 strings with the local
encoding when no splits were found.
• weighted.mean(NA, na.rm=TRUE) and similar now returns NaN again,
as it did prior to R 2.10.0.
• R CMD had a typo in its detection of whether the environment
variable TEXINPUTS was set (reported by Martin Morgan).
• The command-line parser could mistake --file=size... for one of
the options for setting limits for Ncells or Vcells.
• The internal strptime() could corrupt its copy of the timezone
which would then lead to spurious warnings. (PR#14338)
• dir.create(recursive = TRUE) could fail if one of the components
existed but was a directory on a read-only file system. (Seen on
Solaris, where the error code returned is not even listed as
possible on the man page.)
• The postscript() and pdf() devices will now allow lwd values less
than 1 (they used to force such values to be 1).
• Fixed font face for CID fonts in pdf() graphics output.
(PR#14326)
• GERaster() now checks for width or height of zero and does
nothing in those cases; previously the behaviour was undefined,
probably device-specific, and possibly dangerous.
• wilcox.test(x, y, conf.int = TRUE) failed with an unhelpful
message if x and y were constant vectors, and similarly in the
one-sample case. (PR#14329)
• Improperly calling Recall() from outside a function could cause a
segfault. (Reported by Robert McGehee.)
• \Sexpr[result=rd] in an Rd file added a spurious newline, which
was displayed as extra whitespace when rendered.
• require(save = TRUE) recorded the names of packages it failed to
load.
• packageStatus() could return a data frame with duplicate row
names which could then not be printed.
• txtProgressBar(style = 2) did not work correctly.
txtProgressBar(style = 3) did not display until a non-minimum
value was set.
• contour() did not display dashed line types properly when contour
lines were labelled. (Reported by David B. Thompson.)
• tools::undoc() again detects undocumented data objects. Of
course, this also affects R CMD check.
• ksmooth(x,NULL) no longer segfaults.
• approxfun(), approx(), splinefun() and spline() could be confused
by x values that were different but so close as to print
identically. (PR#14377)
CHANGES IN R VERSION 2.11.1:
NEW FEATURES:
• R CMD INSTALL checks if dependent packages are available early on
in the installation of source packages, thereby giving clearer
error messages.
• R CMD INSTALL --build now names the file in the format used for
Mac OS X binary files on that platform.
• BIC() in package stats4 now also works with multiple fitted
models, analogously to AIC().
DEPRECATED & DEFUNCT:
• Use of file extension .C for C++ code in packages is now
deprecated: it has caused problems for some makes on
case-insensitive file systems (although it currently works with
the recommended toolkits).
INSTALLATION:
• Command gnutar is preferred to tar when configure sets TAR. This
is needed on Mac OS 10.6, where the default tar, bsdtar 2.6.2,
has been reported to produce archives with illegal extensions to
tar (according to the POSIX standard).
BUG FIXES:
• The C function mkCharLenCE now no longer reads past len bytes
(unlikely to be a problem except in user code). (PR#14246)
• On systems without any default LD_LIBRARY_PATH (not even
/usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a
trailing colon. (PR#13637)
• More efficient implementation of utf8ToInt() on long multi-byte
strings with many multi-byte characters. (PR#14262)
• aggregate.ts() gave platform-dependent results due to rounding
error for ndeltat != 1.
• package.skeleton() sometimes failed to fix filenames for .R or
.Rd files to start with an alphanumeric. (PR#14253)
It also failed when only an S4 class without any methods was
defined. (PR#14280)
• splinefun(method = "monoH.FC") was not quite monotone in rare
cases. (PR#14215)
• Rhttpd no longer crashes due to SIGPIPE when the client closes
the connection prematurely. (PR#14266)
• format.POSIXlt() could cause a stack overflow and crash when used
on very long vectors. (PR#14267)
• Rd2latex() incorrectly escaped special characters in \usage
sections.
• mcnemar.test() could alter the levels (dropping unused levels) if
passed x and y as factors (reported by Greg Snow).
• Rd2pdf sometimes needed a further pdflatex pass to get
hyperlinked pages correct.
• interaction() produced malformed results when levels were
duplicated, causing segfaults in split().
• cut(d, breaks = <n>) now also works for "Date" or "POSIXt"
argument d. (PR#14288)
• memDecompress() could decompress incompletely rare xz-compressed
input due to incorrect documentation of xz utils. (Report and
patch from Olaf Mersmann.)
• The S4 initialize() methods for "matrix", "array", and "ts" have
been fixed to call validObject(). (PR#14284)
• R CMD INSTALL now behaves the same way with or without
--no-multiarch on platforms with only one installed architecture.
(It used to clean the src directory without --no-multiarch.)
• [<-.data.frame was not quite careful enough in assigning (and
potentially deleting) columns right-to-left. (PR#14263)
• rbeta(n, a, b) no longer occasionally returns NaN for a >> 1 > b.
(PR#14291)
• pnorm(x, log.p = TRUE) could return NaN not -Inf for x near
(minus for lower.tail=TRUE) the largest representable number.
• Compressed data files *.(txt|tab|csv).(gz|bz2|xz) were not
recognized for the list of data topics and hence for packages
using LazyData. (PR#14273)
• textConnection() did an unnecessary translation on strings in a
foreign encoding (e.g. UTF-8 strings on Windows) and so was
slower than it could have been on very long input strings.
(PR#14286)
• tools::Rd2txt() did not render poorly written Rd files
consistently with other renderers.
It computed widths of strings that would be print()ed with
escapes incorrectly, for example in the computation of column
width for \tabular.
• na.action() did not extract the na.action component as
documented.
• do.call()ing NextMethod in erroneous ways no longer segfaults.
(PR#13487)
CHANGES IN R VERSION 2.11.0:
SIGNIFICANT USER-VISIBLE CHANGES:
• Packages must have been installed under R >= 2.10.0, as the
current help system is the only one now supported.
• A port to 64-bit Windows is now available as well as binary
package repositories: see the ‘R Administration and Installation
Manual’.
• Argument matching for primitive functions is now done in the same
way as for interpreted functions except for the deliberate
exceptions
call switch .C .Fortran .Call .External
all of which use positional matching for their first argument,
and also some internal-use-only primitives.
• The default device for command-line R at the console on Mac OS X
is now quartz() and not X11().
NEW FEATURES:
• The open modes for connections are now interpreted more
consistently. open = "r" is now equivalent to open = "rt" for
all connections. The default open = "" now means "rt" for all
connections except the compressed-file connections gzfile(),
bzfile() and xzfile() for which it means "rb".
• R CMD INSTALL now uses the internal untar() function in package
utils: this ensures that all platforms can install bzip2- and
xz-compressed tarballs. In case this causes problems (as it has
on some Windows file systems when run from Cygwin tools) it can
be overridden by the environment variable R_INSTALL_TAR: setting
this to a modern external tar program will speed up unpacking of
large (tens of Mb or more) tarballs.
• help(try.all.packages = TRUE) is much faster (although the time
taken by the OS to find all the packages the first time it is
used can dominate the time).
• R CMD check has a new option --timings to record per-example
timings in file <pkg>.Rcheck/<pkg>-Ex.timings.
• The TRE library has been updated to version 0.8.0 (minor
bugfixes).
• grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit
locales if there is no marked UTF-8 input string: this will be
somewhat faster, and for [g]sub() give the result in the native
encoding rather than in UTF-8 (which returns to the behaviour
prior to R 2.10.0).
• A new argument skipCalls has been added to browser() so that it
can report the original context when called by other debugging
functions.
• More validity checking of UTF-8 and MBCS strings is done by
agrep() and the regular-expression matching functions.
• The undocumented restriction on gregexpr() to length(text) > 0
has been removed.
• Package tcltk now sends strings to Tcl in UTF-8: this means that
strings with a marked UTF-8 encoding are supported in non-UTF-8
locales.
• The graphics engine now supports rendering of raster (bitmap)
images, though not all graphics devices can provide (full)
support. Packages providing graphics devices (e.g., Cairo,
RSvgDevice, cairoDevice) will need to be reinstalled.
There is also support in the graphics engine for capturing raster
images from graphics devices (again not supported on all graphics
devices).
• R CMD check now also checks if the package and namespace can be
unloaded: this provides a check of the .Last.lib() and
.onUnload() hook functions (unless --install=fake).
• prop.table(x) now accepts a one-dimensional table for x.
• A new function vapply() has been added, based on a suggestion
from Bill Dunlap. It requires that a template for the function
value be specified, and uses it to determine the output type and
to check for consistency in the function values.
• The main HTML help page now links to a reformatted copy of this
NEWS file. (Suggested by Henrik Bengtsson.) Package index files
link to the package DESCRIPTION and NEWS files and a list of
demos when using dynamic help.
• The [ method for class "AsIs" allows the next method to change
the underlying class. (Wish of Jens Oehlschlägel.)
• write.csv[2] no longer allow argument append to be changed: as
ever, direct calls to write.table() give more flexibility as well
as more room for error.
• The index page for HTML help for a package now collapses multiple
signatures for S4 methods into a single entry.
• The use of .required by require() and detach() has been replaced
by .Depends which is set from the Depends field of a package
(even in packages with namespaces). By default detach() prevents
such dependencies from being detached: this can be overridden by
the argument force.
• bquote() has been extended to work on function definitions.
(Wish of PR#14031).
• detach() when applied to an object other than a package returns
the environment that has been detached, to parallel attach().
• readline() in non-interactive use returns "" and does not attempt
to read from the ‘terminal’.
• New function file_ext() in package tools.
• xtfrm() is now primitive and internally generic, as this allows
S4 methods to be set on it without name-space scoping issues.
There are now "AsIs" and "difftime" methods, and the default
method uses unclass(x) if is.numeric(x) is true (which will be
faster but relies on is.numeric() having been set correctly for
the class).
• is.numeric(x) is now false for a "difftime" object
(multiplication and division make no sense for such objects).
• The default method of weighted.mean(x, w) coerces w to be numeric
(aka double); previously only integer weights were coerced. Zero
weights are handled specially so an infinite value with zero
weight does not force an NaN result.
There is now a "difftime" method.
• bug.report() now has arguments package and lib.loc to generate
bug reports about packages. When this is used, it looks for a
BugReports field in the package DESCRIPTION file, which will be
assumed to be a URL at which to submit the report, and otherwise
generates an email to the package maintainer. (Suggested by
Barry Rowlingson.)
• quantile() now has a method for the date-time class "POSIXt", and
types 1 and 3 (which never interpolate) work for Dates and
ordered factors.
• length(<POSIXlt>) now returns the length of the corresponding
abstract timedate-vector rather than always 9 (the length of the
underlying list structure). (Wish of PR#14073 and PR#10507.)
• The readline completion backend no longer sorts possible
completions alphabetically (e.g., function argument names) if R
was built with readline >= 6.
• select.list() gains a graphics argument to allow Windows/Mac
users to choose the text interface. This changes the behaviour
of new.packages(ask=TRUE) to be like update.packages(ask=TRUE) on
those platforms in using a text menu: use ask="graphics" for a
graphical menu.
• New function chooseBioCmirror() to set the "BioC_mirror" option.
• The R grammar now prevents using the argument name in signatures
of S4 methods for $ and $<-, since they will always be called
with a character string value for name. The implicit S4 generic
functions have been changed to reflect this: packages which
included name in the signature of their methods need to be
updated and re-installed.
• The handling of the method argument of glm() has been refined
following suggestions by Ioannis Kosmidis and Heather Turner.
• str() gains a new argument list.len with default 99, limiting the
number of list() items (per level), thanks to suggestions from
David Winsenius.
• Having formal arguments of an S4 method in a different order from
the generic is now an error (the warning having been ignored by
some package maintainers for a long time).
• New functions enc2native() and enc2utf8() convert character
vectors with possibly marked encodings to the current locale and
UTF-8 respectively.
• Unrecognized escapes and embedded nuls in character strings are
now an error, not just a warning. Thus option "warnEscapes" is
no longer needed. rawToChar() now removes trailing nuls
silently, but other embedded nuls become errors.
• Informational messages about masked objects displayed when a
package is attached are now more compact, using strwrap() instead
of one object per line.
• print.rle() gains argument prefix.
• download.file() gains a "curl" method, mainly for use on
platforms which have curl but not wget, but also for some
hard-to-access URLs.
• In Rd, \eqn and \deqn will render in HTML (and convert to text)
upper- and lower-case Greek letters (entered as \alpha ...),
\ldots, ..., \ge and \le.
• utf8ToInt() and intToUtf8() now map NA inputs to NA outputs.
• file() has a new argument raw which may help if it is used with
something other than a regular file, e.g. a character device.
• New function strtoi(), a wrapper for the C function strtol.
• as.octmode() and as.hexmode() now allow inputs of length other
than one.
The format() and print() methods for "octmode" now preserve names
and dimensions (as those for "hexmode" did).
The format() methods for classes "octmode" and "hexmode" gain a
width argument.
• seq.int() returns an integer result in some further cases where
seq() does, e.g. seq.int(1L, 9L, by = 2L).
• Added \subsection{}{} macro to Rd syntax, for subsections within
sections.
• n-dimensional arrays with dimension names can now be indexed by
an n-column character matrix. The indices are matched against
the dimension names. NA indices are propagated to the result.
Unmatched values and "" are not allowed and result in an error.
• interaction(drop=TRUE) uses less memory (related to PR#14121).
• summary() methods have been added to the "srcref" and "srcfile"
classes, and various encoding issues have been cleaned up.
• If option "checkPackageLicense" is set to TRUE (not currently the
default), users will be asked to agree to non-known-to-be-FOSS
package licences at first use.
• Checking setAs(a, b) methods only gives a message instead of a
warning, when one of a or b is unknown.
• New function norm() to compute a matrix norm. norm() and also
backsolve() and sample() have implicit S4 generics.
• Files Renviron.site and Rprofile.site can have
architecture-specific versions on systems with sub-architectures.
• R CMD check now (by default) also checks Rd files for
auto-generated content in need of editing, and missing argument
descriptions.
• aggregate() gains a formula method thanks to a contribution by
Arni Magnusson. The data frame method now allows summary
functions to return arbitrarily many values.
• path.expand() now propagates NA values rather than converting
them to "NA".
• file.show() now disallows NA values for file names, headers, and
pager.
• The ‘fuzz’ used by seq() and seq.int() has been reduced from 1e-7
to 1e-10, which should be ample for the double-precision
calculations used in R. It ensures that the fuzz never comes
into play with sequences of integers (wish of PR#14169).
• The default value of RSiteSearch(restrict=) has been changed to
include vignettes but to exclude R-help. The R-help archives
available have been split, with a new option of "Rhelp10" for
those from 2010.
• New function rasterImage() in the graphics package for drawing
raster images.
• stats:::extractAIC.coxph() now omits aliased terms when computing
the degrees of freedom (suggestion of Terry Therneau).
• cor() and cov() now test for misuse with non-numeric arguments,
such as the non-bug report PR#14207.
• pchisq(ncp =, log.p = TRUE) is more accurate for probabilities
near one. E.g. pchisq(80, 4, ncp=1, log.p=TRUE). (Maybe what
was meant in PR#14216.)
• maintainer() has been added, to give convenient access to the
name of the maintainer of a package (contributed by David Scott).
• sample() and sample.int() allow zero items to be sampled from a
zero-length input. sample.int() gains a default value size=n to
be more similar to sample().
• switch() returned NULL on error (not previously documented on the
help page): it now does so invisibly, analogously to
if-without-else.
It is now primitive: this means that argument EXPR is always
matched to the first argument and there is no danger of partial
matching to later named arguments.
• Primitive functions UseMethod(), attr(), attr<-(), on.exit(),
retracemem() and substitute() now use standard argument matching
(rather than positional matching). This means that all
multi-argument primitives which are not internal now use standard
argument matching except where positional matching is desirable
(as for switch(), call(), .C() ...).
• All the one-argument primitives now check that any name supplied
for their first argument is a partial match to the argument name
as documented on the help page: this also applies to replacement
functions of two arguments.
• base::which() uses a new .Internal function when arr.ind is FALSE
resulting in a 10x speedup. Thanks to Patrick Aboyoun for
implementation suggestions.
• Help conversion to text now uses the first part of \enc{}{}
markup if it is representable in the current output encoding. On
the other hand, conversion to LaTeX with the default
outputEncoding = "ASCII" uses the second part.
• A new class "listOfMethods" has been introduced to represent the
methods in a methods table, to replace the deprecated class
"MethodsList".
• any() and all() return early if possible. This may speed up
operations on long vectors.
• strptime() now accepts "%z" (for the offset from UTC in the
RFC822 format of +/-hhmm).
• The PCRE library has been updated to version 8.02, a bug-fix
release which also updates tables to Unicode 5.02.
• Functions which may use a graphical select.list() (including
menu() and install.packages()) now check on a Unix-alike that Tk
can be started (and not just capabilities("tcltk") &&
capabilities("X11")).
• The parser no longer marks strings containing octal or hex
escapes as being in UTF-8 when entered in a UTF-8 locale.
• On platforms with cairo but not Pango (notably Mac OS X) the
initial default X11() type is set to "Xlib": this avoids several
problems with font selection when done by cairo rather than Pango
(at least on Mac OS X).
• New function arrayInd() such that which(x, arr.ind = TRUE) for an
array 'x' is now equivalent to arrayInd(which(x), dim(x),
dimnames(x)).
DEPRECATED & DEFUNCT:
• Bundles of packages are defunct.
• stats::clearNames() is defunct: use unname().
• Basic regular expressions are defunct, and strsplit(), grep(),
grepl(), sub(), gsub(), regexpr() and gregexpr() no longer have
an extended argument.
• methods::trySilent() is defunct.
• index.search() (which was deprecated in 2.10.0) is no longer
exported and has a different argument list.
• Use of multiple arguments to return() is now defunct.
• The use of UseMethod() with more than two arguments is now
defunct.
• In the methods package, the "MethodsList" metadata objects which
had been superseded by hash tables (environments) since R 2.8.0
are being phased out. Objects of this class are no longer
assigned or used as metadata by the package.
getMethods() is now deprecated, with its internal use replaced by
findMethods() and other changes. Creating objects from the
"MethodsList" class is also deprecated.
• Parsing strings containing both octal/hex and Unicode escapes now
gives a warning and will become an error in R 2.12.0.
INSTALLATION:
• UTF-8 is now used for the reference manual and package manuals.
This requires LaTeX ‘2005/12/01’ or later.
• configure looks for a POSIX compliant tr, Solaris's /usr/ucb/tr
having been found to cause Rdiff to malfunction.
• configure is now generated with autoconf 2.65, which works better
on recent systems and on Mac OS X.
PACKAGE INSTALLATION:
• Characters in R source which are not translatable to the current
locale are now handled more tolerantly: these will be converted
to hex codes with a warning. Such characters are only really
portable if they appear in comments.
• R CMD INSTALL now tests that the installed package can be loaded
(and backs out the installation if it cannot): this can be
suppressed by --no-test-load. This avoids installing/updating a
package that cannot be used: common causes of failures to load
are missing/incompatible external software and missing/broken
dependent packages.
• Package installation on Windows for a package with a src
directory now checks if a DLL is created unless there is a
src/Makefile.win file: this helps catch broken installations
where the toolchain has not reported problems in building the
DLL. (Note: this can be any DLL, not just one named
<pkg-name>.dll.)
BUG FIXES:
• Using with(), eval() etc with a list with some unnamed elements
now works. (PR#14035)
• The "quick" dispatch of S4 methods for primitive functions was
not happening, forcing a search each time. (Dispatch for
closures was not affected.) A side effect is that default values
for arguments in a method that do not have defaults in the
generic will now be ignored.
• Trying to dispatch S4 methods for primitives during the search
for inherited methods slows that search down and potentially
could cause an infinite recursion. An internal switch was added
to turn off all such methods from findInheritedMethods().
• R framework installation (on Mac OS X) would not work properly if
a rogue Resources directory was present at the top level. Such a
non-symlink will now be renamed to Resources.old (and anything
previously named Resources.old removed) as part of the framework
installation process.
• The checks for conforming S4 method arguments could fail when the
signature of the generic function omitted some of the formal
arguments (in addition to ...). Arguments omitted from the
method definition but conforming (per the documentation) should
now be ignored (treated as "ANY") in dispatching.
• The computations for S4 method evaluation when ... was in the
signature could fail, treating ... as an ordinary symbol. This
has been fixed, for the known cases.
• Various ar() fitting methods have more protection for singular
fits.
• callNextMethod now works again with the drop= argument in [
• parse() and parse_Rd() miscounted columns when multibyte UTF-8
characters were present.
• Formatting of help pages has had minor improvements: extra blank
lines have been removed from the text format, and empty package
labels removed from HTML.
• cor(A, B) where A is n x 1 and B a 1-dimensional array segfaulted
or gave an internal error. (The case cor(B, A) was PR#7116.)
• cut.POSIXt() applied to a start value after the DST transition on
a DST-change day could give the wrong time for argument breaks in
units of days or longer. (PR#14208)
• do_par() UNPROTECTed too early (PR#14214)
• Subassignment x[[....]] <- y didn't check for a zero-length right
hand side, and inserted a rubbish value. (PR#14217)
• fisher.test() no longer gives a P-value *very* slightly > 1, in
some borderline cases.
• Internal function matchArgs() no longer modifies the general
purpose bits of the SEXPs 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.
• gsub() in 2.10.x could fail from stack overflow for extremely
long strings due to temporary data being allocated on the stack.
Also, gsub() with fixed=TRUE is in some circumstances
considerably faster.
• Several primitives, including attributes(), attr<-()
interactive(), nargs() and proc.time(), did not check that they
were called with the correct number of arguments.
• A potential race condition in list.files() when other processes
are operating on the directory has been fixed; the code now
dynamically allocates memory for file listings in a single pass
instead of making an initial count pass.
• mean(x, trim=, na.rm = FALSE) failed to return NA if x contained
missing values. (Reported by Bill Dunlap.)
• Extreme tail behavior of, pbeta() {and hence pf()}, e.g.,
pbeta(x, 3, 2200, lower.tail=FALSE, log.p=TRUE) now returns
finite values instead of jumping to -Inf too early. (PR#14230).
• parse(text=x) misbehaved for objects x that were not coerced
internally to character, notably symbols. (Reported to R-devel
by Bill Dunlap.)
• The internal C function coerceSymbol now handles coercion to
character, and warns if coercion fails (rather than silently
returning NULL). This allows a name to be given where a
character vector is required in functions which coerce
internally.
• The interpretation by strptime() of "%c" was non-standard (not
that it is ever advisable to use locale- and system-specific
input formats).
• capabilities("X11") now works the same way on Mac OS X as on
other platforms (and as documented: it was always true for R
built with --with-aqua, as the CRAN builds are).
• The X11() device with cairo but not Pango (notably Mac OS X) now
checks validity of text strings in UTF-8 locales (since Pango
does but cairo it seems does not).
• read.fwf() misread multi-line records when n was specified.
(PR#14241)
• all.equal(tolerance = e) passes the numeric tolerance also to the
comparison of the attributes.
• pgamma(0, 0), a boundary case, now returns 0, its limit from the
left, rather than the limit from the right.
• Issuing POST requests to the internal web server could stall the
request under certain circumstances.
• gzcon( <textConnection> ), an error, no longer damages the
connection (in a way to have it segfault). (PR#14237)
• All the results from hist() now use the nominal breaks not those
adjusted by the numeric ‘fuzz’: in recent versions the nominal
breaks were reported but the 'density' referred to the intervals
used in the calculation - which mattered very slightly for one of
the extreme bins. (Based on a report by Martin Becker.)
• If xy[z].coords (used internally by many graphics functions) are
given a list as x, they now check that the list has suitable
names and give a more informative error message. (PR#13936)
CHANGES IN R VERSION 2.10.1 patched:
NEW FEATURES:
• The handling of line textures in the postscript() and pdf()
devices was set up for round end caps (the only type which
existed at the time): it has now been adjusted for butt endcaps.
• lchoose(a, k) is now defined as log(abs(choose(a,k))),
analogously to lfactorial().
• Although \eqn{} in Rd files is defined as a ‘verbatim’ macro,
many packages expected ... and \ldots to be interpreted there (as
was the case in R < 2.10.0), so this is now done (using an
ellipsis in HTML rendering).
• Escaping of braces in quoted strings in R-code sections of Rd
files is allowed again. This had been changed for the new Rd
format in R 2.10.0 but was only documented on the developer site
and was handled inconsistently by the converters: text and
example conversion removed the escapes but HTML conversion did
not.
• The PCRE library has been updated to version 8.01, a bug-fix
release.
• tools::readNEWS() now accepts a digit as the first character of a
news section.
BUG FIXES:
• Using read.table(header=TRUE) on a header with an embedded new
line would copy part of the header into the data. (PR#14103)
• qpois(p = 1, lambda = 0) now gives 0 as for all other p.
(PR#14135)
• Functions related to string comparison (e.g. unique(), match())
could cause crashes when used with strings not in the native
encoding, e.g. UTF-8 strings on Windows. (PR#14114 and PR#14125)
• x[ , drop=TRUE] dropped an NA level even if it was in use.
• The dynamic HTML help system reported the wrong MIME type for the
style sheet.
• tools::codoc() (used by R CMD check) was missing cases where the
function had no arguments but was documented to have some.
• Help links containing special characters (e.g. "?") were not
generated correctly when rendered in HTML. (PR#14155)
• lchoose(a, k) no longer wrongly gives NaN for negative a.
• ks.test() could give a p-value that was off by one observation
due to rounding error. (PR#14145)
• readBin()/readChar() when reading millions of character strings
in a single call used excessive amounts of memory (which also
slowed them down).
• R CMD SHLIB could fail if used with paths that were not
alphanumeric, e.g. contained +. (PR#14168)
• sprintf() was not re-entrant, which potentially caused problems
if an as.character() method called it.
• The quartz() device did not restore the clipping region when
filling the background for a new page. This could be observed in
multi-page bitmap output as stale outer regions of the plot.
• p.adjust(method, n) now works correctly for the rare case n >
length(p), also when method differs from "bonferroni" or "none",
thanks to a patch from Gordon Smyth.
• tools::showNonASCII() failed to detect non-ASCII characters if
iconv() (incorrectly) converted them to different ASCII
characters. (Seen on Windows only.)
• tcrossprod() wrongly failed in some cases when one of the
arguments was a vector and the other a matrix.
• [cr]bind(..., deparse.level=2) was not always giving names when
documented to do so. (Discovered whilst investigating PR#14189.)
• match(incomparables=<non-NULL>) could in rare cases
infinite-loop.
• poisson.test() needed to pass argument conf.level to
binom.test(). (PR#14195)
• The "nls" method for df.residual() gave incorrect results for
models fitted with na.action = na.exclude. (PR#14194)
• A change to options(scipen=) was only implemented when printing
next occurred, even though it should have affected intervening
calls to axis(), contour() and filledcontour().
• prettyNum(drop0trailing=TRUE) did not handle signs of imaginary
parts of complex numbers correctly (and this was used by str():
PR#14201).
• system.time() had the sys.child component wrong (copied
user.child instead) on systems with HAVE_GETRUSAGE. (PR#14210)
• Changing both line texture and line cap (end) resulted in the
latter to be omitted form the PDF code. In addition, line cap
(end) and join are now set explicitly in PDF output to ensure
correct defaults.
• The suppression of auto-rotation in bitmap() and dev2bitmap()
with the "pdfwrite" device was not working correctly.
• plot(ecdf(), log="x") no longer gives an incorrect warning.
• read.fwf() works again when argument file is a connection.
• Startup files will now be found if their paths exceed 255 bytes.
(PR#14228)
• contrasts<- (in the stats package) no longer has an undeclared
dependence on methods (introduced in 2.10.0).
CHANGES IN R VERSION 2.10.1:
NEW FEATURES:
• 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).
INSTALLATION:
• 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.
DEPRECATED & DEFUNCT:
• The 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.
BUG FIXES:
• 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 was 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 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.
• 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 namespace 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.
• 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 returns a estimate component which does not
depend on the alternative used.
• help.search() failed when the package argument was specified.
(PR#14113)
• switch(EXPR = "A") now returns NULL, as does switch(1) (which
used to signal an error).
CHANGES IN R VERSION 2.10.0:
SIGNIFICANT USER-VISIBLE CHANGES:
• 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).
NEW FEATURES:
• polygon(), pdf() and postscript() now have an argument
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
arguments type to be specified (you could always specify
arguments available or contriburl).
• available.packages() by default only returns information on the
latest versions of packages whose version requirements are
satisfied 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 w§ere
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().
• 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 argument 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 file's LinkingTo specs are now recognized as
installation dependencies, and included in package management
computations.
• Standardized DESCRIPTION file 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#13758).
• 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).
REGULAR EXPRESSIONS:
• 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 modified 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.
HELP & Rd FILE CHANGES:
• A 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 arguments 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 namespace 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 argument, 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 \var tag within a quoted string in
R-like text.
• parse_Rd() now treats the argument of \command as LaTeX-like,
rather than verbatim.
COMPRESSION:
• 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 tools::writePACKAGES 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} .
DEPRECATED & DEFUNCT:
• 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 file ~/.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() (in package 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 in favour of 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.
INSTALLATION:
• 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 currently require it.
• A system glob 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.
INTERNATIONALIZATION:
• 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’.
BUG FIXES:
• 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 Francois.
• 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 Latin-1 or UTF-8 encoding would corrupt the
CHARSXP cache.
**************************************************
* *
* 2.9 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.9.2 patched
NEW FEATURES
o On systems using ICU for collation (including Mac OS X), using
Sys.setlocale() to change the LC_COLLATE setting is more
likely to change the collation provided by ICU.
BUG FIXES
o On systems using zipped data and help (Windows) the names of
datasets could clash with temporary filenames used when
running examples, causing errors.
o 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)
o cat() on an unopened connection could close it twice, and
with file() connections segfaulted on some systems.
o Printing a list could segfault if the elements are nested too
deeply.
CHANGES IN R VERSION 2.9.2
NEW FEATURES
o 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).
o 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'.
o 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().
o PCRE has been updated to version 7.9 (for bug fixes).
o 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.)
DEPRECATED & DEFUNCT
o R CMD Rd2txt is deprecated. (It is just a wrapper for
R CMD Rdconv -t txt.)
o tools::Rd_parse() is deprecated and will be removed in 2.10.0
(which will use only Rd version 2).
BUG FIXES
o parse_Rd() still did not handle source reference encodings
properly.
o 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.
o PDF graphics output was producing two instances of anything
drawn with the symbol font face. (Report from Baptiste Auguie.)
o length(x) <- newval and grep() could cause memory corruption.
(PR#13837)
o If model.matrix() was given too large a model, it could crash
R. (PR#13838, fix found by Olaf Mersmann.)
o gzcon() (used by load()) would re-open an open connection,
leaking a file descriptor each time. (PR#13841)
o The checks for inconsistent inheritance reported by setClass()
now detect inconsistent superclasses and give better warning
messages.
o 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).
o A missing PROTECT caused rare segfaults during calls to
load(). (PR#13880, fix found by Bill Dunlap.)
o gsub() in a non-UTF-8 locale with a marked UTF-8 input
could in rare circumstances overrun a buffer and so segfault.
o R CMD Rdconv --version was not working correctly.
o Missing PROTECTs in nlm() caused "random" errors. (PR#13381 by
Adam D.I. Kramer, analysis and suggested fix by Bill Dunlap.)
o 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).
o new.env(hash = TRUE, size = NA) now works the way it has been
documented to for a long time.
o tcltk::tk_choose.files(multi = TRUE) produces better-formatted
output with filenames containing spaces. (PR#13875)
o R CMD check --use-valgrind did not run valgrind on the package tests.
o 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.
o R CMD BATCH garbled options -d <debugger> (useful for
valgrind, although --debugger=valgrind always worked)
o INSTALL with LazyData and Encoding declared in DESCRIPTION
might have left options("encoding") set for the rest of the
package installation.
CHANGES IN R VERSION 2.9.1
NEW FEATURES
o New function anyDuplicated(x) returns 0 (= FALSE) or the index
of the first duplicated entry of x.
o matplot(), matlines() and matpoints() now also obey a 'lend'
argument, determining line end styles. (Wish of PR#13619).
o bw.SJ(), bw.bcv() and bw.ucv() now gain an optional 'tol'
argument allowing more accurate estimates.
o 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).
o 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.
o nlminb() gives better non-convergence messages in some cases.
o 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.
o R CMD INSTALL is more tolerant of (malformed) packages with a
'man' directory but no validly named .Rd files.
o R CMD check now reports where options are used that cause some
of the checks to be skipped.
o 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.)
o 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'.
DEPRECATED & DEFUNCT
o print.atomic() (defunct since 1.9.0) has been removed since it
caused confusion for an S4 class union "atomic".
o png(type="cairo1") is deprecated -- it was only needed for
platforms with 1.0 <= cairo < 1.2.
BUG FIXES
o 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.)
o col2rgb("#00000080", TRUE) would return the background colour.
(Reported by Hadley Wickham.)
o interaction() now ensures that the levels of the result are unique.
o 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.
o smoothScatter() now also works when e.g. xlim[2] < xlim[1].
o Invalid use of sprintf() such as sprintf("%S%") now give an error
instead of a segmentation fault, as do very unusual cases such as
sprintf("%s", tryCatch(stop(), error=identity)). (It was
always documented that misuse could crash R in
platform-dependent ways.)
o 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).
o readNEWS() missed version numbers with more than one digit.
o building R --without-x no longer fails (PR#13665)
o printCoefmat(cbind(0,1)) now works too (PR#13677)
o bw.SJ(c(1:99, 1e6)) now works too.
o 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.
o stars() would do a partial plot when called with plot = FALSE;
it now consistently returns the locations of the stars.
o Rd2latex() could not handle empty sections.
o old.packages() and hence update.packages() would fail on a
repository which contained only one package but with multiple
versions of that package.
o as.character.Rd() added extra braces when displaying two-argument
macros. (Report and fix by Manuel Eugster.)
o unsplit() was misbehaving in the case of single-column data
frames. (Reported by Will Gray.)
o as(I(1), "vector") and similar coercions from objects of
"unregistered" S3 classes now work.
o srcref records produced by parse() and parse_Rd() did not record
the encoding of the source file. (Reported by Romain Francois.)
o The X11 version of View() was misbehaving in MBCS locales, and
PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama.
o 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.
o sprintf() now signals an error when the result of single format
specification would be longer than the limit (8192 bytes); it would
return "somewhat random" results or segfault previously. (PR#13667)
Further, arguments of type "language" or "symbol" are no longer
allowed, as these, e.g., sprintf("%s", quote(list())), typically
lead to unexpected results or hard to understand error messages.
o 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.
o tcrossprod(<1d-array>, <matrix>) now does work when the arguments
are of compatible dimensions.
o qbinom() now is accurate also in (large size, small prob)
cases. (PR#13711)
o The calculation of the Spearman p-value in cor.test() is
slightly more accurate in some cases. (PR#13574)
o The digamma(), trigamma() and psigamma() functions could be
inaccurate for values of x around 1e-15 due to cancellation.
(PR#13714).
o 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.
o 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.
o R CMD INSTALL no longer gives a spurious warning about old R
versions ignoring multiple dependencies, if the conditions are
known to be satisfied.
o 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.
o xtfrm(), rank(), sort() and order() did not always make use of
custom comparison methods specific to the class of elements
being sorted.
o Increase NAMED value on 'seq' value in for() loop so loop code
cannot modify 'seq' value.
o Prevent rectangles of size < 0.5 pixel from disappearing in
Quartz when using rastered backend. (PR#13744)
o Printing _NA_complex_ had a low-level thinko; patch thanks to
Bill Dunlap.
o CP1257 encoding for postscript/PDF has been corrected. (PR#13736)
o 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)
o The print() method for arima() failed if all coefs were fixed.
o R CMD INSTALL --no-latex was not implemented in 2.9.0 (only).
o Added a needed PROTECT call in RunFinalizers to handle cases where
the routine is called recursively from a GC in a finalizer.
o Constructing error messages about unused arguments in calls to
closures no longer evaluates the arguments.
o qr(x, LAPACK=TRUE) did not coerce integer x to numeric.
o 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.)
CHANGES IN R VERSION 2.9.0
NEW FEATURES
o Package 'Matrix' is now a recommended package contained in the
basic R distribution. It provides S4 classes and methods for
dense and sparse matrices, often by using the numerical
libraries Lapack and from the SuiteSparse collection CHOLMOD,
CSparse, and SPQR among others.
o pdf() and postscript() gain a 'useKerning' argument to place
strings using kerning (which had previously been ignored in
display but not in strwidth), based in part on an idea and
code from Ei-ji Nakama. The default is TRUE.
Kerning involving spaces is now ignored (it was previously
only used in the computation of string widths).
o seq.default() and seq.int() ensure that the result is within the
interval [from, to] even when the last value would previously
have been slightly out of range because of the allowance for
rounding error in computing the number of elements.
o boxplot() gains a simple 'matrix' method, enabling boxplot(mat)
instead of boxplot(data.frame(mat)).
o zip.file.extract() gains an optional 'dir' argument (but use
unzip() instead).
o source() with 'encoding' specified (and not as "unknown") marks
the encoding of character strings in Latin-1 and UTF-8
locales.
o parse(text=z) now marks the encoding of character strings in
Latin-1 and UTF-8 locales if 'z' is of known encoding (that is
all elements are either ASCII or marked as Latin-1 or UTF-8).
o sprintf() does stricter error checking on input formats to
avoid passing invalid formats to the OS (which have a tendency
to crash under such inputs).
o expand.grid() gains a 'stringsAsFactors' argument to ask for
automatic conversion of character vectors to factors (which
happened for many years but was not previously documented).
[This did not actually work prior to R 2.9.1.]
o bxp() now computes the 'ylim' including the outliers only if
'outline = TRUE'. (Wish of PR#13196)
o barplot() gains a 'args.legend' argument. (Wish of PR#13265).
o RweaveLatexSetup() now accepts all (and not just some) options
passed through from Sweave()
o cumsum(x) and cumprod(x) for double precision x now use a long
double accumulator where available and so more closely match
sum() and prod() in potentially being more accurate.
o plot() methods for "stepfun" (and hence "ecdf") gain an 'col'
argument, allowing to set all three colors simultaneously.
o Iterating over a factor in a for loop now coerces to a character
vector (rather than using the integer codes).
o data.frame() now recycles columns of list arguments, not just
vectors and factors.
o plot.ts(plot.type="multiple") now makes use of *.lab and
*.axis graphical parameters (wish of PR#13134 and 13135).
o Classes can be exported from a name space using the NAMESPACE
file directive 'exportClassPattern' which has the same syntax
as 'exportPattern'.
o strftime() now converts its first argument with as.POSIXlt()
and so is no longer an alias for format.POSIXLt.
o body<-() now treats list values consistently with other
types: they no longer need to be wrapped in a list() call.
o option("pdfbrowser") is now set on Windows as well as on Unix-alikes.
o object.size() now returns an object of class "object_size" and
has a print() method.
o [col/row]Sums(), *Means() now have an additional '...' argument,
so that they can more easily be turned into generic functions.
o Package 'tools' contains dependsOnPkgs() to compute reverse
dependencies.
o Strict type checking is now turned on: this catches more
internal corruptions, and some badly written contributed code.
o There are new functions in package 'tcltk', tk_choose.files(),
tk_choose.dir() and tk_messageBox(), analogues of functions
available on Windows (the last is an analogue of winDialog).
o Sys.glob() now does tilde expansion on all platforms.
o read.table() and friends gain a 'fileEncoding' argument to
make re-encoding of input just a little bit simpler.
o grep() gains an 'invert' argument mimicking 'grep -v/--invert'.
o strwrap() now allows a separate prefix for the first line.
o grep() has a more efficient sibling grepl() that returns a
logical vector.
o xfig() has new arguments 'defaultFont' and 'textSpecial'
contributed by Sebastian Fischmeister.
o parse() and parse_Rd() now point to syntax errors in the
reported error context, and include the filename and line and
column numbers so smart text editors can jump to the error
location.
o str(<1d-array>) now writes "[1:n(1d)]" instead of the previous
less clear "[, 1:n]".
o New function testInstalledPackage() in package 'tools' allows
the examples (and if they were installed) any package-specific
tests to be run on an installed package.
testInstalledPackages() can run all the examples and tests in
the standard and/or recommended packages. Also
testInstalledBasic() can run the basic tests (if installed).
o file.copy() now has a 'recursive' argument.
o Errors in setOldClass() will cause a previous definition to be restored.
o Ambiguities in class inheritance and method selection resulting
from duplicates in superclasses are now resolved by requiring
(if possible) consistency with all the superclass inheritance. The
rules for method selection have been revised to take advantage of
the improved ordering.
See ?Methods and the reference there related to inheritance.
o New function unzip() in package 'utils' to expand or list zip
archives.
o Replacement functions for class() and oldClass() will unset
the S4 bit when the replacement can't be an S4 object;
oldClass() will return the S3 class for S4 objects with slot
.S3Class.
o clip() takes extra steps to avoid the next graphics call
resetting the clip region.
o New function sample.int() to provide documented access to the
internal part of sample() (sampling from seq_len(n)).
o New version of withVisible() for better handling of cases like
withVisible(eval.parent(....)). Moved to package 'base' with a
view to replace .Internal(eval.with.vis) in source() later.
o showClass() which is also used to auto-print class definitions, now
mentions the package where the class comes from, if there is one.
o simulate(obj) now also works for "glm" objects and for weighted
fits, thanks in part to contributions from Ben Bolker and
Heather Turner. There is now a means to extend the methods
available for "glm" objects, as glm families can have an
optional 'simulate' component.
o S4 classes that inherit from any of the "structure" classes or
from "vector" will turn on methods for all the "Ops" group of
functions when the package containing the classes is
loaded. See class?structure.
o A mechanism now allows S4 classes to inherit from object types
"environment", "externalptr" and symbol ("name"). See ?setClass.
o demo() gains 'echo' and 'ask' arguments, with defaults similar
to example().
o library() no longer checks for the packages merged during the
re-organization of 1.9.0.
o New function poisson.test() in package 'stats' for exact test
of rates and rate ratios.
o New function isdebugged() indicates whether its argument has the
debug flag set or not.
o ls.str() [via print method] now also works when some objects in
the environment are missing().
o Subsetting S4-objects (without an explicit "[" method) no longer
preserves the class in cases like setClass("C",
contains="list"); This reverts a "bug fix" activated in R 2.8.0.
o .packages() and .find.packages() no longer check the package
info for installed packages with dumped metadata, since this
was checked when the package was installed. .packages() only
considers such packages to be validly installed (any others
were installed in a long-obsolete version of R). Both changes
speed up searches in libraries of thousands of packages.
o boxplot() uses butt line endings for its median line
(suggestion of Uwe Ligges, PR#13553).
o S4 objects passed to a non-default S3 method will be converted
to a valid S3 object with the S3 class. See the section on
inheriting from non-S4 classes in ?Classes.
o A new class "nonStructure" has been defined; classes that extend
a vector class but that should lose their slots under Math or
Ops functions should extend this class. See class?nonStructure.
o axis.POSIXct() now plots in the timezone marked for its inputs
(if any) rather than in the local time. The latter was a
deliberate choice, but is easy to select by removing the
'tzone' attribute. (Suggestion of Dan Kelley.)
o A new function classesToAM() returns an adjacency matrix
representing the inheritance of the classes specified. Allows
better human examination of the patterns, e.g. by using the
matrix as input to one of the graph packages (see the
documentation).
o X11options(antialias = "none") now works, for consistency with
X11().
o sprintf() now allows zero-length arguments (with a zero-length
result). (Suggestion of Bill Dunlap.)
o unlink() is now able to remove broken symbolic links on
Unix-alikes.
o New selectSuperClasses() utility in package 'methods'.
o HoltWinters() now allows parameters alpha and beta to be fixed
at 0 and hence beta = FALSE and gamma = FALSE are used to
specify restricted models.
o A new function smoothScatter() has been added to package
'graphics'. It is appropriate for very dense scatter plots
and uses density estimation and color to reflect density of
plotting.
DEPRECATED & DEFUNCT
o allGenerics() is defunct.
o Use of allocVector(CHARSXP ...) is defunct and gives an error.
o The compatibility define for graphics structure NewDevDesc in
GraphicsDevice.h has been removed.
o Support for versioned installs (R CMD INSTALL --with-package-versions
and install.packages(installWithVers = TRUE)) has been removed.
Packages installed with versioned names will be ignored.
o The numeric and power(0.5) forms of argument to make.link()
which were deprecated in 2.4.0 are now defunct: use power()
directly.
o Conversion to Sd and Ssgm by R CMD Rdconv is now defunct.
o Support for R --gui=gnome is now defunct (and package
gnomeGUI has been withdrwan as it used a long-obsolete version
of GNOME).
o R CMD SHLIB on Windows will call the first target (not 'all') in
Makevars[.win] in future versions: so make 'all' the first
target if you have any.
UTILITIES
o R CMD build now also uses a Makevars[.win] file for cleaning
up src/.
o R CMD Rd2dvi and R CMD check are now able to cope with Cyrillic
characters in UTF-8 if environment variable _R_CYRILLIC_TEX_
is set to a non-empty value and the latex system has suitable
fonts (thanks to a hint from Alexey Shipunov).
o New function rtags() in package 'utils' that provides etags-like
indexing capabilities for R code files.
New front-end script R CMD rtags provides an interface to the
rtags() function (see R CMD rtags --help for details).
o New environment variable R_TEXI2DVICMD to hold the path (if any)
to 'texi2dvi' found at configure time: this now provides the
default to option("texi2dvi").
o massage-Examples.pl has been replaced by the R function
tools:::massageExamples().
o R CMD REMOVE now uses remove.packages() and hence removes all
members of a bundle.
o R CMD SHLIB is now an R script and has a new option -n aka
--dry-run to show what commands would be run. The same code
is used on Unix and Windows.
o R CMD Rdconv has new options --package and --version to set the
corresponding fields in HTML conversion.
o R CMD check runs the package tests with a custom startup file,
currently containing 'options(useFancyQuotes = FALSE)'.
Those tests are run by an R script: using a tests/Makefile
(undocumented) no longer works.
o R CMD config now knows about DYLIB_EXT and SHLIB_EXT, for use
in configure files.
o R CMD BATCH has a new option --no-timing to suppress printing
out the session timing.
o R CMD Rd2dvi can now work on an installed package.
o R CMD check no longer loads package 'tcltk' when checking for
code problems, so more problems may be reported.
o For R CMD SHLIB on Windows the default 'all' target only makes
the DLL, and no longer call targets 'before' and 'after'.
Rd CONVERSION
o Rd files have an optional \Rdversion{} section, which if
missing defaults to 1.0. There is support for version 1.1, a
slightly modified version with the following changes:
- The warnings for \code{} inside example are suppressed.
- Whitespace between arguments in \item and \section is
accepted without a warning (see below).
- $ is treated literally in text, even for latex conversions.
- \ is only an escape before % { } \ .
- \R, \dots and \ldots can be followed by {}, and it is
recommended that they when not followed by whitespace.
- The obsolete interpretation of \Alpha etc is no longer done.
o Rd conversion now handles ^ ~ < > | correctly in non-code
environments (such as \samp), and # and _ even in latex
conversion (but $ still needs to be escaped in version 1.0).
o Whitespace between first and second arguments is now accepted
for \item and \section, e.g. \item{foo} {some value}.
Previously arguments after whitespace were silently ignored,
and a warning is given for version 1.0 files.
o The Rd files created by prompt() and friends are declared to be
version 1.1.
o \alias now supports the escaping of { as well as of %, and this
is recommended.
o parse_Rd(), an experimental parser for Rd files, and Rd2txt(),
Rd2HTML(), Rd2latex() and Rd2ex(), even more experimental
converters, have been added to package 'tools'.
o R CMD check runs the package's Rd files through parse_Rd() for a
stricter syntax check. This can be suppressed by setting
_R_CHECK_RD_PARSE_ to FALSE.
o Added markup \verb, which displays like \code, but parses as
verbatim text. Currently only supported by parse_Rd() and
Rd2HTML().
INSTALLATION
o The shell used by the 'R' script and other shell scripts
intended to be run directly can be specified at installation
time by setting the (precious) configure variable R_SHELL.
o libtool has been updated to 2.2.6a.
o --with-ICU is now the default: this means that ICU will be
used for collation on Mac OS >= 10.4.
o make install-tests can be used to install the test files,
to allowed an installed version of R to be tested -- see the
R-admin manual. This is also supported by the function
testInstalledPackages() in package 'tools'.
o 'make install' using a parallel make should now work.
o 'make check' now always re-makes and re-runs the package
examples, which are now collated in the locale's order (and
not ASCII order).
o configure will now set the default optimization level for
gfortran on x86_64 Linux to -O as -O2 has caused problems with
gfortran 4.3.x.
PACKAGE INSTALLATION
o install.packages() is able to infer that repos=NULL was
intended from the extension on the file name specified as 'pkgs'.
On Mac OS X it now supports local binary packages with .tar.gz
extension. Nonetheless .tgz remains the preferred extension
and is expected in repositories.
It now checks >= version dependencies for dependent packages,
and so will install a newer version of a dependency if needed
and available on the repositories.
The library being installed into is considered when looking
for installed packages if it is not already part of
.libPaths() (as INSTALL already does).
It has a new argument 'Ncpus' to support parallel installs of
source packages.
o HTML links will be resolved first to the standard packages: this
avoids other installed packages diverting help on e.g. qr()
and plot() to themselves. The HTML files are only "touched" if
they have changed.
o A check is done that the R files can be parsed: this both
prevents a broken package without lazy-loading from being
installed and gives better diagnostics.
o install.packages() gains a 'configure.vars' argument, and both
this and 'configure.args' get their defaults from options().
o There is a unified R script for INSTALL on both Unix-alike and
Windows that takes option names used by either in the past.
It adds --no-multiarch to disable building other than the main
sub-architecture, and allows multiple instances of
--configure-args and --configure-vars (which will be
concatenated).
New option --install-tests will install any package-specific
tests.
o Times in the Packaged: and Built: fields are now recorded in
UTC, and in most cases in ISO 8601 format.
C-LEVEL FACILITIES
o A helper function, asCharacterFactor, converts from factors to
character vectors.
BUG FIXES
o The postscript() output for setting text is faster and smaller.
o Subsetting a data frame with duplicate column names without
selecting columns (e.g. z[i,]) no longer makes the column
names unique. This was never documented, but some packages
have assumed it.
o data.frame() no longer ignores row names on objects if the
first name is empty. (PR#13230: this has been the behaviour
for a long time, but apparently undocumented.)
o deparse(control="S_compatible") now never uses backticks.
o X-spline drawing is improved for cases where the control
points are located well off the edges of the device.
The symptom of this problem is the error "reached MAXNUMPTS".
o exists() with mode= "any" will no longer run an active binding's
function.
o format(c(1 + 2i, NA)) no longer has extraneous space in " NA".
o mood.test() could fail in 2.8.x on large samples because of
integer overflow.
o heatmap() without a dendrogram could fail. (PR#13512)
o Checks for missing values will no longer occasionally result in
an infinite loop or stack overflow error, depending on the
compiler. Active bindings are now always considered to be
non-missing.
o Rd conversion was not accepting \p (as in \pkg} or (when using
Perl 5.10.x) \k (as in \kbd) in any preamble text in a
\value{} section, since those are nowadays interpreted by
Perl. (PR#13575)
o if(as.raw(1)) TRUE now works as expected. (PR#13630)
Also, c(as.raw(12), TRUE) or c(raw(3), pi) do.
o duplicated(<data frame>, incomparables = NA) now gives the
intended error message. (PR#13632)
o name handling of as.data.frame() has been sanitized somewhat
o Evaluating an assignment expression with a string on the left
hand side no longer destructively changes the string to a symbol
in the expression.
**************************************************
* *
* 2.8 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.8.1 patched
NEW FEATURES
o R CMD check has a new argument '--install-args' to pass
command-line arguments to INSTALL.
E.g. --install-args="--docs=normal" on Windows if the HTML
Help Workshop is not installed.
o R-Forge has been added to R_HOME/etc/repositories, so it will
be available interactively in setRepositories().
o The compiled loess() code has been updated to the current
version of dloess from Netlib. This includes patches from Ben
Tyner which correct some errors when degree = 0 and hence
solve PR#13570.
INSTALLATION
o --with-ICU is now supported (and recommended) on Mac OS X using
Apple's supplied port. Note however that the locale category
LC_COLLATE cannot be changed whilst R is running on Apple's
version of ICU.
Configure supports a wider range of ICU versions on other
OSes: version 3.0 should suffice, and 3.2, 3.8 and 4.0 have
been tested.
BUG FIXES
o grid-based plots no longer reset the base text size to the
default 96dpi in cairo-based bitmap devices.
o Rd conversion was incorrectly parsing \\\* and \\\{ (and other
cases with an odd number of backslashes greater than one).
Text conversion of \code{\ etc} was incorrect (a single
backslash stands for itself inside \code).
\code{} inside \examples{} is now fixed up (but the warning
remains, since it will be handled incorrectly in earlier
versions of R).
o as.matrix.data.frame() could fail if coercion changed the
dimension of one of the columns (as e.g. the coercion of a "Surv"
object to a character vector does).
o When extracting part of a complex list structure using [[]]
with a vector index, the extracted part was not marked for
duplication on change. (PR#13411)
o Assigning an additional element to a pairlist/language element
by x[["foo"]] <- value did not name the additional element.
o .Call() and .External() were not accepting "NativeSymbolInfo"
and "NativeSymbol" objects as claimed. (Patch from Olaf
Mersmann.)
o codoc() was missing some default value mismatches with
unescaped backslashes, e.g. final="\\" needs to be written as
final="\\\\" in the Rd file.
The reports on values now give strings in the original quoted
format (with \ and " escaped).
o The $<- method for pairlists (including language objects)
failed to duplicate if NAMED was 2.
o read.table(blank.lines.skip = FALSE) gave a final empty row on
files with less than 5 lines (PR#13433).
o Workaround for a bug in some versions of iconv that was seen
with output lines of more than 10,000 bytes and with
re-encoding requested on an output connection.
o The fullrefman.{dvi,pdf} duplicated part I in part II (at
least on some systems).
o cbind() could crash with a zero-length input and a list result.
o pdf(colormodel = "gray") was setting the stroke colour for fills.
o file.show() with multiple files would only show multiple
copies of the first one. (PR#13469)
o formatC(mode = "character") was documented to work, but
did not. (PR#13474)
o besselI(x,.., expon.scaled=TRUE) now gives accurate results for
x < 1e5 whereas it previously underflowed for x >~= 1500.
Further, besselJ(x,..) also computes up to 1e5 (instead of 1e4).
o str() was incorrectly warning about its option component
'formatNum' set by strOptions().
o nls(algorithm = "port") did not accept the [factor] notation.
(PR#13650)
o The relational (aka "comparison") operators are now binary, also in
a lower level sense, and an expression as "<"(1) is now erronous.
o The 'offset' argument for lm() and glm() is not longer
documented to be allowed to be of length 1: this has not been
true for a long time.
o format.info(x) is now also correct when x has no finite content.
o predict.lm() now works correctly when the fit had more than
one offset (possibly specified both in the formula and as an
argument). This function is called by predict.glm(), so the
same isses are corrected there.
o besselI(x, nu) with nu a negative integer (a singular case) is now
correct. (PR#13556)
CHANGES IN R VERSION 2.8.1
NEW FEATURES
o sum() now has a method for "difftime" objects (via the Summary
group).
max(), min() and range() applied to "difftime" object(s) now
return a result in the common units of the objects, if there
is one.
o installed.packages() is now tolerant of malformed DESCRIPTION
files in installed packages (it ignores them, with a warning).
o qt() now works for 0 < df < 1.
o For consistency with matrix() and array(), dimnames(x) <-
list() removes the dimnames (as assigning NULL would do).
It was previously an error.
o nlminb() copies names from 'start' to the parameter vector
used (for consistency with optim()).
o legend() gains a 'title.col' argument: the title colour was
previously set from the first element of 'text.col' (which
remains the default).
o In an Rd file, use of top-level \itemize{} inside a \value{}
block is unnecessary and almost always gave a faulty
conversion. Most cases are now detected and corrected, but
give a warning as such code will not work correctly in earlier
versins of R.
Also, use of \code{} inside a code block such as \examples{}
will give a erroneous conversion that is now detected and
warned against.
o Autoflushing of stdout is turned on when Rd processing, so
warnings/error are likely to appear in the right place in
redirected output (such as that from R CMD check).
UTILITIES
o R_PDFLATEXCMD is added to the environment variables set by
'R CMD' and is used by R CMD Rd2dvi.
R_LATEXCMD, R_PDFLATEXCMD, R_MAKEINDEXCMD and R_DVIPSCMD
default to 'latex', 'pdflatex', 'makeindex' and 'dvips'
respectively if no suitable executable was found at configure
time (since they might well be available at run time,
particularly for binary installations of R). This affects
R CMD Rd2dvi and help(offline=TRUE).
R CMD Rd2dvi now gives an explicit error message if latex (or
pdflatex) fails.
R CMD Rd2dvi gains a --no-index argument: processing some
special characters on PDF indices gave errors which used to be
ignored.
DEPRECATED & DEFUNCT
o R CMD INSTALL --with-package-versions is deprecated (and
support has always been incomplete on Windows).
So is install.packages(installWithVers = TRUE).
o Rd conversion to Sd and Ssgm is now deprecated as we no longer
have any means to check the results (and Sd is long obsolete).
BUG FIXES
o add1.glm() no longer warns if applied to a binomial glm with a
factor response.
o aggregate.data.frame() now does something sensible with a
zero-column 'x' rather than failing with an obscure error
message. It gives an explicit error message if called with a
zero-row 'x'.
o integrate() now accepts integer results from f(): as documented,
but only double was accepted.
o contrib.url() produced an incorrect URL for the type
"mac.binary".
o pairwise.wilcox.test() did not pass on the 'paired' argument
(caught by Matthias Kohl)
o bmp(), jpeg(), and png() on unix with type="cairo" would segfault
on closure if the output file could not be opened.
o tiff() on unix would not write the output file for the first page
when multiple pages were plotted.
o str(1 + structure(1, class = "test")) no longer recurses indefinitely.
o pf(x, .., ncp, lower.tail=FALSE, log=TRUE) is much more accurate
for large x now.
o dev2bitmap() failed in 2.8.0 if 'taa' and 'gaa' were both NA.
o Under rare circumstances equality tests for character strings
could fail to report equality in 2.8.0 in the same way as
2.7.2. (This needed a current encoding of Latin-1 or UTF-8,
one string whose encoding was marked as that encoding and one
that was marked as "unknown". In that circumstance the two
strings are not actually known to be equal, but earlier
versions of R assumed that "unknown" meant the current
encoding, and this is done once again.)
o R CMD config could echo messages from GNU make if called from
within a Makefile (as e.g. package Rcpp did), especially from
within a parallel make run.
o Rounding error could affect window(extend=TRUE) when applied
to monthly series. (PR#13272)
o Offline help on a Unix-alike now works even if options
"latexcmd" and "dvipscmd" contain spaces
(e.g. "dvips -Pmy_printer").
Informative error messages are given if running latex or dvips
fail.
o Using plot.lm() on a "glm" object since 2.7.1 with which=5
caused the Pearson rather than deviance residuals to be used
in which=2 or 3 (including in the default case). (Thanks to
Effie Greathouse and Greg Snow.)
plot.lm() did not report on omitting observations with
leverage one if they also had residual exactly zero. This was
seen in example(occupationalStatus).
o deparse(nlines=) no longer pads short results with blank
lines. (PR#13299)
o legend(xpd=) now restores 'xpd' correctly. (PR#12756)
o The "formula" method for lines() now works if 'subset' is
supplied and no 'data' argument (as that for points() did).
o Sweave() now takes the defaults for the options 'pdf.version'
and 'pdf.encoding' of its RweaveLatex driver from pdf.options().
o prettyNum(x, drop0trailing=TRUE) treated "1.1e20" as "1.1e2"
and hence str() did as well, in 2.8.0 only.
o dchisq(x, df, ncp) no longer hangs for large x and ncp > 0,
and is more accurate in some cases (PR#13309).
o installed.packages(lib.loc = D, priority="NA") now also works when
D contains a single package. (PR#13332)
o legend(...., merge=TRUE) now warns and has no effect in the
case where no line segments are drawn. (PR#13340)
o transform.data.frame() works better when two or more columns are
added.
o Deparsing argument lists with non-syntactic names (e.g. that for
transform()) now uses backticks rather than double quotes to
produce syntactically valid output.
o matrix() failed to check for 0-length 'dimnames': it now
treats them as NULL (as array did). (PR#13361)
o 0^NA is now NA, not Inf, consistent with x^NA, x != 1.
o anova.mlm() did not work if T had only one row (including
e.g. the case M = ~1).
o axis.POSIXct() mislabelled for some time ranges of a few hours
(reported by Martin Becker).
o mantelhaen.test() with 'exact=FALSE' was not respecting
'alternative'. It now does one-sided tests similarly to
prop.test().
o anova.mlm() had trouble with some designs where near-zero rows of
the tranformation matrix were not removed (caught by Nils Skutara).
o Rd conversion was handling expressions like
'\item{foo}{see \eqn{x}}' (with one argument to \eqn
immediately followed by a right brace) incorrectly, sometimes
giving a spurious warning about 'missing text'.
o R CMD INSTALL used the C locale to install the DESCRIPTION
file, and so escaped non-ASCII characters in packages with a
declared encoding of "latin1" or "UTF-8". (However, the
installed DESCRIPTION file was rarely used since the dumped
metadata are available.)
o xspline() now respects inline par settings.
It and grid.xspline() now handle the special case of only two
control points, and splines with control points that are
located well outside the device (e.g., a zoomed view of a
larger curve). (Both cases were giving the error "reached
MAXNUMPTS").
o In setClass("C", contains="list"); x <- new("C", 1:3), x[2:3] now
remains of class "C". So does rep(x, 2) or rep.int(x, 3).
[NOTE: This "feature" has been reverted for R 2.9.0, see above]
o median.default() now also works for "numeric"-like vectors.
o The pdf() device can now handle the case where an image uses a
very large number of colours with different levels of
semi-transparency (alpha-values). It used to segfault.
(Also PR#13264.)
o window() failed to apply a fuzz to 'start' or 'end' and so
sometimes warned incorrectly for time series with 'freq' not a
power of two (e.g. 12 or 24).
o unique.default() now preserves the "tzone" attribute on
"POSIXct" objects.
o If all the packages had dependency lists of equal lengths,
occasionally install.packages() would compute an incorrect
sort order.
o col(x, as.factor=TRUE) and row(x, as.factor=TRUE) would fail
if x had no column (row) names. It was documented
incorrectly, and now returns a matrix factor.
o setRepositories() failed if "pkgType" was set to
"mac.binary.leopard".
o formals<-() changed the body of the function if this was a
length-one list.
o body<-() failed if the function had no arguments. It now
warns if discarding elements from a 'value' of type "expression".
o qr.coef() failed in the complex case for non-square systems.
(PR#13305)
o plot.dendrogram(horizontal=TRUE) did not not plot 'edgetext'
at the correct locations. (PR#13313)
o The starting point for plot.acf(ci.type="ma") was lag 0 when it
should have been lag 1. (PR#13071)
o There was an obscure bug with srcrefs, which could put the
parser into a condition giving "Error: bad value" on any input
CHANGES IN R VERSION 2.8.0
SIGNIFICANT USER-VISIBLE CHANGES
o var(), cov(), cor(), sd() etc now by default (when 'use' is not
specified) return NA in many cases where they signalled an
error before.
NEW FEATURES
o abbreviate() gains an optional argument 'strict' allowing cheap
and fast strict abbrevation.
o The "lm" methods of add1(), anova() and drop1() warn if they are
mis-used on an essentially exact fit.
o as.array() is now generic, gains a '...' argument.
o New function as.hexmode() for converting integers in hex format.
format.hexmode() and as.character.hexmode() gain an 'upper.case'
argument.
o bitmap() and dev2bitmap() gain support for anti-aliasing.
The default type has been changed to 'png16m', which supports
anti-aliasing.
o Box.test() gains a 'fitdf' argument to adjust the degrees of
freedom if applied to residuals.
o browseURL() has a new argument 'encodeIfNeeded' to use
URLencode() in cases where it seems likely that would be
helpful. (Unfortunately, those are hard to guess.)
o by() gains a 'simplify' argument, passed to tapply().
o capabilities() gains a new argument "tiff" to report if tiff()
is operational.
o chol2inv() now treats <numeric(1)> as a [1 x 1]-matrix.
o cov() and cor() have the option 'use = "everything"' as default,
and so does var() with its default 'na.rm = FALSE'. This
returns NA instead of signalling an error for NA observations.
Another new option is 'use = "na.or.complete"' which is the default
for var(*, na.rm=FALSE).
var(double(0), na.rm= L) now returns NA instead of signalling an error,
for both L = TRUE or FALSE, as one consequence of these changes.
o data.matrix() now tries harder to convert non-numeric columns,
via as.numeric() or as(, "numeric").
o dev.interactive() is able to recognize the standard screen
devices if getOption("device") is a function (as well as by name).
o dev.new() gains a '...' argument which can be used to pass
named arguments which will be used if appropriate to the
device selected.
o dimnames(x) <- value extends 'value' if it a list and too
short, and 'x' is an array. This allows constructions such as
dimnames(x)[[1]] <- 1:3 to work whether or not 'x' already has
dimnames.
o format(), formatC() and prettyNum() gain a new argument
'drop0trailing' which can be used to suppress trailing "0"s.
o format() now works for environments; also print(env) and str(env)
share the same code for environments.
o It is now possible to create and open a text-mode gzfile()
connection by explicitly using e.g. open="rt".
o New help.request() function for compiling an e-mail to R-help
according to "the rules". It is built on the new utility,
create.post() on which also bug.report() is based now; both
thanks to a contribution by Heather Turner.
o help.search() now assumes that non-ASCII items are in latin1
if that makes sense (all known examples on CRAN are).
o HoltWinters() and decompose() use a (statistically) more
efficient computation for seasonal fits (they used to waste
one period).
o intToUtf8() and intToBits() now accept numeric vectors,
truncating them to integers.
o is.unsorted() gains an argument 'strictly'. It now works for
classed objects with a >= or > method (as incorrectly
documented earlier).
o library() no longer warns about the masking objects that are
identical(.,.) to those they mask.
o lockBinding(), unlockBinding(), lockEnvironment() and
makeActiveBinding() now all return invisibly (they always
return NULL).
o mood.test() now behaves better in the presence of ties.
o na.action() now works on fits of classes "lm", "glm", ....
o optim(.., method="SANN", .., trace=TRUE) is now customizable via
the 'REPORT' control argument, thanks to code proposals by
Thomas Petzoldt.
o The 'factory-fresh' defaults for options("device") have been
changed to refer to the devices as functions in the grDevices
namespace and not as names. This makes it more likely that
the incorrect (since R 2.5.0) assumption in packages that
get(getOption("device"))() will work will catch users of those
packages.
o pch=16 now has no border (for consistency with 15, 17, 18) and
hence is now different from pch=19.
o pdf() has new arguments 'useDingbats' (set this to FALSE for use
with broken viewers) and 'colormodel'. It now only references
the ZapfDingbats font if it is used (for small opaque circles).
The default PDF version is now 1.4, since viewers that do not
accept that are now rare.
Different viewers were rendering consecutive text() calls on a
pdf() device in different ways where translucency was
involved. The PDF generated has been changed to force each
call to be rendered separately (which is the way xpdf or
ghostscript was rendering, but Acrobat was forming a
transparency group), which is consistent with other graphics
devices supporting semi-transparency.
o plot.dendrogram() has new arguments (xlim, ylim) which allows
zooming into a hiearchical clustering dendrogram.
o plot.ecdf() now defaults to pch=19 so as to better convey the
left-closed line segments.
o plot.histogram() gains an 'ann' argument. (Wish from Ben Bolker.)
o plot(<lm_obj>) now warns when it omits points with leverage one
from a plot.
o Plotmath now recognizes 'aleph' and 'nabla' (the Adobe Symbol
'gradient' glyph) as symbol names.
o polyroot() no longer has a maximum degree.
o The alpha/alphamax argument of the 'nls' and 'mle' profile()
methods is used to compute confidence limits for univariate
t-statistics rather than a confidence region for all the
parameters (and not just those being profiled).
o quantile.default() allows 'probs' to stray just beyond [0, 1],
to allow for computed values.
o New functions rawConnection() and rawConnectionValue() allow
raw vectors to be treated as connections.
o read.dcf() now consistently gives an error for malformed DCF.
o read.fwf() no longer passes its default for 'as.is' to
read.table(): this allows the latter's default to be used.
o readBin(), writeBin(), readChar() and writeChar() now open a
connection which was not already open in an appropriate binary
mode rather than the default mode.
readLines(), cat() and sink() now open a connection which was
not already open in an appropriate text mode rather than the
default mode.
o readCitationFile() (and hence citation) now reads a package's
CITATION file in the package's declared encoding (if there is one).
o The behaviour of readLines() for incomplete final lines on
binary-mode connections has been changed to be like blocking
rather than non-blocking text-mode connections.
o A new reorder.character() method has been added. This allows
use of 'reorder(x, ...)' as a shorthand for
'reorder(factor(x), ...)' when 'x' is a character vector.
o round() now computes in long doubles where possible so the
results are more likely to be correct to representation error.
o rug() now uses axis()'s new arguments from 2.7.2, hence no
longer draws an axis line.
o save() (optionally, but by default) checks for the existence
of objects before opening the file/connection (wish of
PR#12543).
o segments(), arrows() and rect() allow zero-length
coordinates. (Wish of PR#11192)
o set.seed(kind=NULL) now takes 'kind' from a saved seed if the
workspace has been restored or .Random.seed has been set in
some other way. Previously it took the 'currently used' value,
which was "default" unless random numbers had been used in
the current session. Similarly for the values reported by
RNGkind(). (Related to PR#12567.)
set.seed() gains a 'normal.kind' argument.
o setEPS() and setPS() gain '...' to allow other arguments to be
passed to ps.options(), including overriding 'width' and 'height'.
o setTimeLimit() function to set limits on the CPU
and/or elapsed time for each top-level computation, and
setSessionTimeLimit() to set limits for the rest of the session.
o splinefun() has a new method = "monoH.FC" for monotone Hermite
spline interpolation.
o sprintf() optionally supports the %a/%A notation of C99 (if the
platform does, including under Windows).
o str()'s default method gains a 'formatNum' function argument which
is used for formatting numeric vectors. Note that this is very
slightly not backward compatible.
o The summary() method for class "ecdf" now uses a print()
method rather than printing directly.
o summary.manova() uses a stabler computation of the test
statistics, and gains a 'tol' argument to allow highly
correlated responses to be explored (with probable loss of
accuracy). Similar changes have been made to anova.mlm() and
anova.mlmlist().
o Sweave() now writes concordance information inside a
\Sconcordance LaTeX macro, which allows it to be inserted into
PDF output.
o system.time() now uses lazy evaluation rather than
eval/substitute, which results in more natural scoping. (PR#11169)
o In table(), 'exclude=NULL' now does something also for factor
arguments. A new 'useNA' argument allows you to control
whether to add NA levels unconditionally or only when present
in data. A new convenience function addNA() gives similar
functionality by adding NA levels to individual factors.
o unlink() tries the literal pattern if it does not match with
wildcards interpreted -- this helps with e.g. unlink("a[b")
which previously needed to be unlink("a\\[b").
o update.packages() gains an argument 'oldPkgs', where
new.packages() and old.packages() get 'instPkgs'. These allow
consideration of only subsets of packages instead of all
installed ones.
o which(b) is somewhat faster now, notably for named vectors, thanks
to a suggestion by Henrik Bengtsson.
o New generic function xtfrm() as an auxiliary helper for
sort(), order() and rank(). This should return a numeric
vector that sorts in the same way as its input. The default
method supports any class with ==, > and is.na() methods but
specific methods can be much faster.
As a side-effect, rank() will now work better on classed
objects, although possibly rather slowly.
o X11() and capabilities("X11") now catch some X11 I/O errors that
previously terminated R. These were rare and have only be
seen with a misconfigured X11 setup on some versions of X11.
o The handling of nuls in character strings has been changed --
they are no longer allowed, and attempting to create such a
string now gives a truncation warning (unless
options("warnEscapes") is false).
o The user environment and profile files can now be specified via
environment variables 'R_ENVIRON_USER' and 'R_PROFILE_USER',
respectively.
o ?pkg::topic and ?pkg:::topic now find help on 'topic' from
package 'pkg' (and not help on :: or :::).
o ??topic now does help.search("topic"); variations such as
??pkg::topic or field??topic are also supported.
o There is support for using ICU (International Components for
Unicode) for collation, enabled by configure option --with-ICU
on a Unix-alike and by a setting in MkRules on Windows.
Function icuSetCollate() allows the collation rules (including
the locale) to be tuned.
o If S4 method dispatch is on and S4 objects are found as
attributes, show() rather than print() is used to print the
S4 attributes.
o Starting package tcltk without access to Tk (e.g. no available
display) is now a warning rather than an error, as Tcl
will still be usable. (On most platforms it was possible to
inhibit Tk by not having DISPLAY set, but not on Windows nor
Mac OS X builds with --with-aqua.)
o Using $ on a non-subsettable object (such as a function) is
now an error (rather than returning NULL).
o Hexadecimal numerical constants (such as 0xab.cdp+12) may now
contain a decimal point.
o PCRE has been updated to version 7.8 (mainly bug fixes).
NEW FEATURES IN PACKAGE 'methods'
o S3 classes that are registered by a call to setOldClass() now
have the S3 class as a special slot, and therefore so do
any S4 classes that contain them. This mechanism is used to
support S4 classes that extend S3 classes, to the extent
possible. See ?Classes, ?setOldClass, and ?S3Class.
The treatment of special pseudo-classes "matrix", "array", and
"ts" as S4 classes has also been modified to be more
consistent and, within limitations imposed by special
treatment of these objects in the base code, to allow other
classes to contain them. See class?ts.
A general feature added to implement "ts" and also
"data.frame" as S4 classes is that an S4 class definition can
be supplied to setOldClass() when the S3 class has known
attributes of known class.
setOldClass() now saves all the S3 inheritance, allowing the
calls to be built up in stages, rather than including all the
S3 classes in each call. Also allows as(x,"S3") to generate
valid S3 inheritance from the stored definition. See ?S3.
o S4 methods may now be defined corresponding to "...", by
creating a generic function that has "..." as its signature.
A method will be selected and called if all the arguments
matching "..." are from this class or a subclass. See ?dotsMethods.
o New functions S3Part() and S3Class() provide access to the
corresponding S3 object and class for S4 classes that extend
either an S3 class or a basic R object type.
o show(<class definition>) now also shows the class name.
INSTALLATION
o If sub-architectures are used, a copy of Rscript is installed
in ${R_HOME}/bin/exec${R_ARCH} (since that in ${R_HOME}/bin
and /usr/bin might be overwritten in a subsequent installation).
PACKAGE INSTALLATION
o LazyLoad: yes is now the default, so packages wanting to avoid
lazy loading must set 'LazyLoad: no' (or an equivalent value) in
the DESCRIPTION file.
o R CMD INSTALL will now fail if it finds a non-executable
'configure' script in the package -- this usually indicates a
file system with insufficient permissions. If a
non-executable 'cleanup' script is found and either
--clean or --preclean is used, a warning is given.
DEPRECATED & DEFUNCT
o Use in packages of the graphics headers Rdevices.h and
Rgraphics.h is defunct: they are no longer installed.
o options("par.ask.default") is defunct in favour of
"device.ask.default".
o The 'device-independent' family "symbol" is defunct: use
font=5 (base) or fontface=5 (grid) instead.
o gammaCody() is defunct.
o par("gamma") is defunct.
o 'methods' package functions getAccess(), getAllMethods(),
getClassName(), getClassPackage(), getExtends(),
getProperties(), getPrototype(), getSubclasses, getVirtual(),
mlistMetaName(), removeMethodsObject() and seemsS4Object() are
defunct.
o Use of a non-integer .Random.seed is now an error. (R itself
has never generated such values, but user code has, and
R >= 2.6.0 has given a warning.)
o methods::allGenerics() is deprecated.
o In package installation, SaveImage: yes is now ignored, and
any use of the field will give a warning.
o unserialize() no longer accepts character strings as input.
o The C macro 'allocString' has been removed -- use 'mkChar' and
variants.
o Use of allocVector(CHARSXP ...) is deprecated and gives a warning.
UTILITIES
o The default for 'stylepath' in Sweave's (default) RweaveLatex
driver is now FALSE rather than TRUE if
SWEAVE_STYLEPATH_DEFAULT is unset : see ?RweaveLatex.
To support this, tools::texi2dvi adds the R 'texmf' directory
to the input search path.
o R CMD Rd2dvi now previews PDF output (as was documented) if
R_PDFVIEWER is set (as it will normally be on a Unix-alike but
not on Windows, where the file association is used by default).
o R CMD check checks for binary executable files (which should not
appear in a source package), using a suitable 'file' if
available, else by name.
o R CMD check now also uses codetools' checks on the body of S4
methods.
C-LEVEL FACILITIES
o R_ReadConsole will now be called with a buffer size of 4096
bytes (rather than 1024): maintainers of alternative
front-ends should check that they do not have a smaller limit.
o Graphics structure NewDevDesc has been renamed to DevDesc.
For now there is a compatibility define in GraphicsDevice.h,
but it will be removed in R 2.9.0.
o PROTECT and UNPROTECT macros now work even with R_NO_REMAP.
BUG FIXES
o @ now gives an error (and not just a warning) if it is being
applied to a non-S4 object.
o R CMD appends (not prepends) R's texmf path to TEXINPUTS.
o Objects generated by new() from S4 classes should now all
satisfy isS4(object). Previously, prototypes not of object
type S4 would not be S4 objects. new() applied to basic,
non-S4 classes still will (and should) return non-S4 objects.
o Functions writing to connections such as writeLines(),
writeBin(), writeChar(), save(), dput() and dump() now check
more carefully that the connections are opened for writing,
including connections that they open themselves.
Similarly functions which read such as readLines(), scan(),
dcf() and parse() check connections for being open for reading.
o Equality comparison of factors with <NA> levels now works
correctly again.
o Repainting of open X11 View() windows is now done whilst an
X11 dataentry window is in use.
o Indexing of data frames with NA column names and a numeric or
logical column index works again even if columns with NA names
are selected.
o on.exit() has been fixed to use lexical scope in determining
where to evaluate the exit action when the on.exit expression
appears in a function argument.
o rank() now consistently returns a double result for
ties.method = "average" and an integer result otherwise.
Previously the storage mode depended on 'na.last' and if any
NAs were present.
o The "lm" methods of add1(), and drop1() now also work on a model
fit with na.action = na.exclude.
o median(c(x = NA_real_)) no longer has spurious names().
o isoreg(x, y) now returns the correct result also when x has ties,
in all cases.
o What na.action() does is now correctly documented.
o source() with echo=TRUE now behaves like ordinary automatic
printing, by using methods::show() for S4 objects.
o Several bugs fixed in `?` with topics: it previously died trying
to construct some error messages; for S4 methods, class "ANY"
should be used for omitted arguments and default methods.
o trace() should create missing traceable classes in the global
environment, not in baseenv() where other classes will not be
found.
o Class inheritance using explicit coerce= methods via setIs()
failed to coerce the argument in method dispatch. With this
fixed, a mechanism was needed to prohibit such inheritance
when it would break the generic function (e.g.,
initialize). See ?setIs and ?setGeneric.
o RSiteSearch() encodes its query (it seems this is occasionally
needed on some platforms, but encoding other fields is harmful).
o 'incomparables' in match() was looking up indices in the wrong
table.
o write.dcf() did not escape "." according to Debian policy
(PR#12816).
o col2rgb() sometimes opened a graphics device unnecessarily, and
col2rgb(NA) did not return a transparent color, as documented.
o pdf(family="Japan") [and other CIDfonts] no longer seg.faults
when writing "western" text strings.
o as.list() applied to an environment now forces promises and
returns values.
o Promises capturing calls to sys.parent() and friends did not
work properly when evaluated via method dispatch for internal
S3 generics.
o The default "pkgType" option for non-CRAN builds of R on Mac OS X
is now correctly "source" as documented.
o The default R_LIBS_USER path in AQUA builds now matches the
Mac-specifc path used by the Mac GUI: ~/Library/R/x.y/library
o splinefun() with natural splines incorrectly evaluated derivatives
to the left of the first knot. (PR#13132, fix thanks to
Berwin Turlach)
o anova(glm(..., y=FALSE)) now works. (PR#13098)
o cut.Date(x, "weeks") could fail if x has only one unique value
which fell on a week boundary. (PR#13159)
**************************************************
* *
* 2.7 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.7.2 patched
BUG FIXES
o within(<dataframe>, { ... }) now also works when '...' removes
more than one column.
o Attempting to open an X11() device on a non-existent display
when one is already open on another display now gives a
warning rather than terminating R via a fatal X11 error.
(PR#12628)
o source() did not respect the setting of options("keep.source")
when setting source references.
o seek() now clears the pushback on a text-mode connection if
used to set a new position. (PR#12640)
o quartz() would segfault if asked to create a file for bitmap
output which could not be created. This applied also to the
type="quartz" versions of bmp(), jpeg(), png() and tiff().
o dnbinom(0, size, mu = <large>) suffered from cancellation in 2.7.2
only.
CHANGES IN R VERSION 2.7.2
NEW FEATURES
o sprintf() returns elements of the result in UTF-8 when the
format or any character input has a corresponding element
declared as UTF-8. Similarly for paste(), elements of the
result are in UTF-8 when any input to that element is declared
as UTF-8.
o axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
the colour and line width of ticks to be set separately from
that of the line (e.g. to set one or the other to transparent
or zero width).
o legend() has a new argument 'box.col' to set the colour of the
enclosing box.
o legend() gains a 'xpd' argument to make it easier to place a
legend in the margins or outer margins.
o stripchart() now passes '...' to title() (as well as to
plot.default() and axis()). (Wish of PR#12202)
o help.search() has new argument 'searchEngine' to go directly
to the search form: this is needed by users of Firefox 3.0.x,
for x <= 6, to workaround a bug in interpreting the search
results pages.
BUG FIXES
o Plotmath computed the glyph metrics for the wrong character (and
perhaps for a non-existent one) if this was a single-byte
character with the top bit set. An example was symbol("\300").
o sink() and cat() could divert output to a non-writable connection.
o phyper(x, 0,0,0) no longer hangs for huge x and gives 1 for x >= 0.
(PR#11813)
o plnorm(x, ..., log.p=TRUE) is now correct for x <= 0. (PR#11867)
o <data.frame>[, ch] gives an error (again!) when ch is a string not
exactly matching the column names, thanks to an oral bug report by
Matthew Dowle.
o data.frame(x=1:2, y=3:4, row.names=c("a","NA"))[c(2,NA),] has
correct row names c("NA","NA.1") again.
o The GUI data editor for dataframes did not handle escape
characters in entries properly. (PR#11897)
o PCRE has been updated to 7.7 (bugfix release).
o package.skeleton() wrongly warned about invalid code_files names
when these were not in the current directory.
o shapiro.test(c(0,0,1)) now has P value >= 0 (instead of barely
negative).
o assign() now warns if given a character vector of length > 1,
rather than silently taking the first element.
o rcond(<exactly singular matrix>) now gives 0 instead of an error.
o There was a memory leak in C function ucstoutf8 used by some
graphics devices.
o Plots of profile.mle() objects (package 'stats4') were
misbehaving when the 'which' argument had been used in their
calculation.
o dnbinom(x, size, mu=*, ..) is now more accurate for very large
'size'. The same applies to pnbinom() and rnbinom().
o axis() was ignoring par() mgp[3] if mgp was set in-line.
o Closing an X11 View() or dataentry window via its frame's
close control now works better on some window managers.
o Calling lapply() was not handling method dispatch correctly for
is.numeric(), is.matrix(), is.array(), log() and the Math2
group. This affected data.matrix() which incorrectly regarded
"Date" and "POSIXct" objects as numeric, and has been adjusted
to do so as exceptions.
o package.skeleton() was not looking for non-function objects in
its 'environment' argument.
o nls() was only finding its 'weights' argument in the case when
all the variables in the formula were of the same length and
hence that model.frame() could be used.
It was silently ignoring 'subset' and 'na.action' except in
that case. Now they are ignored only if 'data' is a list and
variables taken from 'data' are not all of the same length,
in which case a warning is given.
o The 'mle' confint() method now takes 'level' into account when
setting 'alpha' for the profile.
o within() was not handling correctly expressions that produced
NULL columns. (PR#11131)
o dev.print() and dev.copy2{eps,pdf}() now ensure that the current
device is restored as the active device even if an error
occurs. (PR#9801)
o as.Date() could fail to convert character strings representing
days on which midnight did not exist in the current timezone
(as happened in parts of Africa on 1960-01-01).
o The automatic placement of legend() with 'title' and a
reversed 'x' axis was incorrect. (PR#12019)
o The use of multiple packages in 'LinkingTo' works again, and
now works when the dependent packages are in the library to be
installed to (but not in the library path seen by R --vanilla).
o bxp() (and hence boxplot) now respects in-line graphical
parameters 'xaxp'/'yaxp' as appropriate. (PR#11463)
o barplot(log = "y") failed if there were NAs in the 'height'
argument. (PR#11585)
o pbeta() is more accurate in some cases with extreme values of
'ncp'. (PR#11277).
o edit.data.frame() no longer fails if called on a 0-column
data frame and no column is created.
o pchisq(x, df=0) was always one even for x < 0; similarly for
pgamma(x, alpha=0).
o add1() and drop1() now return a P-value of NaN in cases with
df=0 for test="Chisq" (they gave NaN until pchisq was altered
in R 2.6.2).
o The default methods of drop1() and add1() now re-evaluate in the
object's formula environment, rather than simply in the parent
(informal bug report by Werner Stahel).
o The undocumented limit of 8191 bytes on comments (from # to
the end of the line) in R code has been removed.
o qgamma() warns if used with shape < 1e-10, when it may be
unreliable. (PR#12324)
o Installing a source package was not using the package's declared
encoding (if any) as a default encoding for the help.search()
database in Meta/hsearch.rds. This could cause packages with
a default encoding to have some of their entries rejected by
help.search() in a multi-byte locale (such as a UTF-8 locale).
o duplicated() and unique() now handle 'incomparables' better,
and avoid occasional segfaults (PR#12551).
o plot(isoreg(x, y)) now plots the points correctly when 'x'
is unssorted.
o data.frame(row.names=NULL) once again behaves differently from
the default (as documented).
CHANGES IN R VERSION 2.7.1
NEW FEATURES
o tools::texi2dvi() has a new argument 'texinputs' to allow the
TeX and bibtex input paths to be specified (even on MiKTeX).
o dev.copy2pdf() gains an 'out.type' argument to allow it to be
used with cairo_pdf() or quartz(type = "pdf").
o poly() has additional checks against user error (as in PR#11243).
o The Mac OS quartz() device draws contiguous lines much faster.
o A field containing just a sign is no longer regarded as numeric
(it was on all platforms in 2.7.0, but not on most in earlier
versions of R). Similarly, '.' is now always non-numeric.
o CITATION files are now read in Latin-1: quite a few were
failing if used in a multibyte locale such as UTF-8.
o The DESCRIPTION file of a package can specify an 'OS_type' field
as either 'unix' or 'windows' to confine installation to that
OS type.
o HoltWinters() now uses optimize() rather than optim for
one-parameter problems which should be more reliable (PR#11469).
o axis() now respects the setting of par("xpd") when clipping.
o The 'factor' method of format() now preserves names, dims and
dimnames in the same way as for character and numeric inputs.
(PR#11512)
o read.DIF(*, transpose=TRUE) now allows to correctly read DIF files
produced by some versions of Excel.
DEPRECATED & DEFUNCT
o The use of unserialize() on character strings is deprecated:
that was a format used in R < 2.4.0.
o The use of embedded nuls in character strings is deprecated:
They will no longer be allowed in R 2.8.0.
UTILITIES
o R CMD check checks for possible check directories in the
sources -- in mid-2008 there were about 20 examples on CRAN.
o R CMD build tries harder to clean up the inst/doc directory
from the remnants of earlier builds.
It also removes any directories with extension .Rcheck, and
files .DS_Store and ._* (created by tar on Mac OS X under some
circumstances: it now sets environment variables to ask for
such files not to be created by that tar.)
BUG FIXES
o Encoding<- on NA_character_ converted it to "NA".
o Adobe Symbol was missing from the encodings in
tools::charset_to_Unicode.
o diag(matrix(x, 0, 0)) now returns a 0-length vector of the
correct mode, instead of always numeric.
o The parser sometimes accepted invalid quoted strings in a UTF-8
locale.
o plot.default(x, y) now dispatches to Axis() methods whether
y is NULL or not.
o On Mac OS X, the Cocoa Quartz window could close without warning
under certain circumstances (specific autorelease pool flush).
o Plotting symbols with separate border and fill colours (e.g.,
plot(pch = 21)) now works with transparent 'col', but opaque
or semi-transparent 'bg'. Previously, if 'col' was
transparent then 'bg' was ignored and nothing was drawn.
o file.path() did not work correctly in 2.7.0 if the components
had different encodings.
o merge() failed if there were no common columns and one of the
inputs had zero rows.
o expand.grid() failed if an input had length 0.
o match() does again truncate strings at embedded nuls (as newly
documented in 2.7.0).
o Because of a typo, 'pointsize' in png(type="cairo") (and jpeg,
bmp, tiff) devices was being interpreted in pixels not bigpoints.
o is() was wrong for some S3 class objects with class of length
greater than one.
o undoc() / codoc() were not checking all S4 methods in some cases.
o Use of textConnection(NULL, mode="w") could segfault.
o Use of strwidth/height(units="user") (the default) is again an
error before a user coordinate system has been set on the
device, rather than giving nonsensical values (the effect of
r31367).
o Rare string width calculations in package grid were not
interpreting the string encoding correctly.
o hasMethods(f, env) {without specified 'package'} now works better.
o A missing PROTECT could cause segfaults on string
comparisons. (PR#11421)
o str(structure(1, classID = "Pooh")) now works fine.
o A missing PROTECT could cause segfaults in if() if coercion of
the condition was required or a warning was to be given.
o plot(<table>) now uses a sensible default main title.
o validObject() called with complete=TRUE did not use inherited
validity methods for slot classes.
o Several bugs fixed in as(): the initial method lookup was not
using the table with inherited methods (so inheritance had to
be recomputed each time); coerce() should not be called
directly--it can insert invalid inherited methods; the
constructed as() methods were not retaining the function's
environment.
o influence.measures(<glm-object>) now computes the same
Cook's distance approximations as cooks.distance().
o plot(<glm>, which=5) uses more correct Cook's distance contours;
(fix to fix to PR#9316).
o pdf() and postscript() were not working correctly in 2.7.0 with
UTF-8 encoded data in a non-UTF-8 MBCS (e.g. EUC-JP on Unix,
CJK locales on Windows).
o conformMethod(), called by setMethod(), now checks better about
argument names in wrong order. Whereas it only warns currently,
it is planned to become an error in the future.
o The predict() method for prcomp() had an incorrect check for
the number of columns of 'newdata' if the columns were not named.
o The axis() function now distinguishes between setting "at" to
NULL or a zero-length vector, treating the latter as a request
for no ticks. This corrects the handling of the "x" parameter
to rug().
o glob2rx("*[*") now produces a correct regular expression.
o The canvas is no longer painted on copy or save in Cocoa Quartz.
o identify() in Quartz can now be terminated by either using popup
menu equivalent (Ctrl-click or second mouse button) or by pressing
the <Esc> key. The latter was documented but did not work.
o tools:::.check_package_depends() {called from 'R CMD check'} now
also works correctly when directory-name != package-name.
o Source references were sometimes off by a line.
o The quartz() parameter 'antialias' is no longer ignored.
o The Quartz device is now trying hard to remove anti-aliasing
effects for rasterized backends in plots that use adjacent,
borderless rectangles such as image().
o The srcfilecopy() function now adds a timestamp to the object it
creates.
o parse() would lose a token when run on stdin().
o socketConnection() was using internally the class "socket"
and not "sockconn", which caused a conflict with make.socket().
(PR#11515)
o Quartz is now trying harder to find the proper font for a given
family which resolves font issues on Mac OS X 10.4. Full font
names and PostScript names can be used interchangeably. (Note,
however that italic/oblique font faces of Helvetica are not
included in the Mac OS X 10.4 system).
o qf() no longer gives NaN when one of df1 and df2 is large and
the other is infinite (including if both are infinite); it is more
accurate e.g. for qf(1e-18, 2,4).
o qbeta(-1e10, 50, 40, log.p=TRUE) no longer hangs.
o Cocoa Quartz backend autodetection of display DPI was not
correct for screens rotated by 90 or 270 degrees.
o selectMethod("coerce", .) now uses a correct default for
'useInherited', and hence no longer may mess up the method cache.
o show() now also works on "unregistered" S3 class objects.
o formatC(*, format="fg", flag="#") is no longer dropping trailing
zeros.
o read.table(file = stdin()) with invalid input could leave the
connection in an invalid state and hence cause a later
segfault. (PR#11627)
o read.DIF() did not obey the default 'stringsAsFactors = TRUE'.
o The 'noquote' method for c() now works correctly with three or
more arguments.
o symbol() in plotmath expressions works again with non-ASCII
input on devices that use UTF-8 for the symbol font.
CHANGES IN R VERSION 2.7.0
SIGNIFICANT USER-VISIBLE CHANGES
o The default graphics device in non-interactive use is now
pdf() rather than postscript(). [PDF viewers are now
more widely available than PostScript viewers.]
The default width and height for pdf() and bitmap() have been
changed to 7 (inches) to match the screen devices.
o Most users of the X11() device will see a new device that has
different fonts, anti-aliasing of lines and fonts and
supports semi-transparent colours.
o Considerable efforts have been made to make the default output
from graphics devices as similar as possible (and in
particular close to that from postscript/pdf). Many devices
were misinterpreting 'pointsize' in some way, for example as
being in device units (pixels) rather than in points.
o Packages which include graphics devices need to be re-installed
for this version of R, with recently updated versions.
NEW FEATURES
o The apse code used by agrep() has been updated to version
0.16, with various bug fixes.
agrep() now supports multibyte character sets.
o any() and all() avoid coercing zero-length arguments (which
used a surprising amount of memory) since they cannot affect
the answer.
Coercion of other than integer arguments now gives a warning
as this is often a mistake (e.g. writing all(pr) > 0 instead
of all(pr > 0) ).
o as.Date(), as.POSIXct() and as.POSIXlt() now convert numeric
arguments (days or seconds since some epoch) provided the
'origin' argument is specified.
o New function as.octmode() to create objects such as file
permissions.
o as.POSIXlt() is now generic, and it and as.POSIXct() gain a
'...' argument. The character/factor methods now accept a
'format' argument (analogous to that for as.Date).
o New function browseVignettes() lists available vignettes in an
HTML browser with links to PDF, Rnw, and R files.
o There are new capabilities "aqua" (for the AQUA GUI and quartz()
device on Mac OS X) and "cairo" (for cairo-based graphics
devices).
o New function checkNEWS() in package 'tools' that detects common
errors in NEWS file formatting.
o deparse() gains a new argument 'nlines' to limit the number of
lines of output, and this is used internally to make several
functions more efficient.
o deriv() now knows the derivatives of digamma(x), trigamma(x)
and psigamma(x, deriv) (wrt to x).
o dir.create() has a new argument 'mode', used on Unix-alikes
(only) to set the permissions on the created directory.
o Where an array is dropped to a length-one vector by drop() or
[, drop = TRUE], the result now has names if exactly one of
the dimensions was named. (This is compatible with S.)
Previously there were no names.
o The 'incomparables' argument to duplicated(), unique() and
match() is now implemented, and passed to match() from merge().
o dyn.load() gains a 'DLLpath' argument to specify the path for
dependent DLLs: currently only used on Windows.
o The spreadsheet edit() methods (and used by fix()) for data
frames and matrices now warn when classes are discarded.
When editing a data frame, columns of unknown type (that is
not numeric, logical, character or factor) are now converted
to character (instead of numeric).
o file.create() has a new argument 'showWarnings' (default TRUE)
to show an informative warning when creation fails, and
dir.create() warns under more error conditions.
o New higher-order functions Find(), Negate() and Position().
o [dpqr]gamma(*, shape = 0) now work as limits of 'shape -> 0',
corresponding to the point distribution with all mass at 0.
o An informative warning (in addition to the error message) will
be given when the basic, extended or perl mode of grep(),
strsplit() and friends fails to compile the pattern.
o More study is done of perl=TRUE patterns in grep() and friends
when length(x) > 10: this should improve performance on long
vectors.
o grep(), strsplit() and friends with fixed=TRUE or perl=TRUE
work in UTF-8 and preserve the UTF-8 encoding for UTF-8 inputs
where supported.
o help.search() now builds the database about 3x times faster.
o iconv() now accepts "UTF8" on all platforms (many did, but not
e.g. libiconv as used on Windows).
o identity() convenience function to be used for programming.
o In addition to warning when 'pkgs' is not found,
install.packages() now reports if it finds a valid package
with only a case mismatch in the name.
o intToUtf8() now marks the Encoding of its output.
o The function is() now works with S3 inheritance; that is, with
objects having multiple strings in the class attribute.
o Extensions to condition number computation for matrices, notably
complex ones are provided, both in kappa() and the new rcond().
o list.files() gains a 'ignore.case' argument, to allow
case-insensitive matching on some Windows/MacOS file systems.
o ls.str() and lsf.str() have slightly changed arguments and
defaults such that ls.str() {no arguments} works when debugging.
o Under Unix, utils::make.packages.html() can now be used directly
to set up linked HTML help pages, optionally without creating
the package listing and search database (which can be much
faster).
o new.packages() now knows about the front-end package gnomeGUI
(which does not install into a library).
o optim(*, control = list(...)) now warns when '...' contains
unexpected names, instead of silently ignoring them.
o The options "browser" and "editor" may now be set to functions,
just as "pager" already could.
o packageDescription() makes use of installed metadata where
available (for speed, e.g. in make.packages.html()).
o pairwise.t.test() and pairwise.wilcox.test() now more explicitly
allow paired tests. In the former case it is now flagged as an
error if both 'paired' and 'pool.SD' are set TRUE (formerly,
'paired' was silently ignored), and one-sided tests are generated
according to 'alternative' also if 'pool.SD' is TRUE.
o paste() and file.path() are now completely internal, for speed.
(This speeds up make.packages.html(packages=FALSE)
severalfold, for example.)
o paste() now sets the encoding on the result under some
circumstances (see ?paste).
o predict.loess() now works when loess() was fitted with
transformed explanatory variables, e.g, loess(y ~ log(x) + log(z)).
o print(<data.frame>)'s new argument 'row.names' allows to suppress
printing rownames.
o print() and str() now also "work" for 'logLik' vectors longer than
one.
o Progress-bar functions txtProgressBar(), tkProgressBar() in
package tcltk and winProgressBar() (Windows only).
o readChar() gains an argument 'useBytes' to allow it to read a
fixed number of bytes in an MBCS locale.
o readNEWS() has been moved to the tools package.
o round() and signif() now do internal argument matching if
supplied with two arguments and at least one is named.
o New function showNonASCII() in package tools to aid detection
of non-ASCII characters in .R and .Rd files.
o The [dpq]signrank() functions now typically use considerably
less memory than previously, thanks to a patch from Ivo
Ugrina.
o spec.ar() now uses frequency(x) when calculating the
frequencies of the estimated spectrum, so that for monthly
series the frequencies are now per year (as for spec.pgram)
rather than per month as before.
o spline() gets an 'xout' argument, analogously to approx().
o sprintf() now does all the conversions needed in a first pass if
length(fmt) == 1, and so can be many times faster if called
with long vector arguments.
o [g]sub(useBytes = FALSE) now sets the encoding on changed
elements of the result when working on an element of known
encoding. (This was previously done only for perl = TRUE.)
o New function Sys.chmod(), a wrapper for 'chmod' on platforms
which support it. (On Windows it handles only the read-only
bit.)
o New function Sys.umask(), a wrapper for 'umask' on platforms
which support it.
o New bindings ttk*() in package tcltk for the 'themed widgets'
of Tk 8.5. The tcltk demos make use of these widgets where
available.
o write.table(d, row.names=FALSE) is faster when 'd' has millions of
rows; in particular for a data frame with automatic row names.
(Suggestion from Martin Morgan.)
o The parser limit on string size has been removed.
o If a NEWS file is present in the root of a source package, it
is installed (analogously to LICENSE, LICENCE and COPYING).
o Rd conversion to 'example' now quotes aliases which contain
spaces.
o The handling of DST on dates outside the range 1902-2037 has
been improved. Dates after 2037 are assumed to have the same
DST rules as currently predicted for the 2030's (rather than
the 1970s), and dates prior to 1902 are assumed to have no DST
and the same offset as in 1902 (if known, otherwise as in the
1970s).
o On platforms where we can detect that mktime sets errno
(e.g. Solaris and the code used on Windows but not Linux nor
Mac OS X), 1969-12-31 23:59:59 GMT is converted from POSIXlt
to POSIXct as -1 and not NA.
o The definition of 'whitespace' used by the parser is slightly
wider: it includes Unicode space characters on Windows and in
UTF-8 locales on machines which use Unicode wide characters.
o The src/extra/intl sources have been updated to those from
gettext 0.17.
o New flag --interactive on Unix-alikes forces the session to be
interactive (as --ess does on Windows).
o x[<zero-length>] <- NULL is always a no-op: previously
type-checking was done on the replacement value and so this
failed, whereas we now assume NULL can be promoted to any
zero-length vector-like object.
Other cases of a zero-length index are done more efficiently.
o There is a new option in Rd markup of \donttest{} to mark
example code that should be run by example() but not tested
(e.g. because it might fail in some locales).
o The error handler in the parser now reports line numbers for
more syntax errors (MBCS and Unicode encoding errors, line
length and context stack overflows, and mis-specified argument
lists to functions).
o The "MethodsList" objects originally used for method selection
are being phased out. New utilities provide simpler
alternatives (see ?findMethods), and direct use of the mangled
names for the objects is now deprecated.
o Creating new S4 class and method definitions in an environment
that could not be identified (as package, namespace or global)
previously generated an error. It now results in creating and
using an artificial package name from the current date/time,
with a warning. See ?getPackageName.
o Unix-alikes now give a warning on startup if locale settings
fail. (The Windows port has long done so.)
o Parsing and scanning of numerical constants is now done by R's
own C code. This ensures cross-platform consistency, and
mitigates the effects of setting LC_NUMERIC (within base R it
only applies to output -- packages may differ).
The format accepted is more general than before and includes
binary exponents in hexadecimal constants: see
?NumericConstants for details.
o Dependence specifications for R or packages in the Depends
field in a DESCRIPTION file can now make use of operators
< > == and != (in addition to <= and >=): such packages will
not be installable nor loadable in R < 2.7.0.
There can be multiple mentions of R or a package in the Depends
field in a DESCRIPTION file: only the first mention will be
used in R < 2.7.0.
GRAPHICS CHANGES
o The default graphics devices in interactive and
non-interactive sessions are now configurable via environment
variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE
respectively.
o New function dev.new() to launch a new copy of the default
graphics device (and taking care if it is "pdf" or
"postscript" not to trample on the file of an already running
copy).
o dev.copy2eps() uses dev.displaylist() to detect screen
devices, rather than list them in the function.
o New function dev.copy2pdf(), the analogue of dev.copy2eps().
o dev.interactive() no longer treats a graphics device as
interactive if it has a display list (but devices can still
register themselves on the list of interactive devices).
o The X11() and windows() graphics devices have a new argument
'title' to set the window title.
o X11() now has the defaults for all of its arguments set by the
new function X11.options(), inter alia replacing options
"gamma", "colortype" and "X11fonts".
o ps.options() now warns on unused option 'append'.
xfig() no longer takes default arguments from ps.options().
(This was not documented prior to 2.6.1 patched.)
pdf() now takes defaults from the new function pdf.options()
rather that from ps.options() (and the latter was not
documented prior to 2.6.1 patched).
The defaults for all arguments other than 'file' in
postscript() and pdf() can now be set by ps.options() or
pdf.options()
o New functions setEPS() and setPS() as wrappers to ps.options()
to set appropriate defaults for figures for inclusion in other
documents and for spooling to a printer respectively.
o The meaning of numeric 'pch' has been extended where MBCSes are
supported. Now negative integer values indicate Unicode
points, integer values in 32-127 represent ASCII characters,
and 128-255 are valid only in single-byte locales.
(Previously what happened with negative pch values was
undocumented: they were replaced by the current setting of
par("pch").)
o Graphics devices can say if they can rotate text well
(e.g. postscript() and pdf() can) and if so the device's
native text becomes the default for contour labels rather than
using Hershey fonts.
o The setting of the line spacing (par("cra")[2]) on the X11() and
windows() devices is now comparable with postscript() etc, and
roughly 20% smaller than before (it used to depend on the
locale for X11). (So is the pictex() device, now 20% larger.)
This affects the margin size in plots, and should result in
better-looking plots.
o There is a per-device setting for whether new frames need
confirmation. This is controlled by either par("ask") or
grid.prompt() and affects all subsequent plots on the device
using base or grid graphics.
o There is a new version of the X11() device based on cairo
graphics which is selected by type "cairo" or "nbcairo", and
is available on machines with cairo installed and preferably
pango (which most machines with gtk+ >= 2.8 will have). This
version supports translucent colours and normally does a
better job of font selection so it has been possible to
display (e.g.) English, Polish, Russian and Japanese text on
a single X11() window. It is the default where available.
There is a companion function, savePlot(), to save the current
plot to a PNG file.
On Unix-alikes, devices jpeg() and png() also accept
type = "cairo", and with that option do not need a running
X server. The meaning of capabilities("jpeg") and
capabilities("png") has changed to reflect this. On MacOS X,
there is a further type = "quartz". The default type is
selected by the new option "bitmapType", and is "quartz" or
"cairo" where available.
Where cairo 1.2 or later is supported, there is a svg() device
to write SVG files, and cairo_pdf() and cairo_ps() devices to
write (possibly bitmap) PDF and postscript files via cairo.
Some features require cairo >= 1.2, and some which are
nominally supported under 1.2 seem to need 1.4 to work well.
o There are new bmp() and tiff() devices.
o New function devSize() to report the size of the current
graphics device surface (in inches or device units). This
gives the same information as par("din"), but independent of
the graphics subsystem.
o New base graphics function clip() to set the clipping region (in
user coordinates).
o New functions grconvertX() and grconvertY() to convert between
coordinate systems in base graphics.
o identify() recycles its 'labels' argument if necessary.
o stripchart() is now a generic function, with default and
formula methods defined. Additional graphics parameters may
be included in the call. Formula handling is now
similar to boxplot().
o strwidth() and strheight() gain 'font' and 'vfont' arguments and
accept in-line pars such as 'family' in the same way as text()
does. (Longstanding wish of PR#776)
o example(ask=TRUE) now applies to grid graphics (e.g. from
lattice) as well as to base graphics.
o Option "device.ask.default" replaces "par.ask.default" now it
applies also to grid.prompt().
o plot.formula() only prompts between plots for interactive
devices (it used to prompt for all devices).
o When plot.default() is called with y=NULL it now calls Axis()
with the 'y' it constructs rather than use the default axis.
DEPRECATED & DEFUNCT
o In package installation, SaveImage: yes is defunct and
lazyloading is attempted instead.
o $ on an atomic vector or S4 object is now defunct.
o Partial matching in [[ is now only performed if explicitly
requested (by exact=FALSE or exact=NA).
o Command-line completion has been moved from package 'rcompgen'
to package 'utils': the former no longer exists as a separate
package in the R distribution.
o The S4 pseudo-classes "single" and double have been removed.
(The S4 class for a REALSXP is "numeric": for back-compatibility
as(x, "double") coerces to "numeric".)
o gpar(gamma=) in the grid package is now defunct.
o Several S4 class definition utilities, get*(), have been said
to be deprecated since R 1.8.0; these are now formally deprecated.
Ditto for removeMethodsObject().
o Use of the graphics headers Rgraphics.h and Rdevices.h is
deprecated, and these will be unavailable in R 2.8.0.
(They are hardly used except in graphics devices, for which
there is an updated API in this version of R.)
o options("par.ask.default") is deprecated in favour of
"device.ask.default".
o The 'device-independent' family "symbol" is deprecated as it was
highly locale- and device-dependent (it only did something
useful in single-byte locales on most devices) and font=5
(base) or fontface=5 (grid) did the job it was intended to do
more reliably.
o gammaCody() is now formally deprecated.
o Two low-level functions using MethodsList metadata objects
(mlistMetaName() and getAllMethods()) are deprecated.
o Setting par(gamma=) is now deprecated, and the windows()
device (the only known example) no longer allows it.
o The C macro 'allocString' will be removed in 2.8.0 -- use
'mkChar', or 'allocVector' directly if really necessary.
INSTALLATION
o Tcl/Tk >= 8.3 (released in 2000) is now required to build
package tcltk.
o configure first tries TCL_INCLUDE_SPEC and TK_INCLUDE_SPEC
when looking for Tcl/Tk headers. (The existing scheme did
not work for the ActiveTcl package on Mac OS X.)
o The Windows build only supports Windows 2000 or later (XP,
Vista, Server 2003 and Server 2008).
o New option --enable-R-static-lib installs libR.a which can
be linked to a front-end via 'R CMD config --ldflags'.
The tests/Embedding examples now work with a static R
library.
o Netscape (which was discontinued in Feb 2008) is no longer
considered when selecting a browser.
o xdg-open (the freedesktop.org interface to
kfmclient/gnome-open/...) is considered as a possible browser,
after real browsers such as firefox, mozilla and opera.
o The search for tclConfig.sh and tkConfig.sh now only looks in
directories with names containing $(LIBnn) in the hope of
finding the version for the appropriate architecture
(e.g. x86_64 or i386).
o libtool has been updated to version 2.2.
o Use of --with-system-zlib, --with-system-bzlib or
--with-system-pcre now requires version >= 1.2.3, 1.0.5, 7.6
respectively, for security.
UTILITIES
o Rdconv now removes empty sections including alias and keyword
entries, with a note.
o Keyword entries are no longer mandatory in Rd files.
o R CMD INSTALL now also installs tangled versions of all vignettes.
o R CMD check now warns if spaces or non-ASCII characters are
used in file paths, since these are not in general portable.
o R CMD check (via massage-Examples.pl) now checks all examples
with a 7 inch square device region on A4 paper, for
locale-independence and to be similar to viewing examples on
an on-screen device.
If a package declares an encoding in the DESCRIPTION file,
the examples are assumed to be in that encoding when running
the tests. (This avoids errors in running latin1 examples in a
UTF-8 locale.)
o R CMD check uses pdflatex (if available) to check the typeset
version of the manual, producing PDF rather than DVI. (This
is a better check since the package reference manuals on CRAN
are in PDF.)
o R CMD Rd2dvi gains a --encoding argument to be passed to
R CMD Rdconv, to set the default encoding for conversions.
If this is not supplied and the files are package sources and
the DESCRIPTION file contains an Encoding field, that is used
for the default encoding.
o available.packages() (and hence install.packages() etc) now
supports subdirectories in a repository, and
tools::write_PACKAGES() can now produce PACKAGES files
including subdirectories.
o The default for 'stylepath' in Sweave's (default) RweaveLatex
driver can be set by the environment variable
SWEAVE_STYLEPATH_DEFAULT: see ?RweaveLatex.
C-LEVEL FACILITIES
o Both the Unix and Windows interfaces for embedding now make
use of 'const char *' declarations where appropriate.
o Rprintf() and REprintf() now use 'const char *' for their format
argument -- this should reduce warnings when called from C++.
o There is a new description of the interface for graphics
devices in the 'R Internals' manual, and several new entry
points. The API has been updated to version R_GE_version = 5,
and graphics devices will need to be updated accordingly.
o Graphics devices can now select to be sent text in UTF-8, even
if the current locale is not UTF-8 (and so enable text entered
in UTF-8 to be plotted). This is used by postscript(), pdf()
and the windows() family of devices, as well as the new
cairo-based devices.
o More Lapack routines are available (and declared in R_Ext/Lapack.h),
notably for (reciprocal) condition number estimation of complex
matrices.
o Experimental utility R_has_slot supplementing R_do_slot.
o There is a new public interface to the encoding info stored on
CHARSXPs, getCharCE and mkCharCE using the enumeration type
cetype_t.
o A new header 'R_ext/Visibility.h' contains some definitions for
controlling the visibility of entry points, and how to control
visibility is now documented in 'Writing R Extensions'.
BUG FIXES
o pt(x, df) is now even more accurate in some cases (e.g. 12 instead
of 8 significant digits), when x^2 << df, thanks to a remark from
Ian Smith, related to PR#9945.
o co[rv](use = "complete.obs") now always gives an error if there
are no complete cases: they used to give NA if
method = "pearson" but an error for the other two methods.
(Note that this is pretty arbitrary, but zero-length vectors
always give an error so it is at least consistent.)
Since sd(na.rm=TRUE) and var(na.rm=TRUE) both call cov(use =
"complete.obs"), this applies also to them.
cor(use="pair") used to give diagonal 1 even if the variable
was completely missing for the rank methods but NA for the
Pearson method: it now gives NA in all cases.
cor(use="pair") for the rank methods gave a matrix result with
dimensions > 0 even if one of the inputs had 0 columns.
o Supplying edit.row.names = TRUE when editing a matrix without
row names is now an error and not a segfault. (PR#10500)
o The error handler in the parser reported unexpected
& as && and | as ||.
o ps.options(reset = TRUE) had not reset for a long time.
o paste() and file.path() no longer allow NA_character_ for
their 'sep' and 'collapse' arguments.
o by() failed for 1-column matrices and dataframes. (PR#10506)
However, to preserve the old behaviour, the default method
when operating on a vector still passes subsets of the vector
to FUN, and this is now documented.
o Better behaviour of str.default() for non-default
'strict.width' (it was calling str() rather than str.default()
internally); also, more useful handling of options("str").
o wilcox.test(exact=FALSE, conf.int=TRUE) could fail in some
extreme two-sample problems. (Reported by Wolfgang Huber.)
o par(pch=) would accept a multi-byte string but only use the
first byte. This would lead to incorrect results in an MBCS
locale if a non-ASCII character was supplied.
o There are some checks for valid C-style formats in, e.g.
png(filename=). (PR#10571)
o vector() was misinterpreting some double 'length' values, e.g,
NaN and NA_real_ were interpreted as zero. Also, invalid
types of 'length' were interpreted as -1 and hence reported as
negative. (length<- shared the code and hence the same
misinterpretations.)
o A basic class "S4" was added to correspond to the "S4" object
type, so that objects with this type will print, etc. The
class is VIRTUAL, since all actual S4 objects must have a real
class.
o Classes with no slots that contain only VIRTUAL classes are now
VIRTUAL, as was intended but confused by having an empty S4
object as prototype. ## backed out temporarily ##
o format.AsIs() discarded dimnames, causing dataframes with matrix
variables to be printed without using the column names, unlike
what happens in S-PLUS (Tim Hesterberg, PR#10730).
o xspline() and grid::grid.xspline() work in device coordinates
and now correct for anisotropy in the device coordinate
system.
o grid.locator() now indicates to the graphics device that it is
is in 'graphics input' mode (as locator() and identify()
always have). This means that devices can now indicate the
'graphics input' mode by e.g. a change of cursor.
o Locales without encoding specification and non-UTF-8 locales
now work properly on Mac OS X. Note that locales without
encoding specification always use UTF-8 encoding in Mac OS X
(except for specials "POSIX" and "C") - this is different from
other operating systems.
o iconv() now correctly handles to="" and from="" on Mac OS X.
o In diag()'s argument list, drop the explicit default (' = n')
for 'ncol' which is ugly when making diag() generic.
o S4 classes with the same name from different packages were not
recognized because of a bug in caching the new definition.
o jpeg() and png() no longer maintain a display list, as they
are not interactive devices.
o Using attr(x, "names") <- value (instead of the correct
names<-) with 'value' a pairlist (instead of the correct
character vector) worked incorrectly. (PR#10807)
o Using [<- to add a column to a data frame dropped other
attributes whereas [[<- and $<- did not: now all preserve
attributes. (PR#10873)
o File access functions such as file.exists(), file.info(),
dirname() and unlink() now treat an NA filename as a
non-existent file and not the file "NA".
o r<foo>(), the random number generators, are now more consistent
in warning when NA's (specifically NaN's) are generated.
o rnorm(n, mu = Inf) now returns rep(Inf, n) instead of NaN;
similar changes are applied to rlnorm(), rexp(), etc.
o [l]choose() now warns when rounding non-integer 'k' instead of
doing so silently. (May help confused users such as PR#10766.)
o gamma() was warning incorrectly for most negative values as being
too near a negative integer. This also affected other
functions making use of its C-level implementation.
o dumpMethod() and dumpMethods() now work again.
o package.skeleton() now also works for code_files with only
metadata (e.g. S4 setClass) definitions; it handles S4 classes and
methods, producing documentation and NAMESPACE exports if requested.
o Some methods package utilities (implicitGeneric(), makeGeneric())
will be more robust in dealing with primitive functions (not a
useful idea to call them with primitives, though)
o Making a MethodsList from a function with no methods table will
return an empty list, rather than cause an error (questionably
a bug, but caused some obscure failures).
o setAs() now catches 2 arguments in the method definition, if
they do not match the arguments of coerce().
o S4 methods with missing arguments in the definition are handled
correctly when non-signature arguments exist, and check for
conflicting local names in the method definition.
o qgamma() and qchisq() could be inaccurate for small p,
e.g. qgamma(1.2e-10, shape = 19) was 2.52 rather than 2.73.
o dbeta(.., ncp) is now more accurate for large ncp, and typically no
longer underflows for give.log = TRUE.
o coerce() is now a proper S4 object and so prints correctly.
o @ now checks it is being applied to an S4 object, and if not
gives a warning (which will become an error in 2.8.0).
o dump() and friends now warn that all S4 objects (even those
based on vectors) are not source()able, with a stronger wording.
o read.dcf(all = TRUE) was leaking connections.
o scan() with a non-default separator could skip nul bytes,
including those entered as \0 with allowEscapes=TRUE. This
was different from the default separator.
o determinant(matrix(,0,0)) now returns a correct "det" result;
also value 1 or 0 depending on 'logarithm', rather than numeric(0).
o Name space 'grDevices' was not unloading its DLL when the
name space was unloaded.
o getNativeSymbolInfo() was unaware of non-registered Fortran
names, because one of the C support routines ignored them.
o load() again reads correctly character strings with embedded nuls.
(This was broken in 2.6.x, but worked in earlier versions.)
**************************************************
* *
* 2.6 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.6.2 patched
BUG FIXES
o src/extra/pcre has been updated to PCRE 7.6 (bugfix release).
o unlink(..., recursive=TRUE) no longer crashes on some platforms
if a directory cannot be opened.
o Loading in 2.6.2 a saved workspace could give an unimportant
warning in a non-UTF-8 multibyte locale (in particular a CJK
locale on Windows) which is now suppressed.
o print() methods are more consistent in returning the original
argument invisibly.
o Using the X11 data editor (e.g. via edit(), fix() or View())
could crash if the 'End' key was used and all the columns
would have fitted into the window.
o Creating a new page on an X11() device (by plot.new() or
grid.newpage()) did not flush out the XClearWindow call, so
the X11 window might not be refreshed immediately.
o libtool has been updated to version 1.5.26, which avoids
many spurious configure warnings on Darwin/Mac OS X.
o l10n_info() now recognizes how Darwin/Mac OS X reports
Latin-1 locales (as charset ISO8859-1 rather than ISO-8859-1).
o Checking examples which used grid (e.g. via lattice) without
attaching grid no longer give errors from grid_plot_hook().
o kappa(m, exact=TRUE) no longer wrongly uses 'exact=FALSE' when m
is an 'lm' or 'qr' object because the kappa.tri(x, exact=TRUE)
now works correctly.
o help(topic, offline=TRUE) misbehaved when there were multiple
matches to 'topic'. (PR#10859)
o The 'multilib' changes on Linux broke the use of
sub-architectures without a main architecture.
o source(echo=TRUE) would skip lines consisting entirely of the
letter t. (PR#10923)
o bzip2 has been updated to 1.0.5 (security fix).
CHANGES IN R VERSION 2.6.2
NEW FEATURES
o colnames(DF) is now also fast for large dataframes DF with
automatic row.names. Note that the correct usage is
names(DF). (PR#10470)
o tools::texi2dvi() works around the failure of 'texi2dvi --quiet'
to be quiet in texinfo 4.11.
o On Linux, parallel 32/64-bit installations are supported using
multilib.
BUG FIXES
o A compilation problem on one system where glob was not found
has been corrected. (PR#10468)
o The "profile.nls" method of plot() was losing the x axis labels.
o array() computed the total number of entries in the array before
coercing the dimensions to integer. (Reported by Allen McIntosh.)
o persp() misreported errors in the y parameter. (Reported by Allen
McIntosh.)
o source("clipboard", echo=TRUE) and file("clipboard", open="rt")
gave spurious errors. (Reported by Fernando Saldanha.)
o attributes<-() stripped any existing attributes before checking
that all elements of the right-hand side had names.
o rbinom(n, size, *) gave NaN when 'size > .Machine$integer.max'.
o print.summary.lm() is now consistent in the capitalization of
"R-squared".
o confint() misreported on some rank-deficient lm() models.
(PR#10496) This could also occur in the default method.
o \code{\var{<name>}} was not rendered correctly to latex in Rd
files for non-alphabetic arguments <name>.
o In 2.6.1, curve(*, add=TRUE) used a wrong default 'xlim' when x
coordinates were logged.
o The Java-based search in help.start() now only requires a
JVM >= 1.4 (2.6.1 accidentally required >= 1.5).
o The default method for range() was omitting 'na.rm' for
non-numeric objects such as those of class "Date". (PR#10508)
o cut(x, breaks=<n>) misbehaved on a constant vector of negative
values.
o bxp(), the plotting engine of boxplot(), no longer plots staple
ticks multiple times. (PR#10499)
o The automatic detection of the domain for message translation
was not working correctly for messages in message(), warning()
and stop() in packages other than 'base'.
o The profile.nls() function misbehaved when encountering
non-convergence of the "port" algorithm.
o Under certain rare circumstances in R 2.6.x, log(), round()
and trunc() could alter their arguments in the caller. This
involved passing of empty '...' arguments, and was spotted
when using apply(x, 2, log).
o par() no longer warns unnecessarily when asked to set new=FALSE
on an unused graphics device.
o plot.formula() was not passing on '...' when used with a
one-sided formula.
plot.formula() was not accepting expressions for annotations
passed to title(). (PR#10525)
o pchisq(x, df=0, ncp=L) now returns the correct limit exp(-L/2) for
x=0 and is no longer returning NaN for x > 0, L < 80. (PR#10551)
o Non-ASCII characters were only working correctly in Hershey
fonts if these were specified by the 'vfont' argument to
text() and not if specified as a font family.
o There were several errors in Hershey$allowed, but the help
page listed the allowed combinations correctly.
o text() no longer attempts to use 'vfont' with an expression
for 'labels' (it was documented not to work).
o fisher.test(simulate.p.value = TRUE) gave incorrect answers
in some extremely degenerate problems. (PR#10558)
o src/extra/pcre has been updated to PCRE 7.5 (bugfix release).
o capture.output() completes an incomplete final line of
output when file = NULL. (PR#10534)
o capture.output() now returns invisibly if output is written to
a file/connection.
o format.AsIs() did not remove the "AsIs" class and so could go
into an infinite loop.
o summary.mlm() lost the names of the coefficients when there
was only one.
o Rdconv was not marking examples files with an encoding if
this was known from the package's DESCRIPTION file.
o readChar() from a raw vector was reading a number of bytes,
not characters.
o slotNames() was erroneously treating classes that extend
"character" as strings.
o R no longer ignores SIGPIPE signals even in processes launched
by system(). Instead PR#1959 is handled by a simple error
handler which will give an error message in circumstances
where none was given before.
o The AIC() S4 generic in package stats4 no longer disables
dispatch of S3 methods for AIC().
o The conflicts check in library() excluded all S4 generics, even
where they were unrelated to the function masked. It is now
more selective (although still too generous to S4 generics).
o proc.time() was missing a protect and could misbehave if
provoked by gctorture(). (PR#10600)
o The cut() and hist() methods for dates and datetimes are now
more accurate for intervals of "months" and "years", thanks to
Marc Schwarz.
o url()/download.file() could segfault if the HTTP interaction
involved a redirect to an address starting with '/' on the
same server.
o Memory allocations used in format() and in an internal utility
function could be off by one byte. (PR#10635)
o isoreg(x, y) no longer segfaults when y has NAs.
o split(x, g) always returns a list as documented. (It used to
return NULL for a zero-length 'x'.)
o tapply(x, g, ...) misbehaved if the args were of zero length.
(PR#10644)
o hist.POSIXt(*, xaxt = "n") no longer suppresses the y-axis.
o strptime() crashed under certain locales on Mac OS X.
o gregexpr() no longer segfaults when "" is given as the search
pattern. Thanks to Hervé Pagès for the bug report.
o matplot(x, *) with default 'pch' did not plot columns from column
number 37 on (because the default pch was NA for those). (PR#10676)
o print.htest() lost output when used within sink(file, split=TRUE).
o Setting par(col.main=) also set par("col") to the same colour.
o Anonymous fifos were broken (again).
CHANGES IN R VERSION 2.6.1
NEW FEATURES
o The "data.frame" and "factor" methods for [[ now support
the 'exact' argument introduced in 2.6.0.
o plot.lm() gains a new argument 'cex.caption' to allow the
size of the captions to be controlled.
o A series of changes make the CHARSXP cache introduced in 2.6.0
faster (and in some cases many times faster) in sessions with
a large number (e.g. a million) of unique character strings,
and also if there are many empty strings.
o embedFonts(), bitmap() and dev2bitmap() explicitly turn off
auto-rotation in Ghostscript when generating PDF.
o The canonical architecture is no longer checked when loading
packages using a non-empty sub-architecture, since it is
possible to (e.g.) build packages for i386-pc-linux-gnu on both
that architecture and on x86_64-unknown-linux-gnu.
o Deparsing will (if option warnIncomplete is set) warn on
strings longer than the parser limit (8192 bytes).
o url() now uses the UserAgent header in http transactions in
the same way as download.file() (making use of option
"HTTPUserAgent").
BUG FIXES
o iconv() is again able to translate character strings with
embedded nuls (such as those in UCS-2).
o new.packages() and update.packages() failed when called on an
empty library, since old.packages() threw an error.
old.packages() now returns NULL (as documented) in that case.
o Builds on Mac OS X 10.4 or higher now allocate enough space
in the binary headers to relocate dependent libraries into the
framework.
o R CMD build now computes the exclusion list on the copy it
makes: this avoids problems if the original sources contain
symbolic links (which are resolved in the copy). Thanks to
Michael Lawrence for diagnosis and patch.
o object.size() had slightly too low a size for objects of type "S4".
o symbol() in plotmath expressions was only accepting valid
character strings, which made it impossible to specify symbols
such as aleph (obtained by symbol("\300")) in a UTF-8 locale.
o An event handling issue caused autorepeat functions to
misbehave with tcltk (notably scrollbars).
o plot(sin, -5, 5) gives ylab 'sin(x)' again, where it resulted
in 'x(x)' in 2.6.0. Further, plot(sin) again plots from
[0,1] also in cases where a previously used coordinate system
differs.
o curve() with unspecified 'from', 'to' and 'xlim' now reuses the
previous x limits, and not slightly larger ones.
o It was intended that R code filenames in packages should start
with an ASCII letter or digits (and R CMD INSTALL uses that),
but the test used in R CMD build ([A-Za-z0-9]) was
locale-specific (and excluded t to y in Estonian, for
example). (PR#10351)
o 'R CMD build' could misbehave when faced with files with CRLF
line endings *and* no line ending on the final line of the
file, removing the last byte of the file.
o DF[i, j] failed in 2.6.0 if j was a logical vector selecting a
single column.
o Unix x11() would fail if a valid 'display' was specified but
DISPLAY was unset. (PR#10379)
o postscript() was not always ignoring .Postscript.Options in
the workspace (where it should not have occurred).
o help.search() would give an error if it found a badly
installed package, even if 'package' was not specified.
o tclServiceMode() (package tcltk) now works under Unix-alikes.
(Although documented, it used only to work under Windows.)
o As Mac OS X 10.5.x comes with incompatible /bin/sh shell, we
force SHELL=/bin/bash (which is ok) in that case. [Only for
2.6.x: another solution is used in 2.7.0.]
o Deliberately using malformed source attributes no longer
causes deparsing/printing of functions to crash R. (PR#10437)
o R CMD check and R CMD INSTALL now work with (some) directory
names containing spaces.
o choose(n, k) gave incorrect values for negative n and small k.
o plot.ts(x,y) could use wrong default labels; fixed thanks to
Antonio, Fabio di Narzo.
o reshape() got column names out of sync with contents in some
cases; found by Antonio Fabio Di Narzo.
o ar(x) for short 'x' (i.e. length <= 10) could fail because the
default 'order.max' was >= length(x) which is non-sensical.
o Keyboard events in getGraphicsEvent() could cause stack
imbalance errors. (PR#10453)
CHANGES IN R VERSION 2.6.0
SIGNIFICANT USER-VISIBLE CHANGES
o integrate(), nlm(), nlminb(), optim(), optimize() and uniroot()
now have '...' much earlier in their argument list. This
reduces the chances of unintentional partial matching but
means that the later arguments must be named in full.
o The default type for nchar() is now "chars". This is almost
always what was intended, and differs from the previous default
only for non-ASCII strings in a MBCS locale. There is a new
argument 'allowNA', and the default behaviour is now to throw
an error on an invalid multibyte string if type="chars" or
type="width".
o Connections will be closed if there is no R object referring to
them. A warning is issued if this is done, either at garbage
collection or if all the connection slots are in use.
NEW FEATURES
o abs(), sign(), sqrt(), floor(), ceiling(), exp() and the gamma,
trig and hyperbolic trig functions now only accept one
argument even when dispatching to a Math group method (which
may accept more than one argument for other group members).
o abbreviate() gains a 'method' argument with a new option
"both.sides" which can make shorter abbreviations.
o aggregate.data.frame() no longer changes the group variables
into factors, and leaves alone the levels of those which are
factors. (Inter alia grants the wish of PR#9666.)
o The default 'max.names' in all.names() and all.vars() is now
-1 which means unlimited. This fixes PR#9873.
o as.vector() and the default methods of as.character(),
as.complex(), as.double(), as.expression(), as.integer(),
as.logical() and as.raw() no longer duplicate in most cases
where the object is unchanged. (Beware: some code has been
written that invalidly assumes that they do duplicate, often
when using .C/.Fortran(DUP=FALSE).)
o as.complex(), as.double(), as.integer(), as.logical() and
as.raw() are now primitive and internally generic for
efficiency. They no longer dispatch on S3 methods for
as.vector() (which was never documented). as.real() and
as.numeric() remain as alternative names for as.double().
expm1(), log(), log1p(), log2(), log10(), gamma(), lgamma(),
digamma() and trigamma() are now primitive. (Note that logb()
is not.)
The Math2 and Summary groups (round, signif, all, any, max, min,
sum, prod, range) are now primitive.
See under METHODS PACKAGE below for some consequences for S4 methods.
o apropos() now sorts by name and not by position on the search
path.
o attr() gains an 'exact = TRUE' argument to disable partial
matching.
o bxp() now allows 'xlim' to be specified. (PR#9754)
o C(f, SAS) now works in the same way as C(f, treatment), etc.
o chol() is now generic.
o dev2bitmap() has a new option to go via PDF and so allow
semi-transparent colours to be used.
o dev.interactive() regards devices with the displaylist enabled
as interactive, and packages can register the names of their
devices as interactive via deviceIsInteractive().
o download.packages() and available.packages() (and functions
which use them) now support in 'repos' or 'contriburl' either
file: plus a general path (including drives on a UNC path on
Windows) or a file:/// URL in the same way as url().
o dQuote() and sQuote() are more flexible, with rendering
controlled by the new option 'useFancyQuotes'. This includes
the ability to have TeX-style rendering and directional quotes
(the so-called 'smart quotes') on Windows. The default is to
use directional quotes in UTF-8 locales (as before) and in the
Rgui console on Windows (new).
o duplicated() and unique() and their methods in base gain an
additional argument 'fromLast'.
o fifo() no longer has a default 'description' argument.
fifo("") is now implemented, and works in the same way as file("").
o file.edit() and file.show() now tilde-expand file paths on all
interfaces (they used to on some and not others).
o The find() argument is now named 'numeric' and not 'numeric.':
the latter was needed to avoid warnings about name clashes
many years ago, but partial matching was used.
o stats:::.getXlevels() confines attention to factors since some
users expected R to treat unclass(<a factor>) as a numeric
vector.
o grep(), strsplit() and friends now warn if incompatible sets
of options are used, instead of silently using the documented
priority.
o gsub()/sub() with perl = TRUE now preserves attributes from the
argument x on the result.
o is.finite() and is.infinite() are now S3 and S4 generic.
o jpeg(), png(), bmp() (Windows), dev2bitmap() and bitmap() have
a new argument 'units' to specify the units of 'width' and
'height'.
o levels() is now generic (levels<- has been for a long time).
o Loading serialized raw objects with load() is now considerably
faster.
o New primitive nzchar() as a faster alternative to
nchar(x) > 0 (and avoids having to convert to wide chars in
a MBCS locale and hence consider validity).
o The way old.packages() and hence update.packages() handle
packages with different versions in multiple package
repositories has been changed. The first package encountered
was selected, now the one with highest version number.
o optim(method = "L-BFGS-B") now accepts zero-length parameters,
like the other methods. Also, method = "SANN" no longer
attempts to optimize in this case.
o New options 'showWarnCalls' and 'showErrorCalls' to give a
concise traceback on warnings and errors. showErrorCalls=TRUE
is the default for non-interactive sessions. Option
'showNCalls' controls how abbreviated the call sequence is.
o New options 'warnPartialMatchDollar', 'warnPartialMatchArgs'
and 'warnPartialMatchAttr' to help detect the unintended use
of partial matching in $, argument matching and attr()
respectively.
o A device named as a character string in options(device =) is now
looked for in the grDevices name space if it is not visible
from the global environment.
o pmatch(x, y, duplicates.ok = TRUE) now uses hashing and so is
much faster for large x and y when most matches are exact.
o qr() is now generic.
o It is now a warning to have an non-integer object for
.Random.seed: this indicates a user had been playing with it,
and it has always been documented that users should only save
and restore it.
o New higher-order functions Reduce(), Filter() and Map().
o [g]regexpr() gain an 'ignore.case' argument for consistency with
grep(). (This does change the positional matching
of arguments, but no instances of positional matching beyond
the second were found.)
o relist() utility, an S3 generic with several methods, providing
an 'inverse' for unlist(); thanks to a code proposal from
Andrew Clausen.
o require() now returns invisibly.
o The interface to reshape() has been revised, allowing some
simplified forms that did not work before, and somewhat
improved error handling. A new argument 'sep' has been
introduced to replace simple usages of 'split' (the old
features are retained).
o rmultinom() uses a high-precision accumulator where available,
and so is more likely to give the same result on different
platforms (although it is still possible to get different
results, and the result may differ from previous versions of R).
o row() and col() now work on matrix-like objects such as data
frames, not just matrices.
o Rprof() allows smaller values of 'interval' on machines that
support it: for example modern Linux systems support
interval = 0.001.
o sample() now requires its first argument 'x' to be numeric
(in the sense of is.numeric()) as well as of length 1 and >= 1
before it is regarded as shorthand for 1:x.
o sessionInfo() now provides details about package name spaces
that are loaded but not attached. The output of sessionInfo
has been improved to make it easier to read when it is
inadvertently wrapped after being pasted into an email
message.
o setRepositories() has a new argument 'ind' to allow selections
to be made programmatically.
o sprintf() no longer has a output string length limit.
o storage.mode<- is now primitive, and hence makes fewer copies
of an object (none if the mode is unchanged). It is a little
less general than mode<-, which remains available. (See also
the entry under DEFUNCT below.)
o sweep() gains an argument 'check.margin = TRUE' which warns
about mismatched dimensions.
o The mathematical annotation facility (plotmath) now recognises
a symbol() function which forces the font to be a symbol font.
This allows access to all characters in the Adobe Symbol
encoding within plotmath expressions.
o For OSes that cannot unset environment variables, Sys.unsetenv()
sets the value to "", with a warning.
o New function Sys.which(), an interface to 'which' on
Unix-alikes and an emulation on Windows.
o On Unix-alikes, system(, intern = TRUE) reports on very long
lines that may be truncated, giving the line number of the
content being read.
o termplot() has a default for 'ask' that uses dev.interactive().
It allows 'ylim' to be set, or computed to cover all the
plots to be made (the new default) or computed for each plot
(the previous default).
o uniroot(f, *) is slightly faster for non-trivial f() because it
computes f(lower) and f(upper) only once, and it has new optional
arguments 'f.lower' and 'f.upper' by which the caller can pass these.
o unlink() is now internal, using common POSIX code on all platforms.
o unsplit() now works with lists of dataframes.
o The vcov() methods for classes "gls" and "nlme" have migrated to
package 'nlme'.
o vignette() has a new argument 'all' to choose between showing
vignettes in attached packages or in all installed packages.
o New function within(), which is like with(), except that it
returns modified versions back of lists and data frames.
o X11(), postscript() (and hence bitmap()), xfig(), jpeg(), png()
and the Windows devices win.print(), win.metafile() and bmp()
now warn (once at first use) if semi-transparent colours are
used (rather than silently treating them as fully
transparent).
o New function xspline() to provide base graphics support of
X-splines (cf grid.xspline).
o New function xyTable() does the 2D gridding "computations" used by
sunflowerplot().
o Rd conversion to HTML and CHM now makes use of classes, which
are set in the stylesheets. Editing R.css will change the
styles used for \env, \option, \pkg etc. (CHM styles are set
at compilation time.)
o The documented arguments of '%*%' have been changed to be x
and y, to match S and the implicit S4 generic.
o If members of the Ops group (the arithmetic, logical and
comparison operators) and '%*%' are called as functions,
e.g. '>'(x, y), positional matching is always used. (It used
to be the case that positional matching was used for the
default methods, but names would be matched for S3 and S4
methods and in the case of '!' the argument name differed
between S3 and S4 methods.)
o Imports environments of name spaces are named (as
"imports:foo"), and so are known e.g. to environmentName().
o Package 'stats4' uses lazy-loading not SaveImage (which is now
deprecated).
o Installing help for a package now parses the .Rd file only
once, rather than once for each type.
o PCRE has been updated to version 7.2.
o bzip2 has been updated to version 1.0.4.
o gettext has been updated to version 0.16.1.
o There is now a global CHARSXP cache, R_StringHash. CHARSXPs
are no longer duplicated and must not be modified in place.
Developers should strive to only use mkChar (and mkString) for
creating new CHARSXPs and avoid use of allocString. A new
macro, CallocCharBuf, can be used to obtain a temporary char
buffer for manipulating character data. This patch was
written by Seth Falcon.
o The internal equivalents of as.complex, as.double, as.integer
and as.logical used to handle length=1 arguments now accept
character strings (rather than report that this is
'unimplemented').
o Lazy-loading a package is now substantially more efficient (in
memory saved and load time).
o Various performance improvements lead to a 45% reduction
in the startup time without 'methods' (and one-sixth with -
'methods' now takes 75% of the startup time of a default session).
o The [[ subsetting operator now has an argument 'exact' that
allows programmers to disable partial matching (which will in
due course become the default). The default value is exact=NA
which causes a warning to be issued when partial matching
occurs. When exact = TRUE, no partial matching will be
performed. When exact = FALSE, partial matching can occur and
no warning will be issued. This patch was written by Seth
Falcon.
o Many of the C-level warning / error messages (e.g. from
subscripting) have been re-worked to give more detailed
information on either the location or the cause of the
problem.
o The S3 and S4 Math groups have been harmonized. Functions
log1p(), expm1(), log10() and log2() are members of the S3
group, and sign(), log1p(), expm1(), log2(), cummax(),
cummin(), digamma(), trigamma() and trunk() are members of the
S4 group. gammaCody() is no longer in the S3 Math group.
They are now all primitive.
o The initialization of the random-number stream makes use of the
sub-second part of the current time where available.
Initialization of the 1997 Knuth TAOCP generator is now done
in R code, avoiding some C code whose licence status has been
questioned.
o The reporting of syntax errors has been made more user-
friendly.
METHODS PACKAGE
o Packages using 'methods' have to have been installed in R 2.4.0
or later (when various internal representations were changed).
o Internally generic primitives no longer dispatch S4 methods on
S3 objects.
o load() and restoring a workspace attempt to detect and warn on
the loading of pre-2.4.0 S4 objects.
o Making functions primitive changes the semantics of S4
dispatch: these no longer dispatch on classes based on types
but do dispatch whenever the function in the base name space is
called.
This applies to as.complex(), as.integer(), as.logical(),
as.numeric(), as.raw(), expm1(), log(), log1p(), log2(),
log10(), gamma(), lgamma(), digamma() and trigamma(), as
well as the Math2 and Summary groups.
Because all members of the group generics are now primitive,
they are all S4 generic and setting an S4 group generic does
at last apply to all members and not just those already made
S4 generic.
as.double() and as.real() are identical to as.numeric(), and
now remain so even if S4 methods are set on any of them.
Since 'as.numeric' is the traditional name used in S4,
currently methods must be exported from a NAMESPACE for
'as.numeric' only.
o The S4 generic for '!' has been changed to have signature (x)
(was (e1)) to match the documentation and the S3 generic.
setMethod() will fix up methods defined for (e1), with a
warning.
o The "structure" S4 class now has methods that implement the
concept of structures as described in the Blue Book--that
element-by-element functions and operators leave structure
intact unless they change the length. The informal behavior
of R for vectors with attributes was inconsistent.
o The implicitGeneric() function and relatives have been added to
specify how a function in a package should look when methods are
defined for it. This will be used to ensure that generic versions
of functions in R core are consistent. See ?implicitGeneric.
o Error messages generated by some of the functions in the methods
package provide the name of the generic to provide more
contextual information.
o It is now possible to use setGeneric(useAsDefault = FALSE) to
define a new generic with the name of a primitive function
(but having no connection with the primitive).
o showMethods() has a "smart" default for 'inherited' such that
showMethods(<genfun>, incl = TRUE) becomes a useful short cut.
DEPRECATED & DEFUNCT
o $ on an atomic vector now gives a warning that it is 'invalid'.
It remains deprecated, but may be removed in R >= 2.7.0.
o storage.mode(x) <- "real" and storage.mode(x) <- "single" are
defunct: use instead storage.mode(x) <- "double" and
mode(x) <- "single".
o In package installation, SaveImage: yes is deprecated in
favour of LazyLoad: yes.
o seemsS4Object (methods package) is deprecated in favour of isS4().
o It is planned that [[exact=TRUE]] will become the default in
R 2.7.0.
UTILITIES
o checkS3methods() (invoked by R CMD check) now checks the
arguments of methods for primitive members of the S3 group
generics.
o R CMD check now does a recursive copy on the 'tests' directory.
o R CMD check now warns on non-ASCII .Rd files without an
\encoding field, rather than just on ones that are definitely
not from an ISO-8859 encoding. This agrees with the
long-standing stipulation in 'Writing R Extensions', and
catches some packages with UTF-8 man pages.
o R CMD check now warns on DESCRIPTION files with a non-portable
Encoding field, or with non-ASCII data and no Encoding field.
o R CMD check now loads all the 'Suggests' and 'Enhances'
dependencies to reduce warnings about non-visible objects, and
also emulates standard functions (such as shell()) on
alternative R platforms.
o R CMD check now (by default) attempts to latex the vignettes
rather than just weave and tangle them: this will give a NOTE
if there are latex errors.
o R CMD check computations no longer ignore Rd \usage entries for
functions for extracting or replacing parts of an object, so S3
methods should use the appropriate \method{} markup.
o R CMD check now checks for CR (as well as CRLF) line endings in
C/C++/Fortran source files, and for non-LF line endings in
Makefile[.in] and Makevars[.in] in the package 'src'
directory. R CMD build will correct non-LF line endings in
source files and in the make files mentioned.
o Rdconv now warns about unmatched braces rather than silently
omitting sections containing them. (Suggestion by Bill
Dunlap, PR#9649)
Rdconv now renders (rather than ignores) \var{} inside \code{}
markup in latex conversion.
R CMD Rdconv gains a --encoding argument to set the default
encoding for conversions.
o The list of CRAN mirrors now has a new (manually maintained)
column "OK" which flags mirrors that seem to be OK, only those
are used by chooseCRANmirror(). The now exported function
getCRANmirrors() can be used to get all known mirrors or only
the ones that are OK.
o R CMD SHLIB gains arguments --clean and --preclean to clean up
intermediate files after and before building.
o R CMD config now knows about FC and FCFLAGS (used for F9x
compilation).
o R CMD Rdconv now does a better job of rendering quotes in
titles in HTML, and \sQuote and \dQuote into text on Windows.
C-LEVEL FACILITIES
o New utility function alloc3DArray similar to allocMatrix.
o The entry point R_seemsS4Object in Rinternals.h has not been
needed since R 2.4.0 and has been removed. Use IS_S4_OBJECT
instead.
o Applications embedding R can use R_getEmbeddingDllInfo() to
obtain DllInfo for registering symbols present in the
application itself.
o The instructions for making and using standalone libRmath have
been moved to the R Installation and Administration manual.
o CHAR() now returns (const char *) since CHARSXPs should no
longer be modified in place. This change allows compilers to
warn or error about improper modification. Thanks to Hervé
Pagès for the suggestion.
o acopy_string is a (provisional) new helper function that
copies character data and returns a pointer to memory
allocated using R_alloc. This can be used to create a copy of
a string stored in a CHARSXP before passing the data on to a
function that modifies its arguments.
o asLogical, asInteger, asReal and asComplex now accept STRSXP
and CHARSXP arguments, and asChar accepts CHARSXP.
o New entry point R_GE_str2col listed in R_ext/GraphicsEngine.h
for external graphics device developers.
o doKeybd and doMouseevent are now exported in GraphicsDevice.h.
o R_alloc now has first argument of type 'size_t' to support
64-bit platforms (e.g. Win64) with a 32-bit 'long' type.
o The type of the last two arguments of getMatrixDimnames (non-API
but mentioned in R-exts.texi and in Rinternals.h) has been
changed to 'const char **' (from char **).
o R_FINITE now always resolves to the function call R_finite in
packages (rather than sometimes substituting isfinite). This
avoids some issues where R headers are called from C++ code
using features tested on the C compiler.
o The advice to include R headers from C++ inside extern "C" {}
has been changed. It is nowadays better *not* to wrap the
headers, as they include other headers which on some OSes
should not be wrapped.
o Rinternals.h no longer includes a substantial set of C headers.
All but ctype.h and errno.h are included by R.h which is supposed
to be used before Rinternals.h.
o Including C system headers can be avoided by defining NO_C_HEADERS
before including R headers. This is intended to be used from
C++ code, and you will need to include C++ equivalents such as
<cmath> before the R headers.
INSTALLATION
o The 'test-Lapack' test is now part of 'make check'.
o The 'stat' system call is now required, along with 'opendir'
(which had long been used but not tested for). ('make check'
would have failed in earlier versions without these calls.)
o 'evince' is now considered as a possible PDF viewer.
o 'make install-strip' now also strips the DLLs in the standard
packages.
o Perl 5.8.0 (released in July 2002) or later is now required.
(R 2.4.0 and later have in fact required 5.6.1 or later.)
o The C function 'finite' is no longer used: we expect a C99
compiler which will have 'isfinite'. (If that is missing, we
test separately for NaN, Inf and -Inf.)
o A script/executable 'texi2dvi' is now required on Unix-alikes:
it is part of the texinfo distribution.
o Files texinfo.tex and txi-en.tex are no longer supplied in
doc/manual (as the latest versions have an incompatible
licence). You will need to ensure that your texinfo and/or
TeX installations supply them.
o wcstod is now required for MBCS support.
o There are some experimental provisions for building on Cygwin.
PACKAGE INSTALLATION
o The encoding declared in the DESCRIPTION file is now used as
the default encoding for .Rd files.
o A standard for specifying package license information in the
DESCRIPTION License field was introduced, see 'Writing R
Extensions'. In addition, files LICENSE or LICENCE in a package
top-level source directory are now installed (so putting copies
into the 'inst' subdirectory is no longer necessary).
o install.packages() on a Unix-alike now updates
doc/html/packages.html only if packages are installed to
.Library (by that exact name).
o R CMD INSTALL --clean now runs SHLIB --clean to do the clean
up (unless there is a src/Makefile), and this will remove
$(OBJECTS) (which might have been redefined in Makevars).
R CMD INSTALL --preclean cleans up the sources after a
previous installation (as if that had used --clean) before
attempting to install.
R CMD INSTALL will now run R CMD SHLIB in the 'src' directory
if src/Makevars is present, even if there are no source files
with known extensions.
o If there is a file src/Makefile, src/Makevars is now ignored
(it could be included by src/Makefile if desired), and it is
preceded by etc/Makeconf rather than share/make/shlib.mk.
Thus the makefiles read are R_HOME/etc/Makeconf, src/Makefile
in the package and then any personal Makevars files.
o R CMD SHLIB used to support the use of 'OBJS' in Makevars, but
this was changed to 'OBJECTS' in 2001. The undocumented
alternative of 'OBJS' has finally been removed.
o R CMD check no longer issues a warning about no data sets
being present if a lazyload db is found (as determined by the
presence of Rdata.rdb, Rdata.rds, and Rdata.rdx in the 'data'
subdirectory.
BUG FIXES
o charmatch() and pmatch() used to accept non-integer values for
'nomatch' even though the return value was documented to be
integer. Now 'nomatch' is coerced to integer (rather than the
result being coerced to the type of 'nomatch').
o match.call() no longer 'works' outside a function unless
'definition' is supplied. (Under some circumstances it used
to 'work', matching itself.)
o The formula methods of boxplot, cdplot, pairs and spineplot
now attach 'stats' so that model.frame() is visible where
they evaluate it.
o Date-time objects are no longer regarded as numeric by
is.numeric().
o methods("Math") did not work if 'methods' was not attached.
o readChar() read an extra empty item (or more than one) beyond
the end of the source; in some conditions it would terminate
early when reading an item of length 0.
o Added a promise evaluation stack so interrupted promise
evaluations can be restarted.
o R.version[1:10] now nicely prints.
o In the methods package, prototypes are now inherited for the
.Data "slot"; i.e., for classes that contain one of the basic
data types.
o <data frame>[[i, j]] now works if 'i' is character.
o write.dcf() no longer writes NA fields (PR#9796), and works
correctly on empty descriptions.
o pbeta(x, log.p = TRUE) now has improved accuracy in many cases,
and so have functions depending on it such as pt(), pf() and
pbinom().
o mle() had problems with the L-BFGS-B in the no-parameter case
and consequentially also when profiling 1-parameter models
(fix thanks to Ben Bolker).
o Two bugs fixed in methods that in involve the "..." argument in
the generic function: previously failed to catch methods that
just dropped the "..."; and use of callGeneric() with no arguments
failed in some circumstances when "..." was a formal argument.
o sequence() now behaves more reasonably, although not
back-compatibly for zero or negative input.
o nls() now allows more peculiar but reasonable ways of being called,
e.g., with data=list(<uneven lengths>) or a model without variables.
o match.arg() was not behaving as documented when
several.ok=TRUE (PR#9859), gave spurious warnings when 'arg'
had the wrong length and was incorrectly documented (exact
matches are returned even when there is more than one partial
match).
o The data.frame method for split<-() was broken.
o The test for -D__NO_MATH_INLINES was badly broken and returned
true on all non-glibc platforms and false on all glibc ones
(whether they were broken or not).
o LF was missing after the last prompt when --quiet was used without
--slave. Use --slave when no final LF is desired.
o Fixed bug in initialisation code in 'grid' package for
determining the boundaries of shapes. Problem reported
by Hadley Wickham; symptom was error message:
"Polygon edge not found".
o str() is no longer slow for large POSIXct objects. Its output
is also slightly more compact for such objects; implementation
via new optional argument 'give.head'.
o strsplit(*, fixed=TRUE), potentially iconv() and internal string
formatting is now faster for large strings, thanks to report
PR#9902 by John Brzustowski.
o de.restore() gave a spurious warning for matrices (Ben Bolker)
o plot(fn, xlim=c(a,b)) would not set "from" and "to" properly
when plotting a function. The argument lists to curve() and
plot.function() have been modified slightly as part of the
fix.
o julian() was documented to work with POSIXt origins, but did
not work with POSIXlt ones. (PR#9908)
o Dataset HairEyeColor has been corrected to agree with
Friendly (2000): the change involves the breakdown of the
Brown hair / Brown eye cell by Sex, and only totals over Sex
are given in the original source.
o Trailing spaces are now consistently stripped from \alias{}
entries in .Rd files, and this is now documented. (PR#9915)
o .find.packages(), packageDescription() and sessionInfo()
assumed that attached environments named "package:foo" were
package environments, although misguided users could use such
a name in attach().
o spline() and splinefun() with method = "periodic" could return
incorrect results when length(x) was 2 or 3.
o getS3method() could fail if the method name contained a regexp
metacharacter such as "+".
o help(<a character vector>) now uses the name and not the
value of the vector unless it has length exactly one, so
e.g. help(letters) now gives help on 'letters'.
(Related to PR#9927)
o Ranges in chartr() now work better in CJK locales, thanks to
Ei-ji Nakama.
**************************************************
* *
* 2.5 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.5.1 patched
INSTALLATION
o doc/manual now includes the texinfo support file epsf.tex which
basic TeX installations often omit.
BUG FIXES
o Attempting to do in-memory serialization of an object requiring
more than 1Gb might have failed.
o Using formals<- on a function whose body was NULL worked
incorrectly. (PR#9758)
o logb() is now strictly a wrapper for log(), so if S4 methods
are set on log(), logb() will also dispatch on them.
o conflicts(where=) did not work correctly. (PR#9760)
o log(x, base) was intended to handle complex 'base' even for
real 'x', but there was a typo in the code to do so.
o Syntax errors would sometimes misreport the error context.
o qt(p, df=1) is now also correct for very small p. (PR#9804)
qt(p, df=2) ditto; also is more accurate for 0 < |p - 0.5| << 1.
qt(*, log.p=TRUE) now is finite and monotone (again!) where possible.
o Several functions including those making use of printCoefmat(),
layout() and sortedXyData() now work correctly with
non-default settings of options("OutDec").
o S4 method dispatch for group generics (and %*%) failed to pass
arguments to methods as promises and so in some circumstances
methods could change their arguments. (Seen for the 'Math'
group with package Matrix.)
o The print() method for "ts" now handles quarterly and monthly
series which do not start at the beginning of a quarter or
month respectively.
o Deserializing raw objects saved using save(..., ascii=TRUE)
now works correctly.
o ISOLatin7 encoding for postscript/PDF has been corrected.
(PR#9845)
o rbind(x,y) and cbind(x,y) did not dispatch properly when x and
y had multiple S3-style classes.
o The workaround for seeking on > 2Gb files did not work correctly
on Unix-alike 32-bit systems. (PR#9883)
o We had identical(NaN, NA_real_) != identical(NA_real_, NaN),
spotted by Petr Savicky.
CHANGES IN R VERSION 2.5.1
NEW FEATURES
o density(1:20, bw = "SJ") now works as bw.SJ() now tries a larger
search interval than the default (lower, upper) if it does not
find a solution within the latter.
o The output of library() (no arguments) is now sorted by library
trees in the order of .libPaths() and not alphabetically.
o R_LIBS_USER and R_LIBS_SITE feature possible expansion of
specifiers for R version specific information as part of the
startup process.
o C-level warning calls now print a more informative context,
as C-level errors have for a while.
o There is a new option "rl_word_breaks" to control the way the
input line is tokenized in the readline-based terminal
interface for object- and file-name completion.
This allows it to be tuned for people who use their space bar
vs those who do not. The default now allows filename-completion
with +-* in the filenames.
o If the srcfile argument to parse() is not NULL, it will be added
to the result as a "srcfile" attribute.
o It is no longer possible to interrupt lazy-loading (which was
only at all likely when lazy-loading environments), which
would leave the object being loaded in an unusable state.
This is a temporary measure: error-recovery when evaluating
promises will be tackled more comprehensively in 2.6.0.
INSTALLATION
o 'make check' will work with --without-iconv, to accommodate
building on AIX where the system iconv conflicts with
libiconv and is not compatible with R's requirements.
o There is support for 'DESTDIR': see the R-admin manual.
o The texinfo manuals are now converted to HTML with a style
sheet: in recent versions of makeinfo the markup such as @file
was being lost in the HTML rendering.
o The use of inlining has been tweaked to avoid warnings from
gcc >= 4.2.0 when compiling in C99 mode (which is the default
from configure).
BUG FIXES
o as.dendrogram() failed on objects of class "dendrogram".
o plot(type ="s") (or "S") with many (hundreds of thousands)
of points could overflow the stack. (PR#9629)
o Coercing an S4 classed object to "matrix" (or other basic class)
failed to unset the S4 bit.
o The 'useS4' argument of print.default() had been broken by an
unrelated change prior to 2.4.1. This allowed print() and
show() to bounce badly constructed S4 objects between
themselves indefinitely.
o Prediction of the seasonal component in HoltWinters() was one
step out at one point in the calculations.
decompose() incorrectly computed the 'random' component for a
multiplicative fit.
o Wildcards work again in unlink() on Unix-alikes (they did not
in 2.5.0).
o When qr() used pivoting, the coefficient names in qr.coef() were
not pivoted to match. (PR#9623)
o UseMethod() could crash R if the first argument was not a
character string.
o R and Rscript on Unix-alikes were not accepting spaces in -e
arguments (even if quoted).
o Hexadecimal integer constants (e.g. 0x10L) were not being parsed
correctly on platforms where the C function atof did not
accept hexadecimal prefixes (as required by C99, but not
implemented in MinGW as used by R on Windows). (PR#9648)
o libRlapack.dylib on Mac OS X had no version information and
sometimes an invalid identification name.
o Rd conversion of \usage treated '\\' as a single backslash in
all but latex: it now acts consistently with the other
verbatim-like environments (it was never 'verbatim' despite
the documentation).
\code{\.} is now rendered as '\.' in all formats, as
documented (it was not the case for latex conversion).
codoc() (and checkDocStyle() and checkDocUsage()) now apply
the same transformations to \usage as Rd conversion does,
so {, % and \\ in strings in usages will now be related
correctly to the help files.
o rbind() failed if the only data frame had 0 rows. (PR#9657)
o <a data.frame>[i, j] could sometimes select the wrong column
when j is numeric if there are duplicate column names.
o sample(x, size, replace=TRUE, prob) had a memory leak if
10000 < size <= 100000.
o x <- cbind(1:2); rownames(x) <- factor(c("A",NA)) now longer
segfaults.
o R CMD BATCH no longer assumes Sys.unsetenv() is supported (it
is not on older Solaris systems).
o median() returned a logical result when it was 'NA': it now
returns an NA of appropriate type (e.g. integer or double).
o grep(fixed = TRUE, perl = TRUE) ignored 'fixed', although it
was documented to ignore 'perl'
Same for [g]regexpr and [g]sub.
o getNamespaceExports("base") works again.
o runmed(c(), 1) no longer segfaults.
o qr.coef(QR, b) failed for an LAPACK-produced QR if b was
integer or for an over-determined system.
qr.solve() for an under-determined system produces a
solution with 0 and not NA for columns which are unused.
o segments() was not handling full transparency correctly in PDF.
(PR#9694)
Nor was arrows().
o callGeneric() inside a method with extra arguments {and hence
currently defined via .local()} now works.
o [g]sub(fixed=TRUE, useBytes=FALSE) could substitute in the
wrong place in an MBCS locale.
gregexpr() could give incorrect answers in MBCS locales for
perl = TRUE or fixed = TRUE (unless useBytes = TRUE).
o The legacy quartz() device no longer crashes in locator()
if the user attempts to close the window.
o "CGGStackRestore: gstack underflow" warning is no longer shown
in legacy quartz() device.
o formatC() now limits 'digits' to 50 to avoid problems in
C-level sprintf in some OSes.
o seq.int(x, y, by=z) gave 'x' (and not an error) if
0 > (y-x)/z > -1.
o promptClass() now lists methods, including those for generics in
other attached packages.
o Connection-related functions such as readBin() no longer crash
when supplied with a non-connection object.
o as.character.srcref() didn't handle bad srcref objects cleanly.
o predict.nls() no longer requires 'newdata' to contain exactly
the variable names needed to fit the model: variables used on
the LHS only are no longer required and further variables are
allowed.
o plot.hclust() had a 'out by one' error, and ignored the last
object when computing the window region (and could overrun
arrays).
o deriv() was creating results with double (and not integer) dims.
o The unserialize code (e.g. as called by load()) looked for a
function findPackageEnv() to set a saved package environment.
This was missing, but is now supplied.
o [cr]bind could segfault when creating a list matrix result.
(Reported by Martin Morgan.)
o besselI(x, nu, exp=TRUE) and besselY(x, nu) could give wrong
answers for nu < 0. (Reported by Hiroyuki Kawakatsu.)
o [g]sub could confuse a trailing byte '\' for a backreference
in MBCSs where '\' can occur as a trailing byte (not UTF-8 nor
EUC-JP, but SJIS and the CJK character sets used on Windows).
(PR#9751)
CHANGES IN R VERSION 2.5.0
USER-VISIBLE CHANGES
o apropos(x) and find(x) now both only work for character 'x',
and hence drop all non-standard evaluation behaviour.
o Data frames can have 'automatic' row names which are not
converted to dimnames by as.matrix(). (Consequently, e.g.,
t(.) for such data frames has NULL column names.) This
change leads to memory reductions in several places, but can
break code which assumes character dimnames for data frames
derived from matrices.
No existing R object is regarded as having 'automatic' row
names, and it may be beneficial to recreate such objects via
read.table() or data.frame().
o Using $ on an atomic vector now raises a warning, as does use
on an S4 class for which a method has not been defined.
o The Unix-alike readline terminal interface now does
command-completion for R objects, incorporating the
functionality formerly in package 'rcompletion' by Deepayan
Sarkar. This can be disabled by setting the environment
variable R_COMPLETION=FALSE when starting R (e.g. in
~/.Renviron). (Note that when this is enabled, filename
completion no longer works for file paths containing R
operators such as '+' and '-'.)
NEW FEATURES
o abbreviate() no longer has an 8191 byte limit on the size of
strings it can handle.
o abs(x) now returns integer for integer or logical arguments.
o apropos() has a new argument 'ignore.case' which defaults to
TRUE, potentially matching more than previously, thanks to a
suggestion by Seth Falcon.
o args(), str() and print() now give the argument lists of primitive
functions.
o as.matrix() gains the '...' argument that several packages have
assumed it always had (and S-PLUS has).
o Manipulation of integers as roman numerals via as.roman() in
package utils.
o attr() no longer treats name = NA_character_ as meaning
name = "NA".
o binom.test() now allows a 'fuzz' for calculated integer values
in its x and n arguments.
o boxplot(*, notch = TRUE) now warns when notches are outside
hinges; related to PR#7690.
o New function callCC() providing a downward-only version of
Scheme's call with current continuation.
o capabilities() now has a "profmem" entry indicating whether
R has been compiled with memory profiling.
o colnames<-() and rownames<-() now handle data frames explicitly,
so calling colnames<- on a data frame no longer alters the
representation of the row names.
o commandArgs() has a new 'trailingOnly' argument to be used in
conjunction with --args.
o contour() now passes graphical parameters in '...' to axis()
and box().
o New data set 'crimtab' on Student(1908)'s 3000 criminals.
o cut.default() has a new argument 'ordered_result'.
o .deparseOpts() has two new options: "keepNA" to ensure that
different types (logical, integer, double, character and
complex) of NAs are distinguished, and "S_compatible" to
suppress the use of R-specific features such as 123L and to
deparse integer values of a double vector with a trailing
decimal point.
The 'keepInteger' option now uses the suffix 'L' rather than
as.integer() where possible (unless all entries are NA or
"S_compatible" is also set).
Other deparse options can now be added to "all" (which has not
for some time actually switched on all options).
Integer sequences m:n are now deparsed in that form.
o deparse() and dput() now include "keepInteger" and "keepNA" in
their defaults for the 'control' argument.
o detach() now takes another argument, unload, which indicates
whether or not to unload the package and then only cleans
up the S4 methods if the package successfully unloads.
o There are new constants NA_integer_, NA_real_, NA_complex_ and
NA_character_ to denote NAs of those types, and they will be
used in deparsing in place of as.integer(NA) etc unless
.deparseOpts() includes "S_compatible".
o dev.print() now recognizes 'screen devices' as all those with
an enabled display list, rather than a hard-coded set.
o Objects of class "difftime" are now handled more flexibly. The
units of such objects can now be accessed via a units()
function, which also has a replacement form, and there are
conversion methods to and from numeric, which also allow the
specification of units. Objects of this class can also be
stored in data frames now. A format() method has been added,
and the print method was revised.
o New function environmentName() to give the print name of
environments such as "namespace:base".
This is now used by str().
o New function env.profile() provides R level access to summary
statistics on environments. In a related patch, new.env()
now allows the user to specify an initial size for a hashed
environment.
o file() can read the X11 clipboard selection as "X11_clipboard"
on suitable X11-using systems.
o file("stdin") is now recognized, and refers to the process's
'stdin' file stream whereas stdin() refers to the console.
These may differ, for example for a GUI console, an embedded
application of R or if --file= has been used.
o file_test() is now also available in package utils.
(It is now private in package tools.)
o file.show() gains an 'encoding' argument.
o New functions formatUL() and formatOL() in package utils for
formatting unordered (itemize) and ordered (enumerate) lists.
o The statistics reported when gcinfo(TRUE) are now of the amounts
used (in Mb) and not of the amounts free (which are not really
relevant when there are no hard limits, only gc trigger points).
o New function get_all_vars() to retrieve all the
(untransformed) variables that the default method of
model.frame() would use to create the model frame.
o interaction() has a new argument 'lex.order'.
o initialize() (in methods) now tries to be smarter about
updating the new instance in place, thereby reducing
copying.
o install.packages(dependencies = NA) is a new default, which is
to install essential dependencies when installing from
repositories to a single library. As a result of this change,
update.packages() will install any new dependencies of the
packages it is updating (alongside the package in the same
library tree).
If 'lib' is not specified or is specified of length one and
the chosen location is not a writable directory,
install.packages() offers to create a personal library
directory for you if one does not already exist, and to
install there.
o is.atomic, is.call, is.character, is.complex, is.double (== is.real),
is.environment, is.expression, is.function, is.integer,
is.list, is.logical, is.null, is.object, is.pairlist,
is.recursive, is.single and is.symbol (== is.name) are no
longer internally S3 generic, nor can S4 methods be written
for them.
The "factor" methods of is.integer and is.numeric have been
replaced by internal code.
o Added is.raw() for completeness.
o l10n_info() also reports if the current locale is Latin-1.
o levels<-(), names() and names<-() now dispatch internally for
efficiency and so no longer have S3 default methods.
o .libPaths() now does both tilde and glob expansion.
o Functions lm(), glm() loess(), xtabs() and the default method
of model.frame() coerce their 'formula' argument (if supplied)
to a formula.
o max(), min() and range() now work with character vectors.
o message() has a new argument 'appendLF' to handle messages
with and without newlines. There is a new message class
packageStartupMessage() that can be suppressed separately.
o A new function, method.skeleton() writes a skeleton version of
a call to setMethod() to a file, with correct arguments and
format, given the name of the function and the method signature.
o mode<- and storage.mode<- do slightly less copying.
o nls.control(* , printEval = FALSE, warnOnly = FALSE) are two new
options to help better analyze (non-)convergence of nls(),
thanks to Kate Mullen.
nls() and summary(nls()) now contain more information and also
print information about convergence.
o options(device = ) now accepts a function object as well as
the name of a function.
o pdf() supports new values for 'paper' of "US" (same as
"letter"), "a4r" and "USr" (the latter two meaning rotated to
landscape). postscript() also accepts paper = "US".
o persp() now respects the graphical pars 'cex.axis', 'cex.lab',
'font.axis' and 'font.lab'.
o New faster internal functions pmax.int() and pmin.int() for
inputs which are atomic vectors without classes (called by
pmax/pmin where applicable).
pmin/pmax are now more likely to work with classed objects:
they work with POSIXlt datetimes, for example.
o postscript() now by default writes grey colors (including black
and white) via 'setgray', which gives more widely acceptable
output. There are options to write pure RGB, CMYK or gray via
the new argument 'colormodel'.
o rbind.data.frame() now ignores all zero-row inputs, as well as
zero-column inputs (which it used to do, undocumented). This
is because read.table() can create zero-row data frames with
NULL columns, and those cannot be extended.
o readChar() and writeChar() can now work with a raw vector.
o read.table(), write.table() and allies have been moved to package
utils.
o rgb() now accepts the red, green and blue components in a
single matrix or data frame.
o New utility function RShowDoc() in package 'utils' to find and
display manuals and other documentation files.
o New .row_names_info() utility function finds the number of rows
efficiently for data frames; consequently, dim.data.frame()
has become very fast for large data frames with 'automatic'
row names.
o RSiteSearch() now also allows to search postings of the 'R-devel'
mailing list.
o screeplot() is now (S3) generic with a default method, thanks
to a patch from Gavin Simpson.
o Experimental 'verbose' argument for selectMethod(). Might be
replaced later by a better interface for method selection
inspection.
o Added links to source files to the parsing routines, so that
source() can now echo the original source and comments (rather
than deparsing). This affects example() and Sweave() as well.
o stack() and unstack() have been moved to package utils.
o strptime() now sets the "tzone" attribute on the result if
tz != "".
o str.default() typically prints fewer entries of logical vectors.
o The RweaveLatex driver for Sweave() now supports two new
options: expand=FALSE, to show chunk references in the output,
and concordance=TRUE, to output the concordance between input
and output lines.
o system() now takes the same set of arguments on all platforms,
with those which are not applicable being ignored with a
warning. Unix-alikes gain 'input' and 'wait', and Windows
gains 'ignore.stderr'.
o system.time() and proc.time() now return an object of class
"proc_time" with a print() method that returns a POSIX-like
format with names.
o Sys.getenv() has a new argument 'unset' to allow unset and set
to "" to be distinguished (if the OS does). The results of
Sys.getenv() are now sorted (by name).
o New function Sys.glob(), a wrapper for the POSIX.2 function
glob(3) to do wildcard expansion (on systems which have it,
plus an emulation on Windows).
o Sys.setenv() is a new (and preferred) synonym for Sys.putenv().
The internal C code uses the POSIX-preferred 'setenv' rather
than 'putenv' where the former is available.
o New function Sys.unsetenv() to remove environment variables
(on systems where unsetenv is implemented or putenv can remove
variables, such as on Windows).
o text(), mtext(), strheight(), strwidth(), legend(), axis(),
title(), pie(), grid.text() and textGrob() all attempt to
coerce non-language annotation objects (in the sense of is.object)
to character vectors. This is principally intended to cover
factors and POSIXt and Date objects, and is done via the
new utility function as.graphicsAnnot() in package grDevices.
o tcltk:tk_select.list() now chooses the width to fit the widest item.
o {re,un}tracemem() are now primitives for efficiency and so
migrate from 'utils' to 'base'.
o union(), interect(), setdiff() and setequal() now coerce their
arguments to be vectors (and they were documented only to
apply to vectors).
o uniroot() now works if the zero occurs at one of the ends of
the interval (suggestion of Tamas Papp).
o There is a new function View() for viewing matrix-like
objects in a spreadsheet, which can be left up whilst R is
running.
o New function withVisible() allows R level access to the
visibility flag.
o zip.file.extract() has been moved to package utils.
o A few more cases of subassignment work, e.g. <raw>[] <- <list>
and <vector>[] <- <expression>, with suitable coercion of the LHS.
o There is a warning if \ is used unnecessarily in a string when
being parsed, e.g. "\." where probably "\\." was intended.
("\." is valid, but the same as ".".) Thanks to Bill Dunlap
for the suggestion.
o Introduced the suffix L for integer literals to create
integer rather than numeric values, e.g. 100L, 0x10L, 1e2L.
o Set the parser to give verbose error messages in case of
syntax errors.
o The class "LinearMethodsList" has been extended and will be
used to create list versions of methods, derived from the
methods tables (environments). The older recursive
"MethodsList" class will be deprecated (by the release of
2.5.0 if possible).
o There are more flexible ways to specify the default library
search path. In addition to R_LIBS and .Library, there are
.Library.site (defaults to R_HOME/site-library) and
R_LIBS_USER (defaults to a platform- and version-specific
directory in ~/R). See ?.libPaths for details.
o LAPACK has been updated to version 3.1.0. This should cause
only small changes to the output, but do remember that the sign
of eigenvectors (and principal components) is indeterminate.
o PCRE has been updated to version 7.0.
o Several functions handle row names more efficiently:
- read.table() and read.DIF() make use of integer row names
where appropriate, and avoid at least one copy in assigning
them.
- data.frame() and the standard as.data.frame() methods avoid
generating long dummy row names and then discarding them.
- expand.grid() and merge() generate compact 'automatic' row
names.
- data.matrix() and as.matrix.data.frame() have a new argument
'rownames.force' that by default drops 'automatic' row names.
o <data frame>[i, j] is substantially more memory-efficient when
only a small part of the data frame is selected, especially
when (part of) a single column is selected.
o Command-line R (and Rterm.exe under Windows) accepts the options
'-f filename', '--file=filename' and '-e expression' to follow
other script interpreters. These imply --no-save unless
--save is specified.
o Invalid bytes in character strings in an MBCS now deparse/print
in the form "\xc1" rather than "<c1>", which means they can be
parsed/scanned.
o Printing functions (without source attributes) and expressions
now preserves integers (using the L suffix) and NAs (using
NA_real_ etc where necessary).
o The 'internal' objects .helpForCall, .tryHelp and topicName are
no longer exported from 'utils'.
o The internal regex code has been upgraded to glibc 2.5 (from 2.3.6).
o Text help now attempts to display files which have an \encoding
section in the specified encoding via file.show().
o R now attempts to keep track of character strings which are
known to be in Latin-1 or UTF-8 and print or plot them
appropriately in other locales. This is primarily intended
to make it possible to use data in Western European languages
in both Latin-1 and UTF-8 locales. Currently scan(),
read.table(), readLines(), parse() and source() allow
encodings to be declared, and console input in suitable
locales is also recognized.
New function Encoding() can read or set the declared encodings
for a character vector.
o There have been numerous performance improvements to the data
editor on both Windows and X11. In particular, resizing the
window works much better on X11.
o Packages graphics and grid no longer require grDevices, as
they might be used only with third-party devices.
DEPRECATED & DEFUNCT
o symbol.C() and symbol.For() are defunct, and have been replaced
by wrappers that give a warning.
o Calling a builtin function with an empty argument is now always
an error.
o The autoloading of ts() is defunct.
o The undocumented reserved word GLOBAL.ENV has been removed.
(It was yet another way to get the value of the symbol
.GlobalEnv.)
o The deprecated behaviour of structure() in adding a class when
specifying with "tsp" or "levels" attributes is now defunct.
o unix() is now finally defunct, having been deprecated for
at least seven years.
o Sys.putenv() is now deprecated in favour of Sys.setenv(),
following the POSIX recommendation.
o Building R with --without-iconv is deprecated.
o Using $ on an atomic vector is deprecated (it was previously
valid and documented to return NULL).
o The use of storage.mode<- for other than standard types (and
in particular for value "single") is deprecated: use mode<-
instead.
INSTALLATION
o A suitable iconv (e.g. from glibc or GNU libiconv) is
required. For 2.5.x only you can build R without it by
configuring using --without-iconv.
o There is support again for building on AIX (tested on 5.2 and 5.3)
thanks to Ei-ji Nakama.
o Autoconf 2.60 or later is used to create 'configure'. This
makes a number of small changes, and incorporates the changes
to the detection of a C99-compliant C compiler backported for
2.4.1.
o Detection of a Java development environment was added such that
packages don't need to provide their own Java detection. Newly
added make variables are JAVAC, JAVAH, JAR and JAVA_CPPFLAGS.
R CMD javareconf was updated to look for the corresponding
Java tools as well.
In addition, Java detection honors user-supplied environment
variables JAVA_CPPFLAGS, JAVA_LIBS and JAVA_LD_LIBRARY_PATH.
o Added workaround for reported non-POSIX sh on OSF1. (PR#9375)
o 'make install-strip' now works, stripping the executables and
also the shared libraries and modules on platforms where
'libtool' knows how to do so.
o Building R as a shared library and standalone nmath now
installs pkg-config files 'libR.pc' and 'libRmath.pc' respectively.
o Added test for insufficiently complete implementation of sigaction.
C-LEVEL FACILITIES
o Functions str2type, type2char and type2str are now available in
Rinternals.h.
o Added support for Objective C in R and packages (if available).
o R_ParseVector() has a new 4th argument 'SEXP srcfile' allowing
source references to be attached to the returned expression list.
o Added ptr_R_WriteConsoleEx callback which allows consoles to
distinguish between regular output and errors/warnings.
To ensure backward compatibility it is only used if
ptr_R_WriteConsole is set to NULL.
UTILITIES
o Additional Sweave() internal functions are exported to help
writing new drivers, and RweaveLatexRuncode() is now created
using a helper function (all from a patch submitted by Seth
Falcon).
o The following additional flags are accessible from R CMD config:
OBJC, OBJCFLAGS, JAR, JAVA, JAVAC, JAVAH, JAVA_HOME, JAVA_LIBS
and JAVA_CPPFLAGS.
o R CMD build now takes the package name from the DESCRIPTION
file and not from the directory. (PR#9266)
o checkS3methods() (and hence R CMD check) now checks agreement
with primitive internal generics, and checks for additional
arguments in methods where the generic does not have a '...'
argument.
codoc() now knows the argument lists of primitive functions.
o R CMD INSTALL and R CMD REMOVE now use as the default library
(if -l is not specified) the first library that would be used
if R were run in the current environment (and they run R to
find it).
o There is a new front-end Rscript which can be used for #!
scripts and similar tasks. See help("Rscript") and 'An
Introduction to R' for further details.
o R CMD BATCH (not Windows) no longer prepends
'invisible(options(echo = TRUE))' to the input script. This
was the default unless --slave is specified and the latter is
no longer overridden.
On all OSes it makes use of the -f argument to R, so
file("stdin") can be used from BATCH scripts.
On all OSes it reports proc.time() at the end of the script
unless q() is called with options to inhibit this.
o R CMD INSTALL now prepends the installation directory (if
specified) to the library search path.
o Package installation now re-encodes R files and the NAMESPACE
file if the DESCRIPTION file specifies an encoding, and sets
the encoding used for reading files in preparing for
LazyData. This will help if a package needs to be used in
(say) both latin1 and UTF-8 locales on different systems.
o R CMD check now reports on non-ASCII strings in datasets.
(These are a portability issue, which can be alleviated by
marking their encoding: see 'Writing R Extensions'.)
o Rdiff now converts CRLF endings in the target file, and
converts UTF-8 single quotes in either to ASCII quotes.
o New recommended package 'codetools' by Luke Tierney provides
code-analysis tools. This can optionally be used by 'R CMD
check' to detect problems, especially symbols which are not
visible.
o R CMD config now knows about LIBnn .
o New recommended package 'rcompgen' by Deepayan Sarkar
provides support for command-line completion under the Unix
terminal interface (provided readline is enabled) and the
Windows Rgui and Rterm front ends.
BUG FIXES
o gc() can now report quantities of 'Vcells' in excess of 16Gb on
64-bit systems (rather than reporting NA).
o Assigning class "factor" to an object now requires it has
integer (and not say double) codes.
o structure() ensures that objects with added class "factor" have
integer codes.
o The "formula" and "outer" attributes of datasets 'ChickWeight',
'CO2', 'DNase', 'Indometh', 'Loblolly', 'Orange' and 'Theoph'
now have an empty environment and not the environment used to
dump the datasets in the package.
o Dataset 'Seatbelts' now correctly has class c("mts", "ts").
o str() now labels classes on data frames more coherently.
o Several 'special' primitives and .Internals could return
invisibly if the evaluation of an argument led to the
visibility flag being turned off. These included
as.character(), as.vector(), call(), dim(), dimnames(),
lapply(), rep(), seq() and seq_along(). Others (e.g. dput()
and print.default()) could return visibly when this was not
intended.
o Several primitives such as dim() were not checking the number
of arguments supplied before method dispatch.
o Tracing of primitive functions has been corrected. It should
now be the case that tracing either works or is not allowed
for all primitive functions. (Problems remain if you make a
primitive into a generic when it is being traced. To be fixed
later.)
o max.col() now omits infinite values in determining the
relative tolerance.
o R CMD Sweave and R CMD Stangle now respond to --help and --version
like other utilities.
o .libPaths() adds only existing directories (as it was
documented to, but could add non-directories).
o setIs() and setClassUnion() failed to find some existing
subclasses and produced spurious warnings, now fixed.
o data.frame() ignored 'row.names' for 0-column data frames, and
no longer treats an explicit row.names=NULL differently from
the default value.
o identical() looked at the internal structure of the
'row.names' attribute, and not the value visible at R level.
o abline(reg) now also correctly works with intercept-only lm
models, and abline() warns more when it's called illogically.
o warning() was truncating messages at
getOption("warning.length") - 1 (not as documented), with no
indication. It now appends '[... truncated]'.
o Stangle/Sweave were throwing spurious warnings if options
'result' or 'strip.white' were unset.
o all.equal() was ignoring 'check.attributes' for list and
expression targets, and checking only attributes on raw vectors.
Logical vectors were being compared as if they were numeric,
(with a mean difference being quoted).
o Calculating the number of significant digits in a number was
itself subject to rounding errors for digits >= 16. The
calculation has been changed to err on the side of slightly
too few significant digits (but still at least 15) rather than
far too many. (An example is print(1.001, digits=16).)
o unlink() on Unix-alikes failed for paths containing spaces.
o substr() and friends treated NA 'start' or 'stop' incorrectly.
o merge(x, y, all.y = TRUE) would sometimes incorrectly return
logical columns for columns only in y when there were no
common rows.
o read.table(fn, col.names=) on an empty file returned NULL
columns, rather than logical(0) columns (which is what results
from reading a file with just a header).
o grid.[xy]axis(label=logical(0)) failed.
o expression() was unnecessarily duplicating arguments.
o as.expression(<list>) returned a single-element expression
vector, which was not compatible with S: it now copies lists
element-by-element.
o supsmu(periodic = TRUE) could segfault. (PR#9502, detection
and patch by Bill Dunlap.)
o pmax/pmin called with only logical arguments did not coerce to
numeric, although they were documented to do so (as max/min
do).
o methods() did not know that cbind() and rbind() are internally
generic.
o dim(x) <- NULL removed the names of x, but this was always
undocumented. It is not clear that it is desirable but it is
S-compatible and relied on, so is now documented.
o which(x, arr.ind = TRUE) did not return a matrix (as
documented) if 'x' was an array of length 0.
o C-level duplicate() truncated CHARSXPs with embedded nuls.
o Partial matching of attributes was not working as documented
in some cases if there were more than two partial matches or
if "names" was involved.
o data(package=character(0)) was not looking in ./data as
documented.
o summary.mlm() failed if some response names were "" (as can
easily happen if cbind() is used).
o The postscript() and pdf() drivers shared an encoding list
but used slightly different formats. This caused problems if
both were used with the same non-default encoding in the same
session. (PR#9517)
o The data editor was not allowing Inf, NA and NaN to be entered
in numerical columns. It was intended to differentiate
between empty cells and NAs, but did not do so: it now does
so for strings.
o supsmu() could segfault if all cases had non-finite values.
(PR#9519)
o plnorm(x, lower.tail=FALSE) was returning the wrong tail for
x <= 0. (PR#9520)
o which.min() would not report a minimum of +Inf, and
analogously for which.max(). (PR#9522)
o 'R CMD check' could fail with an unhelpful error when checking
Rd files for errors if there was only one file and that had a
serious error. (PR#9459)
o try() has been reimplemented using tryCatch() to solve two
problems with the original implementation: (i) try() would run
non-NULL options("error") expressions for errors within a try, and
(ii) try() would catch user interrupts.
o str(obj) could fail when obj contained a dendrogram.
o Using <data frame>[, <last column>] <- NULL failed (PR#9565)
o choose(n, k) could return non-integer values for integer n and
small k on some platforms.
o nclass.scott(x) and nclass.FD(x) no longer return NaN when var(x)
or IQR(x) (respectively) is zero.
hist() now allows breaks = 1 (which the above patch will
return), but not breaks = Inf (which gave an obscure error).
o strptime("%j") now also works for the first days of Feb-Dec.
(PR#9577)
o write.table() now recovers better if 'file' is an unopened
connection. (It used to open it for both the column names and
the data.)
o Fixed bug in mosaicplot(sort=) introduced by undocumented
change in R 2.4.1 (changeset r39655).
o contr.treatment(n=0) failed with a spurious error message.
(It remains an error.)
o as.numeric() was incorrectly documented: it is identical to
as.double.
o jitter(rep(-1, 3)) gave NaNs. (PR#9580)
o max.col() was not random for a row of zeroes. (PR#9542)
o ansari.test(conf.int=TRUE, exact=FALSE) failed.
o trace() now works on S3 registered methods, by modifying the
version in the S3 methods table.
o rep(length=1, each=0) segfaulted.
o postscript() could overflow a buffer if used with a long
'command' argument.
o The internal computations to copy complete attribute lists did
not copy the flag marking S4 objects, so the copies no longer
behaved like S4 objects.
o The C code of nlminb() was altering a variable without
duplicating it. (This did not affect nlminb() but would have
if the code was called from a different wrapper.)
o smooth(kind = "3RS3R") (the current default) used .C(DUP =
FALSE) but altered its input argument. (This was masked by
duplication in as.double.)
o The signature for the predefined S4 method for as.character()
was missing '...' .
o readBin(<raw vector>) could read beyond the end of the vector
when size-changing was involved.
o The C entry point PrintValue (designed to emulate auto-printing)
would not find show() for use on S4 objects, and did not have
the same search path (for show(), print() and print() methods)
as auto-printing. Also, auto-printing and print() of S4
objects would fail to find 'show' if the methods name space was
loaded but the package was not attached (or otherwise not in
the search path).
o print() (and auto-printing) now recognize S4 objects even when
'methods' is not loaded, and print a short summary rather than
dump the internal structure.
o Sweave and Stangle had problems due to partial matching of code
chunk names when run with split=TRUE.
o install.packages() on a source package now ensures that
R CMD INSTALL sees the same library search path as
install.packages() did when computing dependencies.
o density() now ensures its 'y' values are non-negative. (PR#8876)
o is.finite() and is.infinite() (and many other primitives)
are not internally generic and so do not support S4 methods,
which can no longer be set. (PR#7951)
o nls(algorithm = "port") now accepts a list 'start' argument,
as for the other methods (and as documented).
o Standard errors from the "ar" method of predict() could be
wrong for the last p predictions for models near
non-stationarity. (PR#9614)
**************************************************
* *
* 2.4 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.4.1 patched
NEW FEATURES
o The Simplified Chinese translations have been completed.
BUG FIXES
o co.intervals() sometimes failed to cover the largest value.
o tempfile() is now random across sessions as well as within a
session. (On some systems it would give the same hex suffix
at the start of each session.)
o Added infinite recursion test to internal function isMissing.
(PR#9426)
o The "Date" and "POSIXt" methods for cut() were not choosing
the first day of the year for breaks = "years".
(In part, PR#9433.)
o R is now able to deparse/print invalid multibyte strings in
MBCS locales (such as UTF-8) using hex escapes. This means
that e.g. demo(Hershey) works in all such locales.
o optimize() could give incorrect answers in some rare problems
with exact symmetry about the midpoint of the interval
supplied. (PR#9438)
o The residuals from an lm() fit with no coefficients but an
offset were incorrect.
o oneway.test() was expecting a literal formula and did not
accept a variable containing a formula.
o The legacy Quartz device (used by console R) displayed its
window outside the screen estate in some dual-head setups.
Now it will be always displayed in the center of the main
screen.
o read.ftable() was not functional on non-seekable connections
such as URLs.
o Some large memory allocations could cause segfaults or
crashes (e.g. followup to PR#9557).
o Sweave() would drop characters from the end of chunk names
ending in "R". (PR#9567)
o library(), i.e. its internal checkConflicts(), now (again) prints
"The following object(s) are masked .." only once per masked package.
o methods:::cbind(x) {one argument} now works, calling cbind2(x)
when 'x' is an S4 object.
CHANGES IN R VERSION 2.4.1
INSTALLATION
o The extraction of info from Subversion for an SVN checkout now
also works for svn >= 1.4.0. However, on Windows the 'Last
Changed Date' will be in the local timezone, and not in GMT as
previously.
o configure uses code borrowed from autoconf 2.60 to try harder to
ensure that a C99-compliant compiler is used. (It does so by
appending to CC.) This avoids problems with systems such as FC5
which override CFLAGS and thereby lose flags such as -std=gnu99.
NEW FEATURES
o rainbow(), heat.colors(), terrain.colors(), topo.colors() and
cm.colors() all gain an 'alpha' argument to be passed to hsv().
o dput() will give an incorrect representation of the row names
of a data frame with integer row names. This is now corrected
when the object is recreated.
C-LEVEL FACILITIES
o Using STRICT_R_HEADERS applies to more reported clashes with
Windows headers, including Calloc and Realloc. These and
Free need to be prefixed by R_ when STRICT_R_HEADERS is defined.
DEPRECATED & DEFUNCT
o The previously undocumented behaviour of structure() in adding a
class when specifying "tsp" or "levels" attributes is now
deprecated (with a warning).
BUG FIXES
o Fixed warning() to use .dfltWarn intead of .dfltStop for default
handling (PR#9274).
o R would slow down when the product of the length of a vector and
the length of a character vector used to subset it exceeded 2^31.
(PR#9280)
o merge() now allows zero-row data frames.
o add1.lm() had been broken by other changes for weighted fits.
o axis.POSIXct() would sometimes give the wrong labels.
o Help for a method call would fail. (PR#9291)
o gzfile() returned an object of class "file" not "gzfile". (PR#9271)
o load()ing from a connection had a logic bug in when it closed
the connection. (PR#9271)
o The lowess() algorithm is unstable if the MAD of the residuals
becomes (effectively) zero: R now terminates the iterations at
that point. (This may result in quite different answers.)
The 'delta' argument was incorrectly documented. (PR#9264)
o abbreviate() would only work for strings of up to 8191 bytes,
but this was not checked. Now longer strings are errors.
o Drawing X11 rotated text was buggy for VERY small (negative)
angle of rotation. Reported by Ben Bolker. (PR#9301)
o The X11 data editor would crash in an MBCS locale if R was
compiled with FC's CFLAGS that add buffer overflow and
stack-smashing detection.
o rect() was not accepting border=NA in some cases involving
cross-hatching.
o Fixes to S4 group generics to ensure that the correct number of
active arguments are in the signature of the group and all
members. Also a fix to keep the 'groupMembers' slot up to date.
o S4 group generic "Logic" (with '&', '|', but not '!') has been
created, following the green book (apart from '!').
o removeClass() now takes care to remove any subclass references
to the deleted class.
o mle() (in stats4) might not have worked as intended when the
order of parameters in 'start' differed from that in the
log-likelihood. (PR#9313)
o dotchart() now properly restores par() settings after itself.
o system() on Mac OS X was blocking arbitrary signals during the
call although only SIGPROF was meant to be blocked.
o methods cached via callNextMethod() and (sometimes) as() were
being cached as directly specified although in fact they were
inherited. Caused problems in later search for inherited methods.
o str() works properly for method definitions and other S4-classed
function objects.
o JAVA_LIBS are now set correctly on MacOS X.
o Fix null-termination issue suspected of causing crash with Fedora
Extra RPMS (PR#9339, Justin Harrington, analysis and fix from Bill
Dunlap).
o Name spaces restored via a saved session silently failed to cache
their methods because the methods package was not yet
attached. Fixed by attaching methods before restoring data.
o rbind()ing a list to a data frame generated invalid row names,
which were an error in 2.4.0. (PR#9346)
o boxplot.stats(x) now returns the correct minimum instead of an
error for x <- c(1,Inf,Inf,Inf), and hence boxplot(x) "works".
o promptClass() now uses \linkS4class{<ClassName>} instead of
of \link{<ClassName>-class}.
o gc() no longer reports nonsense values for the number of used
Vcells if the true value exceeds 2^31 (and hence over 16Gb of
heap is in use): it now reports NA. (PR#9345)
o rapply() now detects more user errors in supplying arguments. (PR#9349)
o boxplot() was ignoring argument 'boxfill'. (PR#9352)
o plot.lm(which = 6, id.n = 0) did not work. (PR#9333)
o .deparseOpts("delayPromises") was not matching the C code,
returning 64 rather than 32.
o bxp() could use partial matching on 'pars' when finding
defaults for some of its parameters, e.g. a setting of 'cex.axis'
in 'pars' or inline was used to set a default for 'outcex'.
o acf() now allows lag.max = 0 except when type="partial", and
forces the lag 0 autocorrelation to 1. (PR#9360)
o hist(*, include.lowest=., right=., plot=FALSE) does not warn
anymore, (PR#9356) and more.
o Some bugs in caching superclass/subclass relations and in
removing those relations on detach and on removeClass() have
been fixed.
o readBin() could return one too many strings if 'n' was an
over-estimate. (PR#9361)
o A request for an opaque colour in the pdf() device after a
translucent one did not set the transparency back to opaque in
2.4.0.
Semi-transparent background colours were not being plotted on
the pdf() device.
o plot.lm(which=5) in the case of constant leverage re-ordered
the factor levels but not the residuals, so the labelling by
factor level was often incorrect.
o packBits() was not accepting a logical argument. (PR#9374)
o make install was omitting doc/FAQ and doc/RESOURCES.
o A two-sample t.test(x, y, var.equal=TRUE) did not allow one of the
groups to be of size one.
o The "ts" method for print() failed on some corrupted objects
of class "ts", e.g. those without a "tsp" attribute.
o structure() reordered the "class" value given if there was a
"tsp" value specified.
o pairs() now does pass appropriate parts of '...' to the
'diag.panel' argument. (PR#9384)
o plot.lm() was using an incorrect estimate of dispersion for
some GLMs (including family=binomial and family=poisson).
(PR#9316)
o Subsetting operators were setting R_Visible too early, so
assignments in arguments could make the result invisible.
(PR#9263)
o The tk-GUI was displaying a warning due to an extra comma in
the list of manuals (PR#9396)
o packageDescription() now gives an explicit error on a corrupt
DESCRIPTION file.
o There was a scoping issue with tcltk callbacks given as
unevaluated expressions. This has only been partially fixed, a
complete fix probably requires redesign.
o trace() had its return value documented incorrectly and was
sometimes visible when it should not have been.
o pchisq() would sometimes use the wrong tail when calculating
non-central probabilities with lower.tail = FALSE. (PR#9406)
o rm() could remove the wrong objects when passed an expression.
(PR#9399) Now only names are allowed in the '...' argument,
and the incorrect documentation of what happened with
character objects is corrected.
o url() was not supporting 'encoding' except on file:// URLs.
CHANGES IN R VERSION 2.4.0
USER-VISIBLE CHANGES
o The startup message now prints first the version string and
then the copyright notice (to be more similar to R --version).
o save() by default evaluates promise objects. The old behaviour
(to save the promise and its evaluation environment) can be
obtained by setting the new argument 'eval.promises' to FALSE.
(Note that this does not apply to promises embedded in
objects, only to top-level objects.)
o The functions read.csv(), read.csv2(), read.delim(),
read.delim2() now default their 'comment.char' argument to "".
(These functions are designed to read files produced by other
software, which might use the # character inside fields, but
are unlikely to use it for comments.)
o The bindings in the base environment/name space (currently the
same thing) are now locked. This means that the values of
base functions cannot be changed except via
assignInNamespace() and similar tricks.
o [[ on a factor now returns a one-element factor (and not an
integer), as.list() on a factor returns a list of one-element
factors (and not of character vectors), and unlist() on a list
of factors returns a factor (and not an integer vector).
These changes may affect the results of sapply() and lapply()
applied to factors.
o mauchly.test() now returns the W statistic (for comparability
with SAS and SPSS), rather than the z (which was accidentally
not named in the output)
o sort(x, decreasing = FALSE, ...) is now a generic function.
This means that 'partial' is no longer the second argument,
and calls which used positional matching may be incorrect: we
try to detect them.
o See the section on 'Changes to S4 methods': all packages
depending on 'methods' need to be re-installed.
NEW FEATURES
o agrep(), grep(), strwrap(), strtrim(), substr() and
related functions now coerce arguments which should be
character via as.character() rather than internally (so method
dispatch takes place, e.g. for factors).
chartr(), charfold(), tolower() and toupper() now coerce their
main argument if necessary to a character vector via
as.character().
Functions which work element-by-element on character vectors
to give a character result now preserve attributes including
names, dims and dimnames (as suggested by the Blue Book
p. 144). Such functions include charfold(), chartr(), gsub(),
strtrim(), sub(), substr(), tolower() and toupper(). (Note
that coercion of a non-character argument may lose the
attributes.)
agrep(value = TRUE) preserves names for compatibility with
grep().
nchar() has always preserved dims/dimnames (undocumented
before) and now also preserves names.
o .Deprecated and .Defunct take a new parameter, msg, that allows
for the specification of the message printed and facilitates
deprecation of calling sequences etc.
o .Fortran() will map 'name' to lower case, and will work with
'name' containing underscores.
o The default is now .saveRDS(compress = TRUE)
o The :: operator now also works for packages without name spaces
that are on the search path.
o [[ on a list does not duplicate the extracted element unless
necessary. (It did not duplicate in other cases, e.g. a
pairlist.)
o argsAnywhere() works like args() on non-exported functions.
o as.data.frame() gains a '...' argument.
o Added an as.data.frame() method for class "ftable".
o as.list(<an expression>) is now handled by internal code and
no longer loses attributes such as names.
as.list(<a list>) no longer duplicates (unnecessarily).
o as.POSIX[cl]t can now convert character strings containing
fractional seconds.
o attach() can now attach a copy of an environment.
o available.packages() and installed.packages() gain a 'fields'
argument thanks to Seth Falcon.
o axis.POSIXct() uses a different algorithm for ranges of 2 to 50
days that will mark days at midnight in the current timezone
(even if the graph crosses a DST change).
o body<-() and formals<-() default to envir = environment(fun),
that is they do not by default change the environment.
(Previously they changed it to parent.frame().)
o New function combn(x, m, ..) for computing on all combinations of
size 'm' (for small 'm' !).
o The cumxxx() functions now handle logical/integer arguments
separately from numeric ones, and so return an integer result
where appropriate.
o data.frame() has a new argument 'stringsAsFactor'. This and
the default for read.table(as.is=) are set from the new global
option 'stringsAsFactors' via the utility function
default.stringsAsFactors().
o dev.interactive() now has an optional argument 'orNone'.
o df() now has a noncentrality argument 'ncp', based on a
contribution by Peter Ruckdeschel.
o example() gains an argument 'ask' which defaults to "TRUE when
sensible", but the default can be overridden by setting option
'example.ask'.
o expand.grid() now has an argument 'KEEP.OUT.ATTRS' which can
suppress (the potentially expensive) "out.attrs" attribute. It no
longer returns an extraneous 'colnames' attribute.
o The subset and subassign methods for factors now handle factor
matrices, and dim() can be set on a factor.
o There is now a format() method for class "ftable".
o head(x, n) and tail(x, n) now also work for negative arguments,
thanks to Vincent Goulet.
o head.matrix() and tail.matrix() are no longer hidden, to be used
for building head() and tail() methods for other classes.
o If help() finds multiple help files for a given topic, a menu
of titles is used to allow interactive choice.
o help.search() now rebuilds the database if 'package' specifies a
package not in the saved database.
o hist(*, plot = FALSE) now warns about unused arguments.
o history() gains a 'pattern' argument as suggested by Romain
Francois.
o integer(0) now prints as that rather than "numeric(0)" (it
always deparsed as "integer(0)").
o interaction(..., drop=TRUE) now gives the same result as
interaction(...)[,drop=TRUE] (it used to sometimes give a
different order for the levels).
o lag.plot() produces a conventional plot (not setting mfrow) if
only one plot is to be produced.
o lapply() does much less copying. Vector X are handled without
duplication, and other types are coerced via as.list(). (As a
result, package 'boot' runs its examples 4% faster.)
lapply(<a pairlist>) now coerces to a list (rather than traverse
the pairlist from the beginning for each item).
o legend() has new parameters 'box.lwd' and 'box.lty'.
o lines() gains a simple method for isoreg() results.
o load() no longer coerces pairlists to lists (which was
undocumented, but has been happening since 1998).
o make.link() now returns an object of class "link-glm".
The GLM families accept an object of this class for their
'link' argument, which allows user-specified link functions.
Also, quasi() allows user-specified variance functions.
o mapply() uses names more analogously to lapply(), e.g..
o matplot() now accepts a 'bg' argument similarly to plot.default() etc.
o median() is now generic, and its default method uses mean()
rather than sum() and so is more widely applicable (e.g. to dates).
o Dummy functions memory.size() and memory.limit() are available
on Unix-alikes, for people who have not noticed that documentation
is Windows-specific.
o merge() works more efficiently when there are relatively few
matches between the data frames (for example, for 1-1
matching). The order of the result is changed for 'sort = FALSE'.
o merge() now inserts row names as a character column and not a
factor: this makes the default sort order more comprehensible.
o Raw, complex and character vectors are now allowed in model
frames (there was a previously undocumented restriction to
logical, integer and numeric types.). Character vectors in a
formula passed to model.matrix() are converted to factors and
coded accordingly.
o modifyList() utility, typically for housekeeping nested lists.
o x <- 1:20; y <- rnorm(x); nls(y ~ A*exp(-x^2/sig)) no longer
returns an unhelpful error message. In this and similar cases, it
now tries a wild guess for starting values.
o Ops.difftime() now handles unary minus and plus.
o Ops.Date() and Ops.POSIXt() now allow character arguments
(which are coerced to the appropriate class before comparison,
for Ops.POSIXt() using the current time zone).
o There is a new option(max.contour.segments = 25000) which can be
raised to allow extremely complex contour lines in contour()
and contourLines(). (PR#9205)
o options(max.print = N) where N defaults to 99999 now cuts printing
of large objects after about N entries. print(x, ..., max = N)
does the same for the default method and those building on
print.default().
options("menu.graphics") controls if graphical menus should be
used when available.
options("par.ask.default") allows the default for par("ask")
to be set for a newly-opened device. (Defaults to FALSE, the
previous behaviour.)
The way option("papersize") is set has been changed. On
platforms which support the LC_PAPER locale category, the
setting is taken first from the R_PAPERSIZE environment
variable at run time, then from the LC_PAPER category
("letter" for _US and _CA locales and "a4" otherwise). On
other platforms (including Windows and older Unixen), the
choice is unchanged.
o package.skeleton() gains arguments 'namespace' and
'code_files'.
o par(ask=TRUE) now only applies to interactive R sessions.
o parse() now returns up to 'n' expressions, rather than fill
the expressions vector with NULL. (This is now compatible
with S.)
o The 'version' argument for pdf() is now increased
automatically (with a warning) if features which need a higher
level are used.
o pie() now allows expressions for 'labels', and empty slices.
o There is a new '%.%' operator for mathematical annotations
(plotmath) which draws a centred multiplication dot
(a \cdot in LaTeX), thanks to Uwe Ligges.
o predict.lm() gains a 'pred.var' argument. (Wishlist PR#8877.)
o print.summary.{aov,glm,lm,nls} and print.{aov,glm} make use of
naprint() to report when na.action altered the model frame.
o print.table(T, zero.print=ch) now also replaces 0 by ch when T is
non-integer with integer entries.
o Recursive rapply() which is similar to lapply but used
recursively and can restrict the classes of elements to which
it is applied.
o r2dtable() has been moved to package 'stats'.
o New function read.DIF() to read Data Interchange Format files,
and (on Windows) this format from the clipboard.
o New experimental function readNEWS() to read R's own "NEWS" file
and similarly formatted ones.
o readLines() has a new argument 'warn' to suppress warnings:
the default behaviour is still to warn.
o reg.finalizer() has a new argument 'onexit' to parallel the
C-level equivalent R_RegisterFinalizerEx.
o rep() is now a primitive function and under some conditions
very much faster: rep.int() is still a little faster (but does
less). (Because it is primitive there are minor changes to the
call semantics: see the help page.)
o The 'row.names' of a data frame may be stored internally as an
integer or character vector. This can result in considerably
more compact storage (and more logical row names from rbind)
when the row.names are 1:nrow(x). However, such data frames
are not compatible with earlier versions of R: this can be
ensured by supplying a character vector as 'row.names'.
row.names() will always return a character vector, but direct
access to the attribute may not.
The internal storage of row.names = 1:n just records 'n', for
efficiency with very long vectors.
The "row.names" attribute must be a character or integer
vector, and this is now enforced by the C code.
o The "data.frame" and "matrix" methods for rowsum() gain an 'na.rm'
argument.
o Experimental support for memory-use profiling via Rprof(),
summaryRprof(), Rprofmem() and tracemem().
o save.image() [also called by sys.save.image() and hence from q()]
now defaults to saving compressed binary images. To revert to
the previous behaviour set option "save.image.defaults": see
?save.image.
o There is a new primitive seq.int() which is slightly more
restricted than seq() but often very much faster, and new
primitives seq_along() and seq_len() which are faster still.
o serialize(connection = NULL) now returns a raw vector (and not
a character string). unserialize() accepts both old and new
formats (and has since 2.3.0).
o setwd() now returns the previously current directory (invisibly).
o The function sort() is now sort.int(), with a new generic
function sort() which behaves in the same way (except for the
order of its argument list) for objects without a class, and
relies on the '[' method for objects with a class (unless a
specific method has been written, as it has for class "POSIXlt").
o sort.list() now implements complex vectors (PR#9039), and how
complex numbers are sorted is now documented.
o spline() and splinefun() now follow approx[fun] to have an argument
'ties = mean' which makes them applicable also when 'x' has
duplicated values.
o str(x) does not print the S3 "class" attribute when it is the
same as 'mode' (which is printed anyway, possibly abbreviated)
and it puts it beside mode for atomic objects such as S3 class
"table".
o str(<data.frame>) now outputs 'data.frame' instead of
`data.frame'; this may affect some strict (Package) tests.
o str() now takes also its defaults for 'vec.len' and 'digits.d'
from options('str') which can be set by the new strOptions().
o symnum() has a new argument 'numeric.x' particularly useful for
handling 0/1 data.
o Sys.getlocale() and Sys.setlocale() support LC_MESSAGES,
LC_PAPER and LC_MEASUREMENT if the platform does.
o Sweave has a new options 'pdf.encoding' and 'pdf.version' for
its Rweave driver.
o The character vector used by an output textConnection() has
a locked binding whilst the connection is open.
There is a new function textConnectionValue() to retrieve the
value of an output textConnection().
o traceback() gains a 'max.lines' argument.
.Traceback is no longer stored in the workspace.
o warning(immediate. = TRUE) now applies to
getOption("warn") < 0 and not just == 0.
o warnings() is now an accessor function for 'last.warning' (which
is no longer stored in the workspace) with a print() method.
o The internal internet download functions have some new
features from libxml 2.6.26.
o There is an option "HTTPUserAgent" to set the User Agent in R
download requests etc. Patch from S. Falcon.
o PCRE has been updated to version 6.7.
o The C function substituteList now has tail recursion expanded
out, so C stack overflow is less likely. (PR#8141, fix by
Kevin Hendricks)
o The (somewhat soft) 1023/4 byte limit on command lines is now
documented in 'An Introduction to R'.
o The maximum number of open connections has been increased from
50 to 128.
o There is a new manual 'R Internals' on R internal stuctures
plus the former appendices of 'Writing R Extensions'.
o The autoloads introduced at the package re-organization have been
almost completely removed: the one that remains is for ts().
o The setting of the various Java configuration variables has been
improved to refer to JAVA_HOME, and they are now documented in
the R-admin manual.
o It is (again) possible to calculate prediction intervals from
"lm" objects for the original data frame, now with a warning
that the intervals refer to future observations. Weighted
intervals have also been implemented, with user-specifiable
weights. Warnings are given in cases where the default
behaviour might differ from user expectations. See the
?predict.lm for details.
CHANGES TO S4 METHODS
o The default prototype object for S4 classes will have its own
internal type in 2.4.0, as opposed to being an empty list (the
cause of several errors in the code up to 2.3.1). Note that old
binary objects, including class definitions, will be
inconsistent with the type, and should be recreated.
o S4 method dispatch has been completely revised to use cached
generic functions and to search for the best match among
inherited methods. See ?Methods and
http://developer.r-project.org/howMethodsWork.pdf
o Objects created from an S4 class are now marked by an internal flag,
tested by isS4() in R and by macro IS_S4_OBJECT() in C. This
is an efficient and reliable test, and should replace all
earlier heuristic tests.
o Some changes have been made to automatic printing of S4
objects, to make this correspond to a call to show(), as per
'Programming with Data'.
o S4 generic and class definitions are now cached when the related
package is loaded. This should improve efficiency and also
avoid anomalous situations in which a class or generic cannot
be found.
o trace() now creates a new S4 class for the traced object if
required. This allows tracing of user-defined subclasses of
"function".
DEPRECATED & DEFUNCT
o The re-named tcltk functions tkcmd, tkfile.tail, tkfile.dir,
tkopen, tkclose, tkputs, tkread are now defunct.
o Argument 'col' of bxp() has been removed: use 'boxfill'.
o Use of NULL as an environment is now an error.
o postscriptFont() is defunct: use Type1Font().
o La.chol() and La.chol2inv() are defunct (they were the same as
the default options of chol() and chol2inv).
o La.svd(method = "dgesvd") is defunct.
o Files install.R and R_PROFILE.R in packages are now ignored
(with a warning).
o The following deprecated command-line options to INSTALL have
been removed (use the fields in the DESCRIPTION file instead):
-s --save --no-save --lazy --no-lazy --lazy-data --no-lazy-data
o Graphical parameter 'tmag' is obsolete.
o mauchley.test() (package 'stats') is now defunct.
o symbol.C() and symbol.For() are deprecated. They are required in
S for use with is.loaded(), but are not so required in R.
o load()ing an object saved in one of the formats used prior to
R 1.4.0 is deprecated. Such objects should be re-saved in the
current format.
o save(version = 1) is now deprecated.
C-LEVEL FACILITIES
o The convenience function ScalarLogical now coerces all
non-zero non-NA values to TRUE.
o The vector accessor functions such as INTEGER, REAL and
SET_VECTOR_ELT now check that they are called on the
correct SEXPTYPE (or at least on a compatible one). See
`Writing R Extensions' for the details and for a stricter
test regime.
o It is no longer possible to pass list variables to
.C(DUP = FALSE): it would have given rise to obscure garbage
collection errors.
o allocString is now a macro, so packages using it will need to
be reinstalled.
o R_ParseVector was returning with object(s) protected in the
parser if the status was PARSE_INCOMPLETE or PARSE_ERROR.
o There is a new function Rf_endEmbeddedR to properly terminate
a session started by Rf_initEmbeddedR, and both are now
available on Windows as well as on Unix-alikes. These and
related functions are declared in a new header <Rembedded.h>.
If R_TempDir is set when embedded R is initialized it is
assumed to point to a valid session temporary directory: see
`Writing R Extensions'.
o There is a new interface allowing one package to make C routines
available to C code in other packages. The interface consists
of the routines R_RegisterCCallable and R_GetCCallable. These
functions are declared in <R_ext/Rdynload.h>. This interface
is experimental and subject to change.
In addition, a package can arrange to make use of header
files in another (already installed) package via the
'LinkingTo' field in the DESCRIPTION file: see 'Writing R
Extensions'.
UTILITIES
o R CMD SHLIB now handles (as linker commands) -L*, -l* and *.a.
o R CMD check now:
- warns if there are non-ASCII characters in the R code (as
these will likely be syntax errors in some locale).
- tests Rd cross-references by default, and tests for
(syntactically) valid CITATION metadata.
- tests that the package can be loaded, and that the package
and name space (if there is one) can each be loaded in
startup code (before the standard packages are loaded).
- tests for empty 'exec' or 'inst' directories.
- checks if $(FLIBS) is used when $(BLAS_LIBS) is.
- checks that all packages (except non-S4-using standard
packages) used in ::, :::, library() and require() calls are
declared in the DESCRIPTION file, and 'methods' is declared if
S4 classes or methods are set.
- throws an error if the standard packages 'methods' and
'stats4' are imported from in the NAMESPACE file and not
declared in the DESCRIPTION file.
o The test script produced by massage-Examples.pl no longer
creates objects in the base environment.
o New utilties R CMD Stangle and R CMD Sweave for extracting S/R
code from and processing Sweave documentation, respectively.
o The DESCRIPTION file of packages may contain an 'Enhances:'
field.
o An R CMD javareconf script has been added to allow Java
configuration to be updated even after R has been installed.
INSTALLATION
o The C function realpath (used by normalizePath()) is hidden on
some systems and we try harder to find it.
o There is a new option --enable-BLAS-shlib, which compiles the
BLAS into a dynamic library -lRblas and links against that.
For the pros and cons see the R-admin manual.
The defaults are now --without-blas (so you have explicitly to
ask for an external BLAS), and --enable-BLAS-shlib unless
a usable external BLAS is found or on AIX or on MacOS X 10.2
and earlier.
o MacOS X did not like having LSAME in both BLAS and LAPACK
libraries, so it is no longer part of the R-internal LAPACK.
We now require an external BLAS to provide LSAME: it seems
that nowadays all do.
o The configure test for 'whether mixed C/Fortran code can be
run' has been improved as on one system that test passed but
the Fortran run-time library was broken.
o A precious configure variable DEFS can be set to pass defines
(e.g. -DUSE_TYPE_CHECKING_STRICT) to C code when compiling R.
o There is now a test for visible __libc_stack_end on Linux
systems (since it is not visible on some recent glibc's
built from the sources).
o MacOS X 10.4 and higher now use two-level namespaces, single
module in a shared library and allow undefined symbols to be
resolved at run-time. This implies that common symbols are now
allowed in package libraries. --enable-BLAS-shlib is supported
for internal BLAS, external BLAS framework and external static
BLAS. An external dynamic library BLAS is NOT supported. (But
it can be easily used by replacing internal BLAS library file
later.) MacOS X < 10.4 does not support --enable-BLAS-shlib.
o Dynamic libraries and modules use a flat namespace on MacOS X
10.4 and higher if either Xcode tools don't support dynamic
lookup (Xcode < 2.3) or the FORCE_FLAT_NAMESPACE environment
variable is set. (The latter was introduced temporarily for
testing purposes and may go away anytime.)
o configure now defaults to 'run-time linking' on AIX
(and AIX < 4.2 is no longer allowed), using -bexpall rather
than export/import files. If this works, it allows R to be
built in the same way as other Unix-alikes, including with R
as a shared library and with a shared BLAS.
o The "mac.binary" package type now defaults to universal
binary. If a repository supports architecture-specific Mac
binaries, they can be requested by using "mac.binary.xxx" in
contrib.url(), where xxx is the desired architecture.
o There is a new configure option --enable-memory-profiling to
enable memory profiling with tracemem, Rprof, Rprofmem.
BUG FIXES
o The name of a Fortran symbol reported to be missing by
.Fortran() is now the actual name. (What was reported to be
an 'entry point' was missing the common leading underscore.)
o print() on a MBCS character string now works properly a
character at a time rather than a byte at time. (This does
not affect MBCSs like UTF-8 and the Windows DBCSes which have
non-ASCII lead bytes and always worked correctly.)
o glm() now recalculates the null deviance whenever there is an
offset (even if it is exactly zero to avoid a discontinuity in
that case, since the calculations with and without offset are
done by different algorithms).
o Amongst families, quasi() accepted an expression for link and
no other did. Now all accept an expression which evaluates to
a one-element character vector (although e.g. 'logit' is taken
as a name and not an expression).
o trace() now accepts arguments where= and signature= for the
old-style trace (no tracer or exit, edit==FALSE) and just
prints a message on entry. Also the undocumented feature of
where=function now works for generic functions as well.
o callNextMethod() failed for recursive use when the methods had
nonstandard argument lists. Now enforces the semantic rule
that the inheritance is fixed when the method containing the
callNextMethod() is installed. See Details in the documentation.
o UseMethod() looked for the defining environment of 'generic' as
if it were the current function, although some functions are
generic for methods of a different generic.
Lookup for S3 methods is confined to functions: previously a
non-function 'fun.class' could have masked a function of the
same name.
o Line types (lty) specified as hex strings were documented not to
allow zero, but some devices accepted zero and handled it in a
device-dependent way. Now it is an error on all devices.
(PR#8914)
o Subassignment for a time series can no longer extend the series:
it used to attempt to but failed to adjust the tsp attributes.
Now window() must be used.
o Function AIC() in package 'stats4' was not dispatching correctly
on S4 classes via logLik() because of name space issues.
o Subsetting LANGSXPs could break the call-by-value illusion.
(PR#7924) (patch from Kevin Hendricks).
o parse() with n > 1 gave a syntax error if fewer than n statements
were available.
o parse() with n > 1 gave strange results on some syntax errors.
(PR#8815)
o lag.plot() now respects graphical parameters for the axes.
o Using a wrong link in family() now gives more consistent error
messages.
o sort.list(method="radix") works on factors again.
o object.size() is more accurate for vector objects (it takes into
account the smaller header and also the fixed sizes used in
the node classes for small vector objects).
o addmargins(T, ...) now returns a "table" when 'T' is a "table", as
its help page has always suggested.
o remove() now explicitly precludes removing variables from
baseenv() and throws an error (this was previously ignored).
o Saving the workspace at the end of a session now works as has
long been intended, that is it is saved only if something has
been added/deleted/changed during the current session.
o The search for bindings in <<-, ->> and assign(inherits=TRUE)
was omitting the base package, although this was not
documented. Now the base package is included (but most
bindings there are locked).
o dweibull(0, shape) was NaN not Inf for shape < 1. Also, the
help for dgamma and dweibull gave support as x > 0, but
returned non-zero values for x = 0. (PR#9080)
o Subsetting arrays no longer preserves attributes (it was
removed for matrices in 1998).
o The "factor" method of as.character() no longer maps level
"NA" to "<NA>" (a legacy of before there were NA character
strings).
o terms(keep.order=TRUE) was not returning a valid "order"
attribute.
o The DLL registration code was not freeing .External symbols.
o The internet download routines expected URLs of less than 4096
bytes, but did not check. Now this is checked, and http:// URLs
are allowed to be up to 40960 bytes.
o parse(n=-1) threw a stack-imbalance error, and parse(n=3) did
not cope correctly with EOF during input.
o Zero-column data frames had no names (rather than character(0)).
o by() and acf() could get confused when they used very long
expressions as names.
o residuals(<glm object>, type="working") was NA for cases with
zero weight (whereas they are well-defined even though the
case was not used during the fitting) and the actual value is
now returned. This allows residuals to be computed from fits
with 'y = FALSE'.
The residuals in a fitted "glm" object are computed more
accurately: the previous formula was subject to cancellation.
o loess() now checks the validity of its 'control' argument.
o rownames(<0-row matrix>, do.NULL=FALSE) was wrong. (PR#9136)
o apply() now works as documented when applied over 2 or more
margins with one of zero extent. (It used to drop dimensions.)
o head() and tail() now also work row-wise for "table" and "ftable"
objects.
o NextMethod() could throw an error/crash if called from a method
that was called directly rather than from a generic (so
.Method was unset).
o order(x, na.last = NA) failed for a zero-length x.
o grep(pat, x, value = TRUE, perl = L) preserved names for
L == TRUE && !is.na(pat) but not otherwise. Now it always does.
o [rc]bind() now find registered methods and not just visible ones.
o Printing a factor no longer ignores attributes such as names and
dim/dimnames.
o Command-line arguments after --encoding were ignored.
o The check for impossible confidence levels was off by one in
wilcox.test (PR#8557)
o [[ on an environment could create aliases. (PR#8457)
o pt() with a very small (or zero) non-centrality parameter could
give an unduly stringent warning about 'full precision was not
achieved'. (PR#9171)
o writeChar() could segfault if 'nchars' was given silly values.
o qt() and rt() did not work for vector 'ncp', and qt() did not
work for negative 'ncp'.
o ns() failed to work correctly when 'x' was of length one.
o identical() ignored tags on pairlists (including names of
attributes) and required an identical ordering for
attribute values in their pairlists. Now names are compared
on pairlists, and attribute sets are treated as unordered.
o If they were unused arguments supplied to a closure, only
the first non-empty one was reported, despite the message.
Unmatched empty arguments (such as f(1,,) for a function of
one argument) were ignored. They are now an error.
o Calling a builtin with empty arguments used to silently remove
them (and this was undocumented). Now this is an error unless
builtin is c() or list() or there are only trailing empty
arguments, when it is a warning (for the time being: this will
be made an error in R 2.5.0).
o install.packages() ignored 'configure.args' if the vector was
unnamed.
o biplot() now works if there are missing values in the data.
o biplot() now passes par() values to all four axes (not
just those on sides 1 and 2).
o [.acf now handles an empty first index.
o Deparsing uses backticks more consistently to quote
non-syntactic names.
o Assigning to the symbol in a for() loop with a
list/expression/pairlist index could alter the index. Now the
loop variable is explicitly read-only. (PR#9216)
o Using old.packages() (and hence update.packages()) on an empty
(or non-existent) library failed with an obscure message.
o plot.xy() could segfault if supplied with an invalid 'col'
argument. (PR#9221)
o menu() with graphics=TRUE attempted to use Tcl/Tk on unix even
if DISPLAY was not set (in which case Tk is not available and
so the attempt is bound to fail).
o The print() method for 'dist' objects prints a matrix even for
n = 2.
o The cumxxx functions were missing some PROTECTs and so could
segfault on long vectors (especially with names or where
coercion to numeric occurred).
o The X11() device no longer produces (apparently spurious)
'BadWindow (invalid Window parameter)' warnings when run from
Rcmdr.
o legend() assumed that widths and heights of strings were positive,
which they need not be in user coordinates with reversed axes.
(In part, PR#9236)
o The plot() methods for "profile.nls" objects could get
confused if 'which' had been used in the profile() call. (PR#9231)
o boxplot() did not passed named arguments (except graphics
parameters) to bxp() as documented. (PR#9183)
o Only genuinely empty statements act as 'return' in the
browser, not say those starting with a comment char. (PR#9063)
o summary.mlm() incorrectly used accessor functions to fake an
"lm" object. (PR#9191)
o prettyNum() was not preserving attributes, despite being
explicitly documented to. (PR#8695)
o It was previously undocumented what happened if a graphical
parameter was passed in both '...' and 'pars' to boxplot()
and bxp(), and they behaved differently. Now those passed in
'...' have precedence in both cases.
o A failed subassignment could leave behind an object '*tmp*'.
The fix also sometimes gives better error messages.
o Using SIGUSR1 on Unix now always terminates a session, and no
longer is caught by browser contexts and restarts (such as try()).
o In the 'graphics' package, in-line 'font=5' was being ignored
(report by Tom Cook).
o nls() looked for non-parameter arguments in a function call in
the wrong scope (from the body of nls).
o Printing of complex numbers could misbehave when one of the
parts was large (so scientific notation was used) and the
other was so much smaller that it had no significant digits
and should have been printed as zero (e.g. 1e80+3e44i).
o Using install.packages with type="mac.binary" and target path
starting with ~ failed with a cryptic message while unpacking.
o getwd() now works correctly when the working directory is
unavailable (e.g. unreadable).
o The alternative hypothesis in wilcox.test() was labelled by an
unexplained quantity 'mu' which is now spelled out.
The alternative hypothesis in ks.test() is clearer both in the
documentation and in the result. (PR#5360)
**************************************************
* *
* 2.3 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.3.1 patched
BUG FIXES
o help.search() incorrectly documented where the data base was
saved and what was in it.
o str(<data.frame>, strict.width=.) produced an extraneous first line.
o Improve bessel[IJKY]() out-of-range checks; for instance,
besselI(0, nu) no longer warns.
o cbind() on some non-vector objects (e.g. names) segfaulted.
o xy.coords(numeric(0)) gave a misleading error message.
o INSTALL has been changed to avoid a few problems with the
base (not XPG4) Solaris sed.
o There were problems in src/main/printutils.c on some platforms
that did not have va_copy.
o [pq]unif allowed infinite ranges but handled them
inconsistently. (PR#8958)
[pq]unif claimed to allow min == max but did not do so.
o Subassignment within raw arrays of 3 or more dimensions was not
implemented.
o environment<-() did not even check if duplication was required.
o rt() was wrong for non-central t-distributions. qt() was wrong
for non-central distributions far enough in the left tail
(reported by Long Qu). (PR#9050)
o R CMD Rdconv --type=Ssgm no longer drops a \keyword{} if it is the
only one (one letter typo patch by Bill Dunlap). (PR#9051)
o poly(x, y, .., raw = TRUE) now does follow 'raw'.
o plot(0/ -1:1, type = "s") now works. (PR#9046)
o write.table(row.names=FALSE) does now quote column names. (PR#9044)
o rf() was wrong for non-central F (PR#9055). qf() was wrong for
non-central F with denominator df > 1e8.
o The C function dummy_vfprint had a potential memory leak. This
showed up with some connections when used with output of more
than 100,000 bytes in a single call.
o vignette() did not work if more than one vignette with the
same name was installed (PR#9069).
o mget() did not check that 'ifnotfound' was a list, and worked
incorrectly if it was a list of length > 1. Now 'ifnotfound'
is (if possible) coerced to a list.
o The internal check for conformance of time series assumed that the
'tsp' attribute was integer, whereas it was enforced to be
numeric by the attribute-setting code.
o Sweave() did not treat \begin{document} in comments correctly
(PR#9073).
o diff(x) gave wrong result when x was "POSIXlt" object.
o title() could crash R when passed a long non-character vector.
(PR#9115)
o Functions rgb(), hsv() and hcl() lost names unless 'alpha' was
specified. (In part, PR#9118)
o The residuals() method for "glm" failed unless 'y = TRUE' for
the fit: it now works for "working" and "partial" residuals
and gives a useful error message for other types. (PR#9124)
o R CMD Rdconv did not close the .Rd file, which matters on Windows.
(PR#9126)
o anova.mlm() could fail if applied to a single model.
o stopifnot(<FALSE-expr>) now gives a better message for a *long*
expression.
CHANGES IN R VERSION 2.3.1
NEW FEATURES
o In lm() and glm(), offsets are allowed to be length 1 (and
if so are replicated to the number of cases).
o The \uxxxx notation for Unicode characters in input strings
can now be used on any platform which supports MBCS, even if
the current locale is not MBCS (provided that the Unicode
character is valid in the current character set).
o The quasibinomial() family now allows the "cauchit" link. (PR#8851)
o edit.data.frame() no longer (silently) coerces character columns
to factor.
C-LEVEL FACILITIES
o The variables controlling stack checking are made available via
Rinterface.h to front-ends embedding R: see 'Writing R Extensions'
o R_SignalHandlers (defined in Rinterface.h) can be set to 0 to
suppress the R signal handlers in front-ends embedding R.
INSTALLATION CHANGES
o There have been a number of changes to help installation on
platforms that no one had beta-tested.
- Changes related to older header files, e.g. on Redhat 8.0/9.
- Problems with 'make install' on older (<3) versions of bash
on Solaris and elsewhere.
- AIX 5.2/gcc issues with needing -lm when making modules X11
and vfonts.
- Some versions of Solaris and AIX had an fcntl.h that
redefined 'open' to be 'open64' and thereby broke
compilation of src/main/connections.c and elsewhere.
o 'make uninstall' works better on a build using a named
subarchitecture.
BUG FIXES
o min(), max(), sum() and prod() gave nonsensical answers with
an empty list or raw argument.
o sum() on a data frame did not allow multiple arguments. (PR#8385)
o charmatch() and pmatch() did not specify they applied only to
character vectors. Now they do, and attempt to coerce 'x' and
'target' to character before attempting matching.
o The Summary() methods for data.frame, Date, POSIXct, POSIXlt
and difftime all required an argument which can match 'x',
although the generics did not.
o regexpr() now accepts 0-length 'text' inputs.
o help.search() no longer errors out on a wrongly installed package
(with no "hsearch.rds" file).
o The LaTeX version of the package reference manual was omitting
some topics, and was not sorting the foo-package topic first.
o Serializing (e.g. via save()) is better protected against C
stack overflow, which will now abort the conversion but no
longer crashes the R process on some platforms.
o rbind()ing dataframes with a single row could lead to a
corrupt data frame (a problem with the fix to PR#8506).
o plot(lm(y ~ 1)) now works also for 'which = 5'.
o dbeta(0, 1, a, 0) now correctly gives 'a' (limit) instead of 0,
and dbeta(0, a, b, ncp) now returns Inf instead of NaN.
o demo(Hershey) was failing on the Cyrillic octal codes in locales
(e.g. UTF-8) in which these are invalid.
o mean() on an integer (or logical) vector was treating NAs as
actual values (unless na.rm = TRUE).
o mean() on a complex vector was calculated incorrectly in
code to improve precision (PR#8842, John Peters).
o Graphical parameters bg, cex, col, lty, and lwd were being
checked as being of length one even by functions such as
title() that ignored them. (Functions such as lines() and
points() allow them to be of length > 1, so they might be
passed through ... to other high-level graphical functions
which then used to reject them.)
o str() now is fast again for large character vectors.
o edit() would default the environment of a function to .BaseEnv,
instead of to .GlobalEnv.
o lm() and glm() coerce their 'weights' and 'offset' values to
vector to avoid problems with specifying them as 1D or n x 1
arrays.
o image() with one or both axes on log scales would give a
spurious warning; contour() would give an error.
o legend() with log axes would place the title in the wrong place.
o edit.data.frame() was not returning factors edited with
factor.mode="numeric" to factors.
o edit.matrix() tried to set rownames and colnames from the
original matrix even if the sizes had been altered, and
ignored changes made to the column names. 'edit.row.names' has
a more sensible default (if the rownames are non-NULL).
o bindingIsLocked() was returning invalid values of a logical
vector on some platforms.
o merge.data.frame() did not make the column names unique (by
appending elements of 'suffixes') when performing a Cartesian
product. (PR#8676)
o rbind.data.frame() matches up the names of columns (which was
undocumented), but failed to do so when checking if it was
dealing with a factor column. (PR#8868)
If rbind() was used on data frames with duplicated names it
produced a corrupt data frame.
o dt(x, df, ncp= not.0) no longer gives erratic values for
|x| < ~1e-12. (PR#8874)
o \code{\linkS4class{.}} now works.
o ccf() aligns time series by ts.intersect() rather than
ts.union() and so is less likely to need a non-default
na.action. (PR#8893)
o optim(method="CG") could return a value that did not
correspond to $par for very badly behaved functions on which
the second phase of the line search failed. (PR#8786)
o print.ts() could fail on a corrupt time series: it now warns and
does the best it can.
CHANGES IN R VERSION 2.3.0
USER-VISIBLE CHANGES
o In the grid package there are new 'arrow' arguments to
grid.line.to(), grid.lines(), and grid.segments()
(grid.arrows() has been deprecated).
The new 'arrow' arguments have been added BEFORE
the 'name', 'gp' and 'vp' arguments so existing code that
specifies any of these arguments *by position* (not by name)
will fail.
o all.equal() is more stringent, see the PR#8191 bug fix below.
o The data frame argument to transform() is no longer called 'x',
but '_data'. Since this is an invalid name, it is less likely
to clash with names given to transformed variables. (People
were getting into trouble with transform(data, x=y+z).)
NEW FEATURES
o arima.sim() has a new argument 'start.innov' for compatibility
with S-PLUS. (If not supplied, the output is unchanged from
previous versions in R.)
o arrows() has been changed to be more similar to segments():
for example col=NA omits the arrow rather than as previously
(undocumented) using par("col").
o as.list() now accepts symbols (as given by as.symbol() aka
as.name()).
o atan2() now allows one complex and one numeric argument.
o The 'masked' warnings given by attach() and library() now only
warn for functions masking functions or non-functions masking
non-functions.
o New function Axis(), a generic version of axis(), with Date and
POSIX[cl]t methods. This is used by most of the standard
plotting functions (boxplot, contour, coplot, filled.contour,
pairs, plot.default, rug, stripchart) which will thus label x
or y axes appropriately.
o pbeta() now uses TOMS708 in all cases and so is more accurate
in some (e.g. when lower.tail = FALSE and when one of the
shape parameters is very small).
o [qr]beta(), [qr]f() and [qr]t() now have a non-centrality parameter.
o [rc]bind and some more cases of subassignment are implemented
for raw matrices. (PR#8529 and PR#8530)
o The number of lines of deparsed calls printed by browser() and
traceback() can be limited by the option "deparse.max.lines".
(Wish of PR#8638.)
o New canCoerce() utility function in "methods" package.
o [pq]chisq() are considerably more accurate for moderate (up to
80) values of ncp, and lower.tail = FALSE is fully supported
in that region. (They are somewhat slower than before.)
o chol(pivot = TRUE) now gives a warning if used on a (numerically)
non-positive-definite matrix.
o chooseCRANmirror() consults the CRAN master (if accessible) to
find an up-to-date list of mirrors.
o cov.wt() is more efficient for 'cor = TRUE' and has a new 'method'
argument which allows 'Maximum Likelihood'.
o do.call() gains an 'envir' argument.
o eigen() applied to an asymmetric real matrix now uses a
tolerance to decide if the result is complex (rather than
expecting the imaginary parts of the eigenvalues to be exactly
zero).
o New function embedFonts() for embedding fonts in PDF or
PostScript graphics files.
o fisher.test() now uses p-values computed via hypergeometric
distributions for all 2 by 2 tables. This might be slightly
slower for a few cases, but works much better for tables with
some large counts.
There is a new option to simulate the p-value for larger than
2 x 2 tables.
o for() now supports raw vectors as the set of indices.
o getNativeSymbolInfo() is vectorized for the 'name' argument. It
returns a named list of NativeSymbolInfo objects, but is
backward compatible by default when called with a character
vector of length 1, returning the NativeSymbolInfo object.
o help.search() no longer attempts to handle packages installed
prior to R 2.0.0, and reports the current path to the
package (rather than where it was originally installed: this
information is not shown by the print() method).
o Added "hexmode" to parallel "octmode".
o install.packages() now does tilde expansion on file paths
supplied as 'pkgs'.
o install.packages() has additional arguments 'configure.args' and
'clean' which allow the caller to provide additional arguments
to the underlying R CMD INSTALL shell command when installing
source packages on a Unix-alike.
o is.loaded() has a new argument 'type' to confine the search to
symbols for .C, .Fortran, .Call or .External: by default it
looks for a symbol which will match any of them. It is now
internal and not primitive, so argument matching works in the
usual way.
o The symmetry test for matrices used in eigen() has been ``exported''
as the 'matrix' method of a new S3-generic 'isSymmetric().
o .leap.seconds and the internal adjustment code now know about
the 23rd leap second on 2005-12-31: the internal code uses a
run-time test to see if the OS does.
o The 'col' argument of legend() now defaults to par("col")
(which defaults to "black", the previous default), so that
the lines/symbols are shown in the legend in the colour that
is used on the plot.
o log2() and log10() call C functions of the same name if
available, and will then be more likely to be precise to
machine accuracy.
o new.packages() gains a ... argument to pass e.g. 'destdir' to
install.packages(). (Wish of PR#8239.)
o nls() now supports 'weights'.
o The vector passed as the first argument of the 'fn' and 'gr'
arguments of optim() has the names (if any) given to argument
'par'.
o options(expressions) is temporarily increased by 500 during
error-handling. This enables e.g. traceback() to work when
the error is reaching the limit on the nesting of expressions.
o page() accepts general R objects, not just names (and
previously undocumented) character strings. This allows the
object to be specified as a call, for example. More options
are allowed in its '...' argument.
o pairs() allows a wider class of inputs, including data frames
with date and date-time columns.
o par() and the in-line use of graphical parameters produce more
informative error messages, distinguishing between
non-existent pars and inappropriate use of valid pars.
Graphical parameters 'family', 'lend', 'ljoin' and 'lmitre'
can now be set in-line.
There is no longer a warning if non-settable pars are used
in-line, but there is an appropriate warning if unknown pars
are passed.
The length limit for the 'family' parameter has been increased
to 200 bytes, to allow for the names of some CID-keyed fonts
in multi-byte locales.
o The pdf() device now allows 'family' to be specified in the same
generality as postscript().
o The pdf() device writes /FontDescriptor entries for all fonts
except the base 14, and does not write font entries for unused
fonts.
o Plotmath allows 'vartheta', 'varphi' and 'varsigma' (or 'stigma')
as synonyms for 'theta1', 'phi1' and 'sigma1', and the help
page has a note for TeX users.
o plot.xy() now takes its default arguments from the
corresponding par() settings, so points(type="l") and
lines(type="p") behave in the same way (and more obviously,
also for type="b").
o poly() has a new argument 'raw', mainly for pedagogical purposes.
o The class "POSIXlt" now supports fractional seconds (as
"POSIXct" has always done). The printing of fractional seconds
is controlled by the new option "digits.secs", and by default is off.
o postscript() supports family = "ComputerModernItalic" for
Computer Modern with italic (rather than slanted) faces.
o The postscript()/pdf() font metrics for the 14 standard fonts
(only, not the rest of the common 35) have been updated to
versions from late 1999 which cover more glyphs. There are
also a few differences in the metrics and hence the output
might be slightly different in some cases.
o The way families can be specified for postscript() and pdf()
has been expanded to include CID-keyed fonts, with new
functions Type1Font() and CIDFont() to set up such fonts
families.
o prettyNum() has new arguments 'preserve.width' and 'zero.print'.
When the former is not "none", as in calls from format() and
formatC(), the resulting strings are kept at the desired width
when possible even after adding of 'big.mark' or 'small.mark'.
o proc.time() and system.time() now record times to 1ms accuracy
where available (most Unix-like systems).
o The initialization methods for the quasi() family have been
changed to depend on the variance function, and in particular
to work better for the "mu(1-mu)" variance function. (PR#8486)
o read.table() gains a 'flush' argument passed to scan().
o require() now takes a 'lib.loc' argument.
o The second argument 'size' to sample() is required to have
length 1, so that errors when supplying arguments are more
easily detected.
o The default is now compress = !ascii in save() (but not save.image).
o scan() and write.table() now have some interruptibility, which
may be useful when processing very large files.
o A new heuristic test, seemsS4Object() is supplied, along with a
similar C-level test, R_seemsS4Object(object). The test
detects probable S4 objects by their class's attribute. See
the help page.
o S3 classes can now be made non-virtual S4 classes by supplying a
prototype object in the arguments to setOldClass().
o splinefun() returns a function that now also has a 'deriv' argument
and can provide up to the 3rd derivative of the interpolating
spline, thanks to Berwin Turlach.
o stopifnot(A) now gives a better error message when A has NAs, and
uses "not all TRUE" when A has length >= 2.
o str()'s default method has a new argument 'strict.width' which can
be used to produce strict 'width' conforming output. A new
options(str = list(strict.width = *)) setting allows to control
this for a whole session.
o summary.nls() has a new argument 'correlation' that defaults
to FALSE (like summary.lm).
o Sys.sleep() has sub-millisecond resolution on Unix-alikes
with gettimeofday().
o Sys.time() now has sub-millisecond accuracy on systems
supporting the POSIX call gettimeofday, and clock-tick
accuracy on Windows.
o The new function timestamp() adds a time stamp to the saved
command history on consoles which support it.
o New function tcrossprod() for efficiently computing x %*% t(x)
and x %*% t(y).
o The suffix used by tempfile() is now in hex on all platforms
and guaranteed to be at least 6 hex digits (usually 8).
o trace() now works more consistently and more like its
documentation, in particular the assertions about old tracing
being removed for new. For debugging purposes (of R) a
mechanism for debugging the trace computations themselves was
added. See trace.R.
o The implementation of trace() has beem made more general by
calling a function to do the trace interaction, and recover()
now detects trace calls to trim the irrelevant code underneath.
o unserialize() can now also read a byte stream from a raw vector.
o The useDynLib() directive in the NAMESPACE file now accepts the
names of the native/foreign symbols that are to be resolved in
the DLL for use in .C/.Call/.Fortran/.External calls. These
can be used as regular R variables instead of the (routine
name, PACKAGE) pairs currently recommended. Alternative names
can be given for the R variables mapping to these symbols.
The native routine registration information can also be used
directly via useDynLib(name, .registration = TRUE). See the
'Writing R Extensions' manual for more details.
checkFF() (package 'tools') has been updated accordingly.
o validObject() has an option complete=TRUE that recursively
checks the objects in the slots. Not used when new(...)
checks validity.
o New Vectorize() function, a wrapper for mapply().
o write.ftable() has gained an argument 'append = FALSE' (thanks to
Stephen Weigand).
o On Unix-alikes, X11() now has arguments to request the initial
position of the window, and 'gamma' defaults to the value of
getOptions("gamma"). These changes are consistent with the
windows() device.
o X11() and the Unix-alike data entry window can have properties
(including geometry) set by X resources: see their help files.
o xy.coords() & xyz.coords() now have NULL defaults for their 'y' or
'y' and 'z' arguments. This is more consistent with their earlier
documentation, and may be convenient for using them.
o Non-syntactic names of list elements are now printed quoted by
backticks rather than double quotes.
o There is some basic checking for imminent C stack overflow (when
the evaluation depth and the user interrupts are checked).
On systems with suitable OS support (not Windows), segfaults
from C stack overflow are caught and treated as an R error.
New function Cstack_info() reports on stack size and usage.
options(expressions) reverts to the default of 5000 now
stack checking is in place.
o Package tcltk does not try to initialize Tk on Unix-alikes
unless a DISPLAY variable is present. This allows packages
dependent on tcltk to be installed without access to an X server.
o The code used to guess timezone offsets where not supplied by
the OS uses a different algorithm that is more likely to guess
the summer-time transitions correctly.
o Package tools contains translation tables 'Adobe_glyphs' and
'charset_to_Unicode'.
o Changed the environment tree to be rooted in an empty
environment, available as emptyenv(). baseenv() has been
modified to return an environment with emptyenv() as parent,
rather than NULL.
o gettext has been updated to 0.14.5.
o PCRE has been updated to version 6.4.
o The method $.DLLInfo resolves the specified symbol in the DLL,
returning a NativeSymbolInfo object. Use [[ to access the actual
values in the DLLInfo object.
o On systems with either vasprintf or both va_copy and a vsnprintf
which reports the size of buffer required, connections such as
gzfile() and bzfile() can now write arbitrarily long lines,
not just 100000 chars.
o The R session temporary directory is now set in C code using
the same algorithm whether or not the shell front-end is used
and on all platforms. This looks at environment variables
TMPDIR, TMP and TEMP in turn, and checks if they point to a
writable directory.
o Some of the classical tests put unnecessary restrictions on the
LHS in the formula interface (e.g., t.test(x+y ~ g) was not
allowed).
o On suitably equipped Unix-alike systems, segfaults, illegal
operations and bus errors are caught and there is a simple
error-handler which gives the user some choice as to what to
do in interactive use.
On Windows access violations and illegal instructions are
caught with a simple error handler.
o Tracebacks now include calls such as .C/.Fortran/.Call, which
will help if errors occur in R code evaluated by compiled code
and in tracebacks presented by the segfault etc handlers.
o Treatment of signature objects and method definition objects has
been modified to give cleaner printing and more consistency in
the treatment of signatures. A sometimes useful utility,
methodSignatureMatrix(), is now exported.
o Printing the results of codoc() from package tools now helpfully
summarizes the found code/documentation mismatches.
o R refrains from printing a final EOL upon exiting the main loop
if the quiet flag is on and if the save action is known (e.g. this
is true for --slave).
DEPRECATED & DEFUNCT
o The deprecated and undocumented use of atan() with two arguments
has been removed: instead use atan2().
o write.table0() is defunct in favour of write.table().
o format.char() is defunct in favour of format.default().
o Support for the long-deprecated (and no longer documented)
arguments --min-vsize --min-nsize --max-vsize --max-nsize
--vsize --nsize of R CMD BATCH has been removed.
o The 'debian' subdirectory has been removed from the sources.
o The 'vfont' argument of axis() and mtext() has been removed:
use par(family=) instead.
o The unused graphical parameter "type" has been removed: it
invited confusion with the 'type' argument to default methods
of plot(), points() and lines().
o nlsMethod() and profiler() are no longer exported from the stats
name space (and nlsMethod.plinear() is no longer registered as
a method, as nlsMethod() was not generic).
o The re-named tcltk functions tkcmd, tkfile.tail, tkfile.dir,
tkopen, tkclose, tkputs, tkread are now formally deprecated.
o Argument 'col' of bxp() is now formally deprecated.
o Use of NULL as an environment is deprecated and gives a warning.
o postscriptFont() is deprecated in favour of Type1Font() (which
is just a change of name).
o La.chol() and La.chol2inv() are deprecated (they have since R
1.7.0 been the same as the default options of chol() and chol2inv).
o La.svd(method = "dgesvd") is deprecated.
o The use of install.R and R_PROFILE.R files in packages is
deprecated: use the DESCRIPTION file instead to arrange to
save an image or to load dependent packages.
The following command-line options to INSTALL are deprecated
(use the fields in the DESCRIPTION file instead):
-s --save --no-save --lazy --no-lazy --lazy-data --no-lazy-data
o Graphical parameter 'tmag' (which is long unused) is deprecated.
INTERNATIONALIZATION
A set of patches supplied by Ei-ji Nakama has been incorporated.
o New postscript encodings for CP1253, CP1257 and Greek (ISO 8859-7).
o Support for East Asian CID-keyed fonts in pdf() and postscript().
Although these usually contain Latin characters no accurate
AFMs are available and so CID-keyed fonts are intended only
for use with CJK characters.
o Wide-character width functions wc[s]width are provided that
overcome problems found with OS-supplied ones (and those
previously used by R on Windows). This means that
double-width CJK characters are now supported on all
platforms. It seems that the width of some characters (and
not just CJK characters) depends on which CJK locale's fonts
are in use and also on the OS.
Revised wide-character classification functions are
provided for use on Windows, AIX and MacOS X to replace
deficient OS-supplied ones.
o There is support for MBCS charsets in the pictex() graphics
device, and rotated (by 90 degrees) text may work better.
o The \u (and \U except on Windows) notation for characters which
is supported by the parser in all MBCS charsets is now always
interpreted as a Unicode point, even on platforms which do not
encode wchar_t in Unicode. These are now a syntax error in
single-byte locales.
o The default encoding for postscript() and pdf() is chosen to
be suitable for the current locale, if that is a single-byte
locale which is supported. This covers European (including
Greek) and Cyrillic languages.
In UTF-8 locales, a suitable single-byte encoding is chosen
for postscript() and pdf(), and text translated to it.
o xfig() gains an 'encoding' argument.
o There are some message translations into Spanish.
INSTALLATION CHANGES
o The encoding files for pdf()/postscript() have been moved to
directory 'enc' in package 'grDevices'.
o Support for MBCS is only enabled if iconv is found and it
supports enough conversions. (libiconv does.)
o In an MBCS locale, make check now translates the graphics
examples from Latin-1. This ensures that they will work
correctly in UTF-8: it is possible that in other MBCS locales
they will now fail (rather than work completely incorrectly).
o There is a new test, 'test-Docs', which as part of 'make
check-devel' tests the code in the documentation. Currently
it runs doc/manual/R-{exts,intro}.R and the compiled code in
R-exts.c.
o The workaround to allow an external LAPACK-containing BLAS
such as libsunperf to be used with the internal LAPACK has
been removed. If you have such a library you may now need
to use --with-lapack. It is no longer possible to use some
older versions of libsunperf, e.g. Forte 7 on 64-bit builds.
o A substitute for mkdtemp is provided, so it is now always
used for R_TempDir.
o Most of the functions checked for by 'configure' also have
declarations checked for in the appropriate header.
o The top-level documentation files AUTHORS COPYING.LIB COPYRIGHTS
FAQ RESOURCES THANKS have been moved to doc, and COPYING and NEWS
are installed there. The file Y2K has been removed from the
distribution.
o The extension .lo is no longer used in building R (only in
the optional build of libRmath.so): this allows a considerable
simplification of the Makefiles.
o Direct support for f2c has been removed: it can still be used
via a script which makes it look like a Fortran compiler.
(src/scripts/f77_f2c is an example of such a script.)
o There is a new flag SAFE_FFLAGS which is used for the
compilation of dlamc.f. It is set by configure for known
problem cases (recent g77 and gfortran), but can be overridden
by the user.
o The standard autoconf macros for large-file support are now used,
and these are enabled unless --disable-largefile is specified.
This replaces --enable-linux-lfs (and is now selected by default).
o Visibility attributes are used where supported (gcc4/gfortran on
some platforms, also gcc3/g77 on FC3 and partially elsewhere).
The main benefit should be faster loading (and perhaps better
optimized code) in some of the dynamic shared objects (e.g.
libR.so and stats.so).
o The *PICFLAGS are taken to be -fpic rather than -fPIC where
possible. This will make no difference on most platforms:
-fPIC is needed on Sparc (and still used there), but -fpic
should give slightly better performance on PowerPC (although
-fPIC is used on PPC64 as it is needed to build libR.so there).
o More use is made of inlining for small utility functions such
as isReal. Because this can only be done portably with C99
constructs (and we know of no actual implementation), this is
only done for the GNU C compiler.
o There is an experimental feature to allow shared installations
of sub-architectures. See the R-admin manual.
o All platforms now use R's internal implementation of strptime,
which allows fractional seconds. (The major platforms were
already using it.)
o The dlcompat work-around for old Mac OS X systems (<= 10.2)
has been removed. External dlcompat must be installed if needed.
UTILITIES
o R CMD check now uses an install log by default.
o R CMD check works for packages whose package name is different
from the directory name in which it is located.
o R CMD INSTALL now uses more randomness in the temporary
directory name even on systems without mktemp -d.
o R CMD f77 has been removed now f2c is no longer supported.
o The version string shown in the startup message and by
"R --version", and that stored in variable R.version.string
are now in exactly the same format.
o The base name of a help file needs to be valid as part of a file://
URL, so R CMD check now checks the names are ASCII and do not
contain % .
o R CMD check now warns about unknown sections in Rd files, and
invalid names for help, demo and R files, as well as unlikely
file names in the 'src' directory. The latter is controlled
by option --check-subdirs and by default is done if checking a
tarball without a configure script.
R CMD build excludes invalid files in the 'man', 'R' and 'demo'
subdirectories.
o \usepackage[noae]{Sweave} in the header of an Sweave file
supresses auto-usage of the ae package ("almost European"
fonts) and T1 input encoding.
DOCUMENTATION
o Rd format now allows \var{} markup inside \code{} and \examples{}.
o Markup such as --, ---, < and > is handled better when
converting .Rd files to [C]HTML.
o There is new markup \link[=dest]{name} to generate a link to topic
'dest' which is shown as 'name', and \linkS4class{abc} which
expands to \link[=abc-class]{abc}, for cross-referencing the
recommended form of documentation for S4 classes.
PACKAGE INSTALLATION
o There is now some support for Fortran 90/95 code in packages:
see `Writing R Extensions'.
o Installation of man sources and demos is now done by R code.
The restrictions on the names of help files, R files and
of demos are now enforced (see `Writing R Extensions').
o Packages which contain compiled code can now have more than
one dot in their name even on Windows.
o The Meta/hsearch.rds database saved now contains LibPath="".
This information is now always recreated when help.search() is
run, but the field is retained for back-compatibility.
o update.packages() now has a '...' argument to be passed to
install.packages(), including the formerly separate arguments
'destdir' and 'installWithVers'.
o Make macros AR and RANLIB are now declared in etc/Makeconf for
use by packages which wish to make static libraries.
C-LEVEL FACILITIES
o qgamma and rgamma in Rmath.h now check for non-positive arguments.
o The BLAS which ships with R now contains the complete set of
double-complex BLAS routines, rather than just those used in R.
<R_ext/BLAS.h> has been corrected to add the missing
double-precision BLAS functions drotmg and drotm, and to
exclude lsame (which is a Lapack auxiliary function and is now
declared in <R_ext/Lapack.h>). It also includes the double
complex routines added for this release of R provided Fortran
doublecomplex is usable on the platform.
o <R_ext/BLAS.h> and <R_ext/Lapack.h> now declare all the entry
points as 'extern'.
o The flag SAFE_FFLAGS is made available to packages via
etc/Makeconf and R CMD config. It can be used where
optimization needs to be defeated, e.g. in LAPACK setup.
o getNativeSymbolInfo has a withRegistrationInfo argument which
causes the address field to be a reference to the registration
information if it is available for that symbol. If the
registration information is not available, the address is a
reference to the native symbol. The default is FALSE which is
backward compatible, returning just the address of the symbol
and ignoring registration information.
o errorcall and warningcall are now declared in <Rinternals.h>
(they might be needed in front-ends).
o R_FlushConsole and R_ProcessEvents are now declared in <R.h>.
o The R_Sock* functions supporting socket connections are no
longer declared in R-ftp-http.h as they are not loaded into R
itself, and are now hidden in the module's DLL on suitable systems.
BUG FIXES
o Quoted arguments to the R script after --args are now
passed quoted to the R executable and so will be shown as
expected by commandArgs(). (They were previously split at
whitespace even inside quotes on Unix-alikes but not on
Windows.)
o axis() now supports pars 'xaxp'/'yaxp' as inline arguments.
o sort() now does not return inappropriate attributes such as
"dim" and "tsp": it only returns names.
sort(x, partial=) no longer returns unsorted names, and drops
names (since it is supplied for efficiency).
o Use of non-central F in pf() gives accurate values for larger ncp.
o R CMD build --binary does a better job of cleaning up after
failure to re-make vignettes.
o reg-test-1.R tested system(intern=TRUE) which depends on popen
and so is not supported on all platforms.
o Changed apparent mis-spelling of "Gibraltar" in dataset 'eurodist'.
o sysconf() is now used to find the number of clock ticks/second:
under some circumstances glibc reported CLK_TCK = 60 when the
true value was 100.
o identical() was not allowing for embedded nuls in character
strings. (NB: the comparison operators including == do not,
and never will.)
o The profile() and profiler() methods for "nls" objects now
support algorithm = "plinear" and algorithm = "port".
o The signal handlers for signals USR1 and USR2 where not
restored if the signal arrived when interrupts were suspended.
o Certain combinations of S4 inheritance could cause inherited
methods to override some directly specified methods.
o Some cases of named signatures in calls to setMethod() caused errors.
o all.equal() is now more consistent and "picky" about mismatching
attributes, in particular names(); this is a part of the
propositions by Andy Piskorkski (PR#8191).
o load() when applied to a connection leaves it open/not as it
found it, and checks explicitly for having a binary readable
connection.
o The p-values given by stat.anova() (called from several
anova() methods) are now NA (rather than spurious) if
non-nested models give rise to changes in deviance with a
different sign from changes in degrees of freedom.
o Built-ins were reported as the relevant call in C-level error()s
iff R profiling was in progress. Now they are never reported.
o Too-long signatures (with no names) were not being caught
in setMethod().
o Slot names in prototype() are being more thoroughly checked.
o signif() is more likely to follow the 'round to even' rule for
exactly representable numbers, e.g. signif(0.25, 1). (Related
to PR#8452.)
o nls() now works correctly with some low-dimensional fits,
e.g. with one or zero non-linear parameters.
o glm() could give an inappropriate error message if all
possible coefficients were invalid (e.g. a log-linear binomial
model with no intercept and a not all positive predictor).
o solve() gives clearer error messages for some incorrect usages.
(PR#8494 and similar)
o The gaussian() family was missing the 'valideta' component
(which could be needed for the "inverse" link function).
The starting values supplied by the gaussian family could be
invalid for the "log" and "inverse" link functions. This is
now reported.
o data.matrix() did not work correctly on zero-row data frames.
(PR#8496 and other problems.)
o The DSC comments in the files from postscript(onefile=FALSE) now
label all files as having page 1 of 1, as some other software
seems to expect that.
o The axis labels chosen for logarithmic axis are now less
likely to be linear and inappropriate (when the range is more
than 10 and less than 100). (PR#1235)
o Staircase lines (types "s" and "S") are now drawn
continuously rather than a point at a time and so line types,
mitring and so on work. (PR#2630)
o Calling par(mfg) before doing any plotting resulted in NewPage
never being called on the device, which in turn resulted in
incorrect output for postcript() and pdf() devices. (Reported
by Marc Schwartz in discussion of the non-bug PR#7820.)
o terms.formula needed to add parentheses to formulae with
terms containing '|'. (PR#8462)
o pbirthday() and qbirthday() now also work for very improbable
events {those you are typically *not* interested in}.
o Only source help files starting with an upper- or lower-case
letter or digit and extension .Rd or .rd are documented to be
processed. This is more liberal in that starting with a digit
is now also allowed, but rule is now enforced.
o nls(algorthm="port") was always taking positive numeric
differences and so could exceed the upper bounds.
o methods:::.asEnvironmentPackage() was not allowing for
versioned installs.
o .find.package() now reports which package(s) it cannot find in
the case it stops with an error.
o The standard Unix-alike version of file.show() gives an
informative message if it cannot open a file rather than the
(possibly incorrect) 'NO FILE'.
o window() did not allow non-overlapping ranges with
extend = TRUE. (PR#8545)
o pbinom(size = 0) now returns correct values (not NaN). (PR#8560)
o [dp]binom(x, *) for x < 0 now always returns 0. (PR#8700)
analogous change in pgeom(), pnbinom() and ppois().
o [dqpr]geom and [dpqr]nbinom() now all consistently accept prob = 1
but not prob = 0. qgeom(prob=1) now gives the correct values
(not -1).
o INSTALL on Unix-alikes was not loading dependent packages when
preparing for lazy-loading.
o qcauchy(1) now gives +Inf instead of just a very large number.
o df(0, f1, *) now properly returns Inf, 1, or 0 for f1 < , = , or > 2.
o qbinom(), qnbinom() and qpois() now use a better search and
normally reach the answer very quickly when it is large
(instead of being slow or infinite-looping).
o pt(x, df) lost accuracy in the far tails (when |x| > 1e154) for
small df (like df = 0.001 for which such extremes are not unlikely).
o dbeta(x, a, b) underflowed internally and incorrectly gave 0
for very small x and a.
o None of the warnings about convergence failures or loss of
precision in nmath (distribution and special functions) were
being reported to the R user.
o dnt was missing from standalone nmath (under Unix-alikes).
o split() now accepts factors with numeric (but not storage mode
integer) codes.
o The utilities such as 'check' now report active version numbers
again, as SVN 'last changed revision' numbers.
o addmargins() did not accept a name for 'FUN', only an expression.
o '+' for POSIXt objects now takes the tzone from whichever
object has it, so date+x is the same as x+date if x is numeric.
o mean.default() and var() compute means with an additional pass
and so are often more accurate, e.g. the variance of a
constant vector is (almost) always zero and the mean of such a
vector will be equal to the constant value to machine
precision. (PR#1228)
sum(), prod(), mean(), rowSums() and friends use a long double
accumulator where available and so may be more accurate. (This
is particularly helpful on systems such as Sparc and AMD64
where long double gives considerably greater exponent range
and precision than double.)
o read.dcf() now gives a warning on malformed lines.
o add1.[g]lm now try harder to use the environment of the
formula in the orginal fit to look for objects such as the
'data' and 'subset' arguments.
o gaussian()$aic was inconsistent with e.g. the lm results from
AIC() and extractAIC() for weighted fits: it treated the weights
as case weights and not variance factors.
o system() on Unix-alikes ignored non-logical values of 'intern' and
treated 'intern = NA' as true.
o as.table() now produces non-NA rownames when converting a
matrix of more than 26 rows. (PR#8652)
o Partial sorting used an algorithm that was intended only for a
few values of 'partial' and so could be far slower than a full
sort. It now switches to a barebones full sort for more than
10 values of 'partial' and uses a more efficient recursive
implementation for 2...10.
o summary.glm() returned an estimate of dispersion of Inf for a
gaussian glm with zero residual degrees of freedom and then
treated that as a known value. It now uses the estimate NaN,
which is consistent with summary.lm().
o Sys.sleep() on Unix-alikes was restricted to about 2147 seconds
and otherwise might never have returned. (PR#8678)
o is(obj, Cl) could wrongly report TRUE when Cl was a classUnion and
multiple inheritance was involved.
o confint[.lm / .default] used label "100 %" for level = 0.999
o Empty entries (i.e., extraneous ",") in NAMESPACE files now give
a better error message early at parsing time instead of a less
comprehensible one later at load time.
o all.equal(n1, n2) could erroneously return NA when n1, n2
contained large integers.
o anova.mlm() didn't handle multi-df effects properly in the
single-model case (PR#8679)
o anova.mlm() had its colnames mangled by data.frame() (needed
check.names=FALSE).
o summary.glm() gave an NA estimate of dispersion for fits with
zero weights. (PR#8720)
o qhyper() had too small a tolerance for right-continuity on
some platforms so was not always an inverse to phyper().
o rownames<-.data.frame() and dimnames<-.data.frame() tested the
length(s) of the replacement value(s) before coercion, which
can change the length (e.g. for class "POSIXlt").
o max() and min() ignored the largest/smallest representable
integer, as well as Inf/-Inf. (PR#8731)
o write.table() assumed factors had integer codes: it now allows
malformed factors with numeric codes (and otherwise throws an
error).
o Worked around a Solaris restriction which meant that
Sys.sleep() was only effective for times of up to one second.
o sink(, split=TRUE) now works correctly, but is allowed only on
platforms that support va_copy or __va_copy. (PR#8716)
o factanal(), prcomp() and princomp() now only check that columns
in the model frame that will be used are numeric (they
previously also checked columns which were part of negative terms
in the formula).
o Misuse of $ in apply could corrupt memory. (PR#8718)
o apply() could fail if the function returned NULL (e.g. if
there was a single row).
o registerS3method() failed due to a typo. (It was almost never
used.)
o Registering an S3 method for an S3 generic in another package
that was converted to an S4 generic in the same package as the
S3 method, registered the method in the wrong place.
o Recall() used lookup for the function in use and so could fail
if that was an S3 method not on the search path.
o Rdconv -t Ssgm failed if it encountered \link[opt]{arg}.
o uniroot() did not give a warning (as documented) if it failed
to converge in 'maxiter' steps. (PR#8751)
o eapply() (and as.list.environment()) did not work for the base
environment/name space. (PR#8761)
o Added protection in configure against systems for which using
xmkmf fails to report a C or C++ compiler.
o expand.grid() was constructing a data frame 'by hand' and so
setting integer row.names (which are documented to be
character). It now sets character row names, and
row.names.data.frame() coerces to character.
o qbeta() used == on volatile doubles for its convergence test,
which failed with gcc 3.3.x on ix86 Linux. We now use a less
fragile test (and lose a negligible amount of accuracy).
o ls.str() was missing inherits=FALSE, and so could have
reported on an object of the same name but a different mode in
the enclosure of the given environment.
o logLik.nls assumed that sigma^2 had been estimated, but did
not count this in the 'df' attribute.
**************************************************
* *
* 2.2 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.2.1 patched
INSTALLATION CHANGES
o The macro SOCKLEN_T has been replaced by R_SOCKLEN_T to work
around a problem with the headers of AIX 5.3.
BUG FIXES
o sub(fixed = TRUE) could get wrong the length of the character
string for elements of the result after the first.
o legend() worked out which elements of 'lty' were valid before
resizing 'lty', and so could fail if 'lty' was a different
length from 'legend'.
o str(<dendrogram>) sometimes used much too many spaces (in 2.2.x).
o eigen(eispack=TRUE) accessed areas off the matrix in some
circumstances (some asymmetric matrices with both complex
conjugate pair and real eigenvalues).
o strptime() in 2.2.1 sometimes did not set $isdst when it was
previously set.
o Another case of infinite influence has been worked around.
(An addendum to PR#8367.)
o qr.coef() worked incorrectly with multiple rhs in the
LAPACK-using cases. (PR#8476/8)
o rbind.data.frame() gave a corrupt data frame if one of the
named arguments was a zero-row data frame. (PR#8506)
o Checks for NULL in the rho argument of the C-level findVar
function have been added.
o The C-level substitute function was handling NULL in its 'rho'
argument incorrectly.
o The code for pgamma() introduced in 2.1.0 failed for large
values of 'shape' where the previous code was perfectly
acceptable, despite the claim to be uniformly better. For
example, pgamma(0.9e100, 1e100) was NaN. (PR#8528)
o There was no command 'ls' in browser() nor 'next' in debug(),
despite the documentation (which has been corrected).
Command 'where' in the browser() no longer changes to
step-though mode.
o factor.scope() could report incorrectly that interaction terms
were not in the upper scope when such terms in the model and
the upper scope had different orders for the main effects.
(Another manifestation of PR#7842.)
o The "lm" method of drop1() was giving incorrect results for
weighted fits (since deviance.lm() was called on a non-"lm" object).
o dotchart() was miscalculating the space for the labels in the
left margin. (PR#8681)
o r <- glm(.....); all.equal(r,r) # now gives TRUE instead of an error
o plot.acf() with a multiple time series was sometimes
miscalculating the 'ylim' value for the plot after the first.
(PR#8705)
CHANGES IN R VERSION 2.2.1
USER-VISIBLE CHANGES
o options("expressions") has been reduced to 1000: the limit
of 5000 introduced in 2.1.0 was liable to give crashes from C
stack overflow.
NEW FEATURES
o Use of 'pch' (e.g. in points) in the symbol font 5 is now
interpreted in the single-byte encoding used by that font.
Similarly, strwidth now recognizes that font 5 has a different
encoding from that of the locale. (These are likely to affect
the answer only in MBCS locales such as UTF-8.)
o The URW font metrics have been updated to versions from late
2002 which cover more glyphs, including Cyrillic.
o New postscript encodings for CP1250 (Windows East European),
ISO Latin-7 (8859-13, Latvian, Lithuanian and Maori), Cyrillic
(8859-5), KOI8-R, KOI8-U and CP1251.
o configure has more support for the Intel and Portland Group
compilers on ix86 and x86_64 Linux.
o R CMD INSTALL will clean up if interrupted (e.g. by ctrl-C from
the keyboard).
o There is now a comprehensive French translation of the messages,
thanks to Philippe Grosjean, Frederic Lehobey, Jean Thioulouse
and Emmanuel Paradis.
DEPRECATED & DEFUNCT
o The undocumented use of atan() with two arguments is deprecated:
instead use atan2() (as documented).
o The 'vfont' argument of axis() and mtext() is deprecated
(it currently warns and does nothing).
o The function mauchley.test() is deprecated (was a misspelling)
and replaced by mauchly.test()
BUG FIXES
o The malloc's of AIX and OSF/1 which return NULL for size 0
are now catered for in src/main/regex.c.
o Names of list elements which are missing are now printed as
$<NA> and not $"NA" (which is how the non-missing name "NA" is
printed). (Brought up in discussion of PR#8161.)
o help.start() was not linking R.css for use by its front page and
immediate links (2.2.0 only).
o Indexing by character NA matched the name "NA".
o The arith-true test used random inputs and did not set the seed, so
it could fail very occasionally.
o arima() with 'fixed' supplied and p=0 for the non-seasonal
part could give spurious warnings about 'some AR parameters
were fixed'.
o summary.matrix() could give an infinite recursion on some
classed objects (e.g. those of class "Surv").
o The 255th character in an 8-bit character set was not handled
correctly as a letter on some platforms where C char is
signed: for example it was printed as \377 and not allowed in
variable names. (Spotted by Alexey Shipunov in Russian
encodings.)
o Conversion from POSIXct to POSIXlt is done more accurately
around the change of DST in years not supported by the OS
(pre-1970 on Windows and some others, and in the far past or
future).
o chisq.test(cbind(1:0, c(7,16)), simulate.p = TRUE) gave wrong
P-values on some platforms. (PR#8224)
o pdf() was not writing details of the encoding to the file
correctly. (Spotted by Alexey Shipunov in Russian encodings.)
o image() was failing with an error when plotting a matrix
of all NA values. (PR#8228)
image() could fail if called with add=FALSE (the default) and
length(x)=1 for either x or y, as it uses the plot coordinates of
the previous plot (if any).
o tools::checkMD5sums was not accepting file names with spaces in.
o The plot() method for TukeyHSD() needed updating after adding
adjusted p-values. (PR#8229)
o read.fwf() did not work for header = TRUE. (PR#8226)
o diag() failed when its argument had NA values in its dimnames.
o [g]sub(pcre=TRUE) did not work correctly with \U and \L in a
UTF-8 locale, even on the example on the help page.
o promptMethods() was failing if the "methods" argument was supplied.
o is.loaded() now finds Fortran symbols whether or not the
registration mechanism has been used.
o ISODateTime() mistakenly corrected non-existent times (when
DST was being started) in the current time zone.
o Some replacement operations on data frames gave incorrect
answers, e.g. DF[3:4, "y"] if column "y" did not exist or was
a matrix.
o getGraphicsEvent() would cause memory corruption if passed an
empty prompt.
o qr() and chol() now pivot the colnames of the result when
pivoting is used. (PR#8258)
o example(points) omitted pch=0, although it was valid and
said in the text to be illustrated.
o plot.default() had an unused 'lab' argument, thereby preventing
the 'lab' graphics parameter being passed through '...' .
o Although polygon(col = NA) was the stated default, specifying
NA was not equivalent to omitting the argument (but col=NULL
was equivalent).
o Im(-1) was pi. (PR#8272, a side effect from all previous
versions of R returning the same value for Im and Arg of
non-complex numbers.)
o symbols(fg) defaulted to colour 1, not par("col") as documented.
It does now defaults to par("col").
o par("family") did not check the length of the value (up to 49
bytes) and so could segfault.
o aggregate.ts() did not allow for rounding in frequencies such
as 1/5.
o prcomp(tol=) was not dropping the sdev's corresponding to
dropped columns.
o Subassignment of a vector which increased the length of the
vector _and_ had the wrong length of replacement could
occasionally segfault. (This has been there since at least
mid 1997.)
o The registration of .Fortran symbols was broken: these could
only be looked up if there were also .Call symbols registered!
o R CMD build was incorrectly rejecting the recommended form of
name for a translation package, 'Translation-ll'. (PR#8314)
o numericDeriv() gave nonsense results unless the variables were
real, which was not checked.
o predict.prcomp() would sometimes give an error when predicting
a single observation. (PR#8324)
o mapply() could segfault if MoreArgs was not a list. (PR#8332)
o The arith-true test used identical() on floating-point results,
and this allowed a failure when the relative difference was
less than .Machine$double.eps but non-zero.
o qbinom() was not accepting p = -Inf when log.p = TRUE, although
it is a legitimate value.
o write.csv[2] only accepted logical constants for 'row.names', and
now accepts variables.
o Conversion of .Rd files did not correctly match braces
enclosing a whole argument, e.g. \eqn{{\bf a}}{a}.
o The C function pythag (used if hypot was not available) would
infinite-loop on systems with effective optimizing compilers.
o Writing long formats (more than 1000 bytes) with connections
that use dummy_vfprintf could fail on some systems. The limit
has been changed to 100000 bytes pending a more complete fix in R
2.3.0.
o Making in src/nmath/standalone without making R was not
making Rmath.h.
o Both the R front-end and INSTALL could find the attempted
temporary directory name already in use on platforms without
mktemp (and a genuine Bourne shell /bin/sh, not bash). Now
both the process ID and a timestamp are used to create the
directory name.
o [dpqr]gamma now return NaN for an invalid 'shape' parameter
(rather than throw an error), for consistency with other
distribution functions.
o t() now longer drops dimnames 'list(NULL,NULL)' or 'list(NULL)'.
o Influence measures such as rstandard() and cooks.distance()
could return infinite values rather than NaN for a case which
was fitted exactly. Similarly, plot.lm() could fail on such
examples. plot.lm(which = 5) had to be modified to only plot
cases with hat < 1. (PR#8367)
lm.influence() was incorrectly reporting 'coefficients' and
'sigma' as NaN for cases with hat = 1, and on some platforms
not detecting hat = 1 correctly.
o Rmath.h for standalone Rmath was not recording HAVE_WORKING_LOG,
so R_log was not available on platforms defining it.
o HoltWinters() was using a slightly incorrect formula in the C code.
o dir.create() could be confused by a trailing slash on the
path, and by paths containing drives on Windows.
o The search for tcl/tkConfig.sh looked in 'lib' before 'lib64'
directories (and not at all in /usr/local/lib64) and so might
prefer 32- to 64-bit versions if both are available.
o nlminb() used an uninitialized variable unless bounds were supplied,
and so failed on 64-bit Solaris.
CHANGES IN R VERSION 2.2.0
USER-VISIBLE CHANGES
o plot(<lm object>) uses a new default 'which = 5'
for the fourth panel when 'which' is not specified.
o The SVN revision number will appear after the date in the
welcome message. The date shown is now the date of the last
change to the sources rather than the date the sources were
prepared.
o is.null(expression()) now returns FALSE. Only NULL gives TRUE
in is.null().
o graphics::xy.coords, xyz.coords and n2mfrow have been moved to
the grDevices name space (to be available for grid as well).
graphics::boxplot.stats, contourLines, nclass.*, and chull
have been moved to the grDevices name space. The C code
underlying chull() has been moved to package grDevices.
o split(x, f), split<-() and unsplit() now by default split by all
levels of a factor f, even when some are empty.
Use split(x, f, drop = TRUE) if you want the old behavior of
dropping empty levels. split() and split<-() are S3 generic
functions with new arguments 'drop' and '...' and all methods now
should have 'drop' and '...' arguments as well.
o The default for 'allowEscapes' in both read.table() and scan()
has been changed to FALSE.
o The default for 'gcFirst' in system.time() is now TRUE.
NEW FEATURES
o .Platform has a new component 'path.sep', the separator used
between paths in environment variables such as PATH and TEXINPUTS.
o anova.mlm() now handles the single-model case.
o Hexadecimal values are now allowed for as.numeric() and
as.integer() on all platforms, and as integer constants in R code.
o attach() now prints an information message when objects are
masked on the search path by or from a newly attached database.
o axis() now returns 'at' positions.
o axis() has a new argument 'hadj' to control horizontal
adjustment of labels.
o axis.Date() and axis.POSIXct() now accept a 'labels' argument
(contributed by Gavin Simpson).
o barplot() now has arguments 'log = ""' and 'add = FALSE'
(as in barplot2() from package 'gplots').
o baseenv() has been added, to return the base environment. This
is currently still NULL, but will change in a future release.
o boxplot() now responds to supplying 'yaxs' (via bxp()).
(Wish of PR#8072.)
o capabilities() has a new component 'NLS'.
o cbind() and rbind() now react to 'deparse.level' = {0,1,2}
(as in another system not unlike R).
o Experimental versions of cbind() and rbind() in methods package,
based on new generic function cbind2(x,y) and rbind2(). This will
allow the equivalent of S4 methods for cbind() and rbind() ---
currently only after an explicit activation call, see ?cbind2.
o New functions cdplot() and spineplot() for conditional density
plots and spine plots or spinograms. Spine plots are now used
instead of bar plots for x-y scatterplots where y is a factor.
o checkDocFiles() in package 'tools' now checks for bad \usage
lines (syntactically invalid R code).
o The nonparametric variants of cor.test() now behave better in
the presence of ties. The "spearman" method uses the asymptotic
approximation in that case, and the "kendall" method likewise,
but adds a correction for ties (this is not necessary in the
Spearman case).
o The X11 dataentry() now has support for X Input Methods
(contributed by Ei-ji Nakama).
o density() is now an S3 generic where density.default() {former
density()} has new argument 'weights' for specifying observation
masses different than the default 1/N -- based on a suggestion and
code from Adrian Baddeley.
o download.packages() now carries on if it encounters a download
error (e.g. a repository with a corrupt index).
o dump() now skips missing objects with a warning rather than
throw an error.
o Added "POSIXlt" methods for duplicated() and unique().
o Function encoded_text_to_latex() in package tools translates
Latin 1,2,9 and UTF-8 encoded character vectors to LaTeX
escape sequences where appropriate.
o encodeString() allows justify = "none" for consistency with
format.default(). Some argument names have been lengthened
for clarity.
o file(), fifo() and pipe() now (if possible) report a reason
if they fail to open a connection.
o format.default() now has a 'width' argument, and 'justify' can
now centre character strings.
format.default() has new arguments 'na.encode' to control
whether NA character strings are encoded (true by default),
and 'scientific' to control the use of fixed/scientific
notation for real/complex numbers.
How format() works on a list is now documented, and uses
arguments consistently with their usage on an atomic vector.
o format.info() now has a 'digits' argument, and is documented
to work for all atomic vectors (it used to work for all but
raw vectors.).
o New function glob2rx() for translating `wildcard' aka `globbing'
to regular expressions.
o There is a new function gregexpr() which generalizes regexpr()
to search for all matches in each of the input strings (not
just the first match).
o [g]sub() now have a 'useBytes' argument like grep() and regexpr().
o [g]sub(perl = TRUE) support \L and \U in the replacement.
o iconv() has been moved from 'utils' to 'base'.
o identify()'s default method has additional arguments 'atpen'
and 'tolerance' (following S).
o KalmanForecast() and KalmanLike() now have an optional argument
fast=FALSE to prevent their arguments being modified.
o Exact p-values are available in ks.test() for the one-sided and
two-sided one-sample Kolmogorov-Smirnov tests.
o labels() now has a method for "dist" objects (replacing that
for names() which was withdrawn in 2.1.0).
o library() now explicitly checks for the existence of
directories in 'lib.loc': this avoids some warning messages.
o loadNamespace(keep.source=) now applies only to that name space
and not others it might load to satisfy imports: this is now
consistent with library().
o match.arg() has a new argument 'several.ok = FALSE'.
o max.col() has a new argument for non-random behavior in the
case of ties.
o memory.profile() now uses the type names returned by typeof()
and no longer has two unlabelled entries.
o methods() now warns if it appears to have been called on a
non-generic function.
o The default mosaicplot() method by default draws grey boxes.
o nlminb(), similar to that in S-PLUS, added to package 'stats'.
o New algorithm "port" (the nl2sol algorithm available in the
Port library on netlib) added to the nls() function in the
'stats' package.
o object.size() now supports more types, including external
pointers and weak references.
o options() now returns its result in alphabetical order, and is
documented more comprehensively and accurately. (Now all
options used in base R are documented, including
platform-specific ones.)
Some options are now set in the package which makes use of
them (grDevices, stats or utils) if not already set when the
package is loaded.
o New option("OutDec") to set the decimal point for output conversions.
o New option("add.smooth") to add smoothers to a plot, currently
only used by plot.lm().
o pie() has new optional arguments 'clockwise' and 'init.angle'.
o plot.lm() has two new plots (for 'which' = 5 or 6), plotting
residuals or cook distances versus (transformed) leverages - unless
these are constant. Further, the new argument 'add.smooth' adds a
loess smoother to the point plots by default, and 'qqline = TRUE'
adds a qqline() to the normal plot.
The default for 'sub.caption' has been improved for long calls.
o R.home() has been expanded to return the paths to components
(which can as from this version be installed elsewhere).
o readbin() and writeBin() now support raw vectors as well as
filenames and connections.
o read.dcf() can now read gzipped files.
o read.table() now passes 'allowEscapes' to scan().
o sample(x, size, prob, replace = TRUE) now uses a faster
algorithm if there are many reasonably probable values. (This
does mean the results will be different from earlier versions
of R.) The speedup is modest unless 'x' is very large _and_
'prob' is very diffuse so that thousands of distinct values
will be generated with an appreciable frequency.
o scatter.smooth() now works a bit more like other plotting
functions (e.g., accepts a data frame for argument 'x').
Improvements suggested by Kevin Wright.
o signif() on complex numbers now rounds jointly to give the
requested number of digits in the larger component, not
independently for each component.
o New generic function simulate() in the 'stats' package with
methods for some classes of fitted models.
o smooth.spline() has a new argument 'keep.data' which allows to
provide residuals() and fitted() methods for smoothing splines.
o Attempting source(file, chdir=TRUE) with a URL or connection
for 'file' now gives a warning and ignores 'chdir'.
o source() closes its input file after parsing it rather than
after executing the commands, as used to happen prior to
2.1.0. (This is probably only significant on Windows where
the file is locked for a much shorter time.)
o split(), split<-(), unsplit() now have a new argument 'drop = FALSE',
by default not dropping empty levels; this is *not* back compatible.
o sprintf() now supports asterisk `*' width or precision
specification (but not both) as well as `*1$' to `*99$'. Also the
handling of `%' as conversion specification terminator is now
left to the system and doesn't affect following specifications.
o The plot method for stl() now allows the colour of the range
bars to be set (default unchanged at "light gray").
o Added tclServiceMode() function to the tcltk package to allow
updating to be suspended.
o terms.formula() no longer allows '.' in a formula unless there
is a (non-empty) 'data' argument or 'allowDotAsName = TRUE' is
supplied. We have found several cases where 'data' had not
been passed down to terms() and so '.' was interpreted as a
single variable leading to incorrect results.
o New functions trans3d(), the 3D -> 2D utility from persp()'s
example, and extendrange(), both in package 'grDevices'.
o TukeyHSD() now returns p-values adjusted for multiple comparisons
(based on a patch contributed by Fernando Henrique Ferraz P. da Rosa).
o New functions URLencode() and URLdecode(), particularly for use
with file:// URLs. These are used by e.g. browse.env(),
download.file(), download.packages() and various help() print
methods.
o Functions utf8ToInt() and intToUtf8() to work with UTF-8
encoded character strings (irrespective of locale or OS-level
UTF-8 support).
o [dqp]wilcox and wilcox.test work better with one very large sample
size and an extreme first argument.
o write() has a new argument 'sep'.
o write.csv[2] now also support row.names = FALSE.
o The specification of the substitutions done when processing
Renviron files is more liberal: see ?Startup. It now
accepts forms like R_LIBS=${HOME}/Rlibrary:${WORKGRP}/R/lib .
o Added recommendation that packages have an overview man page
<pkg>-package.Rd, and the promptPackage() function to create a
skeleton version.
o Replacement indexing of a data frame by a logical matrix index
containing NAs is allowed in a few more cases, in particular
always when the replacement value has length one.
o Conversion of .Rd files to latex now handles encoding more
comprehensively, including some support for UTF-8.
o The internal regex code has been upgraded to glibc-2.3.5.
Apart from a number of bug fixes, this should be somewhat
faster, especially in UTF-8 locales.
o PCRE has been updated to version 6.2.
o zlib has been updated to version 1.2.3.
o bzip2 has been updated to version 1.0.3.
o Complex arithmetic is now done by C99 complex types where
supported. This is likely to boost performance, but is
subject to the accuracy with which it has been implemented.
o The printing of complex numbers has changed, handling numbers
as a whole rather than in two parts. So both real and
imaginary parts are shown to the same accuracy, with the
'digits' parameter referring to the accuracy of the larger
component, and both components are shown in fixed or
scientific notation (unless one is entirely zero when it is
always shown in fixed notation).
o Error messages from .C() and .Fortran(), and from parsing errors,
are now more informative.
o The date and date-time functions work better with dates more
than 5000 years away from 1970-01-01 (by making dubious
assumptions about the calendar in use).
o There is now a traditional Chinese translation, and a much more
extensive Russian translation.
DEPRECATED & DEFUNCT
o Capability "IEEE754" is defunct.
o loadURL() is defunct: use load(url()).
o delay() is defunct: use delayedAssign() instead.
o The 'CRAN' argument to update.packages(), old.packages(),
new.packages(), download.packages() and install.packages() is
defunct in favour of 'repos'.
o write.table0() is deprecated in favour of the much faster
write.table().
o format.char() is deprecated in favour of format.default().
o R_HOME/etc/Rprofile is no longer looked for if
R_HOME/etc/Rprofile.site does not exist. (This has been
undocumented since R 1.4.0.)
o CRAN.packages() is deprecated in favour of available.packages().
o Rd.sty no longer processes pre-2.0.0 conversions containing \Link.
o The stubs for the defunct device GNOME/gnome have been removed.
o print.matrix() (which has been identical to print.default since
R 1.7.0) has been removed.
INSTALLATION
o LDFLAGS now defaults to -L/usr/local/lib64 on most Linux
64-bit OSes (but not ia64). The use of lib/lib64 can be
overridden by the new variable LIBnn.
o The default installation directory is now ${prefix}/${LIBnn}/R,
/usr/local/lib64/R on most 64-bit Linux OSes and /usr/local/lib/R
elsewhere.
o The places where the doc, include and share directory trees are
installed can be specified independently: see the R-admin manual.
o We now test for wctrans_t, as apparently some broken OSes have
wctrans but not wctrans_t (which is required by the relevant
standards) .
o Any external BLAS found is now tested to see if the complex
routine zdotu works correctly: this provides a compatibility
test of compiler return conventions.
o Installation without NLS is now cleaner, and does not install
any message catalogues.
o src/modules/lapack/dlamc.f is now compiled with -ffloat-store
if f2c/gcc are used, as well as if g77 is used.
o All the Fortran code has been checked to be fully F77
compliant so there are no longer any warnings from F95
compilers such as gfortran.
o The (not-recommended) options --with-system-zlib,
--with-system-bzlib and -with-system-pcre now have 'system' in
the name.
o If a Java runtime environment is detected at configure time
its library path is appended to LD_LIBRARY_PATH or equivalent.
New Java-related variables JAVA_HOME (path to JRE/JDK), JAVA_PROG
(path to Java interpreter), JAVA_LD_PATH (Java library path)
and JAVA_LIBS (flags to link against JNI) are made available
in Makeconf.
o Ei-ji Nakama was contributed a patch for FPU control with the
Intel compilers on ix86 Linux.
MAC OS X INSTALLATION
o --with-blas="-framework vecLib" --with-lapack and
--with-aqua are now the default configure options.
o The default framework version name was changed to not contain
the patch level (i.e. it is now 2.2 instead of 2.2.0). Also
it can be overridden at configure time by setting FW_VERSION
to the desired name.
o The Rmath stand-alone library is now correctly installed inside
the R.framework if R was configured as a framework. In
addition, make install-Rmath-framework will install a
stand-alone Rmath framework in /Library/Frameworks (unless
overridden by RMATH_FRAMEWORK_DIR specifying full framework
path and name including the .framework extension).
PACKAGE INSTALLATION
o The encoding for a packages' 00Index.html is chosen from the
Encoding: field (if any) of the DESCRIPTION file and from the
\encoding{} fields of any Rd files with non-ASCII titles.
If there are conflicts, first-found wins with a warning.
o R_HOME/doc/html/packages.html is now remade by R not Perl code.
This may result in small changes in layout and a change in
encoding (to UTF-8 where supported).
o The return value of new.packages() is now updated for any
packages which may be installed.
o available.packages() will read a compressed PACKAGES.gz file in
preference to PACKAGES if available on the repository: this
will reduce considerably the download time on a dialup connection.
The downloaded information about a repository is cached for the
current R session.
o The information about library trees found by
installed.packages() is cached for the current session, and
updated only if the modification date of the top-level
directory has been changed.
o A data index is now installed for a package with a 'data' dir
but no 'man' dir (even though it will have undocumented data objects).
o contrib.url path for type="mac.binary" has changed from
bin/macosx/<version> to bin/macosx/<arch>/contrib/<version>
where <arch> corresponds to R.version$arch
UTILITIES
o checkFF() used by R CMD check has since R 2.0.0 not reported
missing PACKAGE arguments when testing installed packages with
name spaces. It now
- treats installed and source packages in the same way.
- reports missing arguments unless they are in a function in
the name space with a useDynLib declaration (as the
appropriate DLL for such calls can be searched for).
o Rd2dvi sets the encoding(s) used appropriately. If UTF-8
encoding is used, latex >= 2003/12/01 is required.
o codoc() allows help files named pkg_name-defunct.Rd to have
undocumented arguments (and not just base-defunct.Rd).
C-LEVEL FACILITIES
o C function massdist() {called from density()} has new argument
'xmass' (= weights).
o Raw vectors passed to .C() are now passed as unsigned char *
rather than as SEXPs. (Wish of Keith Frost, PR#7853)
o The search for symbols in a .C/.Call/... call without a
package argument now searches for an enclosing name space and
so finds functions defined within functions in a name space.
o R_max_col() has new (5th) argument '*ties_meth' allowing
non-random behavior in the case of ties.
o The header files have been rationalized: the BLAS routine
LSAME is now declared in BLAS.h not Linpack.h, Applic.h no
longer duplicates routines from Linpack.h, and Applic.h is
divided into API and non-API sections.
o memory.c has been instrumented so that Valgrind can track R's
internal memory management. To use this, configure using
--with-valgrind-instrumentation=level
where level is 1 or 2. Both levels will find more bugs with
gctorture(TRUE). Level 2 makes Valgrind run extremely slowly.
o Some support for raw vectors has been added to Rdefines.h.
o R_BaseEnv has been added, to refer to the base environment.
This is currently equal to R_NilValue, but it will change in
a future release.
BUG FIXES
o %/% has been adjusted to make x == (x %% y) + y * ( x %/% y )
more likely in cases when extended-precision registers were
interfering.
o Operations on POSIXct objects (such as seq(), max() and
subsetting) try harder to preserve time zones and warn if
inconsistent time zones are used.
o as.function.default() no longer asks for a bug report when
given an invalid body. (PR#1880, PR#7535, PR#7702)
o Hershey fonts and grid output (and therefore lattice output)
now rescale correctly in fit-to-window resizing on a Windows
graphics device. Line widths also scale now.
o Plotmath has more support for multibyte characters (contributed
by Ei-ji Nakama).
o The X11() device now hints the window manager so that decorations
appear reliably under e.g. the GNOME WM (contributed
by Ei-ji Nakama).
o Subsetting a matrix or an array as a vector used to attempt to
use the row names to name the result, even though the
array might be longer than the row names. Now this is only
done for 1D arrays when it is done in all cases, even matrix
indexing. (Tidies up after the fix to PR#937.)
o Constants in mathlib are declared 'const static double' to
avoid performance issues with the Intel Itanium compiler.
o The parser checks the format of numeric constants more
thoroughly so for example '123E-' is no longer valid.
o contourLines() no longer requires an open device (used to
start a device unnecessarily). Fix suggested by Barry Rowlingson.
o capabilities() used partial matching but was not documented
to: it no longer does so.
o kernel(1,0) printed wrongly; kernel(<name-string>, *) now returns
a named kernel in all cases; plot(kernel(.),..) is more flexible.
o qgamma(1,s) didn't give +Inf for some s.
o installed.packages() and download.packages() now always
return a matrix as documented, possibly with 0 rows (rather than
a 0-length character vector or NULL).
o Arithmetic operations on data frames no longer coerce the
names to syntatically valid names.
o Units are now properly recycled in grid layouts
when 'widths' or 'heights' are shorter than the number of
columns or rows (PR#8014).
o DF <- data.frame(A=1:2, B=3:4); DF[1, 1:3] <- NULL gave a wrong
error message.
o spline()/spinefun()'s C code had a memory access buglet which
never lead to incorrect results. (PR#8030)
o sum() was promoting logical arguments to double not integer
(as min() and other members of its group do).
o loess() had a bug causing it to occasionally miscalculate
standard errors (PR#7956). Reported by Benjamin Tyner, fixed
by Berwin Turlach.
o library(keep.source=) was ignored if the package had a
name space (the setting of options("keep.source.pkgs") was
always used).
o hist.POSIXct() and hist.Date() now respect par("xaxt").
o The 'vfont' argument was not supported correctly in title(),
mtext(), and axis(). The 'vfont' argument is superseded by
the par(family=) approach introduced in 2.0.0. This bug-fix
just updates the warning messages and documentation to
properly reflect the new order of things.
o The C-level function PrintGenericVector could overflow if
asked to print a length-1 character vector of several thousand
characters. This could happen when printing a list matrix,
and was fatal up to 2.1.1 and silently truncated in 2.1.1 patched.
o What happened for proc.time() and system.time() on
(Unix-alike) systems which do not support timing was
incorrectly documented. (They both exist but throw an error.)
Further, systen.time() would give an error in its on.exit
expression.
o weighted.residuals() now does sensible things for glm() fits:
in particular it now agrees with an lm() fit for a Gaussian glm()
fit. (PR#7961).
o The 'lm' and 'glm' methods for add1() took the weights and
offset from the original fit, and so gave errors in the
(dubious) usage where the upper scope resulted in a smaller
number of cases to fit (e.g. by omitting missing values in new
variables). (PR#8049)
o demo() had a 'device' argument that did nothing (although it
was documented to): it has been removed.
o Setting new levels on a factor dropped all existing
attributes, including class "ordered".
o format.default(justify="none") now by default converts NA
character strings, as the other values always did.
o format.info() often gave a different field width from format()
for character vectors (e.g. including missing values or
non-printable characters).
o axis() now ensures that if 'labels' are supplied as character
strings or expressions then 'at' is also supplied (since the
calculated value for 'at' can change under resizing).
o Defining S4 methods for "[" had resulted in changed behavior of S3
dispatch in a very rare case which no longer happens.
o Fixed segfault when PostScript font loading fails, e.g., when
R is unable to find afm files (reported by Ivo Welch).
o R CMD BATCH <file> now also works when <file> does not end in a
newline on Unix-alike platforms.
o terms.formula() got confused if the 'data' argument was a list with
non-syntactic names.
o prompt() and hence package.skeleton() now produce *.Rd files that
give no errors (but warnings) when not edited, much more often.
o promptClass() and promptMethods() now also escape "%" e.g. in '%*%'
and the latter gives a message about the file written.
o wilcox.test() now warns when conf.level is set higher than
achievable, preventing errors (PR#3666) and incorrect answers
with extremely small sample sizes.
o The default (protection pointer) stack size (the default for
'--max-ppsize') has been increased from 10000 to 50000 in order to
match the increased default options("expressions") (in R 2.1.0).
o The R front-end was expecting --gui=tk not Tk as documented,
and rejecting --gui=X11.
o Rdconv -t latex protected only the first << and >> in a chunk
against conversion to guillemets.
o callNextMethod() and callGeneric() have fixes related to
handling arguments.
o ls.diag() now works for fits with missing data. (PR#8139)
o window.default() had an incorrect tolerance and so sometimes
created too short a series if 'start' or 'end' were zero.
o Some (fairly pointless) cases of reshape left a
temporary id variable in the result (PR#8152)
o R CMD build used 'tar xhf' which is invalid on FreeBSD systems
(and followed tar chf, so there could be no symbolic links in
the tarball).
o Subassignment of length zero vectors to NULL gave garbage
answers. (PR#8157)
o Automatic coercion of raw vectors to lists was missing, so for a
list (or data frame) z, z[["a"]] <- raw_vector did not work
and now does. This also affected DF$a <- raw_vector for a
data frame DF.
o The internal code for commandArgs() was missing PROTECTs.
o The width for strwrap() was used as one less than specified.
o R CMD INSTALL was not cleaning up after an unsuccessful
install of a non-bundle which was not already installed.
**************************************************
* *
* 2.1 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.1.1 patched
BUG FIXES
o runmed(x, k = -1) now gives an error instead of a seg.fault.
o File creation errors in pdf(), postscript(), xfig() resulted
in a pointer being freed twice. (Reported by Matt McCall)
o model.matrix(~ .^2, data=foo) now works as most people would
expect (it used to expand '.' after using the a^2 = a rule).
o ftable() and xtabs() had a check for interactions that would
not work correctly with '.' in the formula.
o The formula method for pairs() was ignoring the na.action argument.
o scan() with the default separator (only) was stripping backslashes
inside quoted string inputs even if allowEscapes = FALSE.
o The "col" parameter to pairs() is now treated consistently with
plot(): it affects the data, not the axes. (Patch submitted
by Olaf Mersmann)
o Sweave failed for \Sexpr{character(0)}. Sweave-test-1.Rnw
contained a print() statement that is no longer needed.
o Typo meant that R_alloc was limited to 2^31 not 2^34 on 64-bit
builds of R.
o pgamma(Inf, shape) did not terminate for shape = 1.1 and some
other values (but not all) (PR#8001). This affected
pchisq(Inf, df1) and pf(Inf, df1, Inf) for some values of df1.
o regexpr("[a-z]", ...) could cause a buffer overrun with multi-byte
character sets, leading to random errors later.
o Installing a package with a 'data' directory which contains
files but those files generate no objects (e.g. the BioC
package makecdfenv) created an incorrectly formatted data
index that data(package="pkg") could not read.
o density(1/(0:2)) now works again (PR#8033).
o make.names() was not respecting the allow_=FALSE argument.
o Arg(-1) now gives pi, not 0; Arg(0i + -1) always worked.
o --enable-linux-lfs had been broken at 2.1.0.
o Printing was not allowing for double-width characters in its
layout.
o axTicks() is now also correct for reverse axis. (PR#7973)
o signif() rounded some numnbers near 1e-308 to the wrong
number of places (this showed up in the print-tests.R), and made
unnecessary rounding errors on some platforms on e.g. signif(18000, 3).
o window() was sometimes failing incorrectly due to representation
errors when the new and old deltat were not both integers
(e.g. multiples of 0.1).
o The 'lm' methods for add1() and drop1() ignored offsets (which
were added for lm() after they written). (PR#8049)
o atan2(0+1i, 0+0i) was incorrectly NA (from a typo in complex.c).
o The POSIXct method for as.Date() was rounding part days
before 1970-01-01 upwards rather than discarding them.
o qpois() was using an incorrect starting point and so could be
unnecessarily slow for large lambda. (PR#8058)
o Formatting of complex numbers with nsmall > 0 could be
incorrect (and was in print-tests.Rout) because of a typo.
o The test for new levels when predicting using model.frame()
sometimes reported levels that were not actually used.
o order(c("5","6",NA,"4",NA), na.last=FALSE) was incorrect.
o Coercion to raw could give spurious messages about discarding
imaginary parts.
Coercion of a list to raw was behaving inconsistently for
out-of-range values (and not warning).
o cor.test(method = "spearman") gave NA p-values for _very_ long
vectors. (PR#8087)
o Switching to the Mersenne-Twister RNG could cause a segfault on
first use.
A user-supplied RNG without user_unif_{nseed,seedloc} was
being re-initialized at each call.
o Reading very short tables from stdin() with read.table would
fail because of a typo.
CHANGES IN R VERSION 2.1.1
NEW FEATURES
o bug.report() now reports the locale in use.
o upgrade.packageStatus() allows user input "c" to cancel the
upgrade, just as update.packages() does.
o glm() now accepts 1D arrays (e.g. tables) as a response,
dropping them to a vector whilst preserving names.
o df() with one infinite df now works (to match pf()).
o Added tclServiceMode() function to the tcltk package to allow
updating to be suspended.
o The Encoding: field of a DESCRIPTION file is now documented,
and used by packageDescription() and library(help=).
o There has been progress on translations: existing translations
have been revised and expanded, and French and Korean have
been added.
The Windows installer supports a wide range of languages for
installation.
BUG FIXES
o lm(qr=FALSE) now works.
o predict.glm() not longer loses names for "response" predictions.
(PR#7792)
o Typo in menu(graphics=TRUE) meant it failed on Unix if tcltk
was not available.
o When names.dist() was removed, the result of cmdscale() lost
its rownames. The example also lost the labels.
o R CMD check assumed 'tar' was GNU tar and so supported -z.
o read.table() was not handing escaped quotes inside quoted fields
in the first five lines of the file. (PR#7789)
It was also not handling correctly EOF in the first five lines
when reading from stdin(). (PR#7772)
o 'make uninstall' was incomplete.
o make.packages.html() called by help.start() was failing if
there were installed packages with help titles invalid in the
current locale.
o printCoefmat(signif.legend = FALSE) was non-functional. (PR#7802)
o Some as.date.frame() methods failed because the expression
deparsed into multiple lines. (PR#7808)
o setRepositories() had a typo. (PR#7810)
o Printing arrays/data frames with multibyte characters in the
column labels was sometimes misaligned or using excessive space.
(PR#7803)
o The Tcl/Tk console did not support multibyte characters.
o as.POSIXlt() could give infinite recursion if passed a corrupt
"POSIXct" object (generated by an incorrect call to c.POSIXct,
PR#7826).
o update.packages() was not passing 'type' correctly to
install.packages().
o Printing the result of an unbalanced model.tables() call
sometimes got confused if terms() had rearranged interaction
terms. (PR#7829)
o .Platform$pkgType was wrong on the CRAN MacOS X build, and
.install.macbinary() was missing.
o as.personList() as used by citation() got confused by names
containing "and". (PR#7797)
o Subscripting an array by a matrix containing zero or negative
values or the wrong number of columns was not handled
consistently. (PR#7824)
o select.list(multiple=TRUE) now detects and tries again for invalid
text input.
o add1.[g]lm could give strange results with interaction terms
when the model and the upper scope had different orders for
the main effects. (PR#7842)
o A bug had sneaked into the anova.mlmlist() code, affecting the
Greenhouse-Geisser epsilon. Code wrongly assumed a matrix to
be symmetric. (Thanks to Bela Bauer.)
o anova.mlmlist() and mauchley.test() are now more tolerant to rank
deficiency in the M and X matrices (also when they are implicitly
generated via model.matrix()).
o anova.mlm had a scoping issue (PR#7898)
o pf() with infinite df is allowed again. It is now more accurate
for extreme ratios of dfs, especially when there is a
non-centrality parameter.
o df() was inaccurate for large df (1e16 or greater).
o dt() was inaccurate for large df (1e9 or greater) with a
non-centrality parameter.
o runmed(*, algorithm="Turlach") seg.faulted in rare cases.
o strwrap() now makes a reasonable job of text that is invalid in the
current locale.
o Reading with encoding "UCS-2LE" will remove any Byte Order
Mark, as most implementations of iconv fail to handle BOMs
(which are present in 'Windows Unicode' files).
o unique() for a list was incorrectly reporting `unimplemented'.
o The parser's contextstack was not protected against overflow,
e.g. more than 50 unmatched '('. (PR#7859)
o source(file, chdir = TRUE) was not checking that 'file' was a
filepath (rather than a URL). For 2.1.0 only, it did not work
even if 'file' was a filepath.
o Hershey fonts were being sized based on pixels not points so came
out too small on devices where pixels were noticeably different
from points (e.g., win.printer() and high-resolution screens).
Fix means that default size of Hershey fonts may be slightly
different, for example, smaller by default on PostScript and PDF.
o The branch cuts in the complex versions of the inverse
trigonometric and hyperbolic functions were non-standard.
(PR#7871)
o truncate() on file() connections was limited to files < 2Gb. It
now works for larger files at least on 64-bit OSes and others
where ftruncate supports such files. (Related to PR#7879)
o proj.aovlist() did not work correctly on objects fitted from a
data frame with row names.
o The coding standards recommendations had
nuke-trailing-whitespace where newer versions of ESS need
ess-nuke-trailing-whitespace. (PR#7888)
o package.skeleton() missed the first newline in the DESCRIPTION file.
o pbirthday() reported p = 1 too often when coincident > 2.
o plot(1:3, exp(1:3), log = "y", ylim = c(30,1)) {reversed
log-scale axis} now works, based on Uwe Ligges' suggestions.
(PR#7894)
o install.packages() was aborting when a package in a bundle was
chosen from a menu. It failed if more than one package in a
bundle was chosen from the command line.
o qcauchy() suffered from underflow in the extreme tails. (PR#7902)
o Printing of raw matrices/arrays was not implemented. (PR#7912)
o getCallingDLL()'s default first argument did not correspond to
its description and has been changed. The mismatch caused
symbols in .C/.Call/.Fortran calls without a PACKAGE= argument
to be potentially looked up in the wrong name space.
o Binary save() of raw vectors was not working correctly on
big-endian platforms. (PR#7812)
o as.Date.factor() now accepts a format argument.
o Workaround added for FreeBSD which does not have alloca.h _and_
does not allow alloca() to be declared.
o identify() now respects 'cex'. (PR#660)
Warnings from identify() are now printed immediately even on
consoles with delayed printing.
CHANGES IN R VERSION 2.1.0
USER-VISIBLE CHANGES
o box plots {by boxplot() or bxp()} now have the median line three
times the normal line width in order to distinguish it from the
quartile ones.
o Unix-alike versions of R can now be used in UTF-8 locales on
suitably equipped OSes. See the internationalization section
below.
o The meaning of 'encoding' for a connection has changed: See the
internationalization section below.
o There has been some rationalization of the format of
warning/error messages, to make them easier to translate.
Generally names of functions and arguments are single-quoted,
and classes double-quoted.
o Reading text files with embedded "\" (as in Windows file names)
may now need to use scan(* , allowEscapes = FALSE), see also below.
NEW FEATURES
o %% now warns if its accuracy is likely to be affected by lack
of precision (as in 1e18 %% 11, the unrealistic expectation of
PR#7409), and tries harder to return a value in range when it is.
o abbreviate() now warns if used with non-ASCII chars, as the
algorithm is designed for English words.
o The default methods for add1() and drop1() check for changes
in the number of cases in use.
The "lm" and "glm" methods for add1() quoted the <none> model
on the original fitted values when using (with a warning) a
smaller set of cases for the expanded models.
o Added alarm() function to generate a bell or beep or visual alert.
o all/any() now attempt to coerce their arguments to logical, as
documented in the Blue Book. This means e.g. any(list()) works.
o New functions for multivariate linear models: anova.mlm(),
SSD(), estVar(), mauchley.test() (for sphericity).
vcov() now does something more sensible for "mlm" class objects.
o as.data.frame.table() has a new argument 'responseName'
(contributed by Bill Venables).
o as.dist() and cophenetic() are now generic, and the latter has a
new method for objects of class "dendrogram".
o as.ts() is now generic.
o binomial() has a new "cauchit" link (suggested by Roger Koenker).
o chisq.test() has a new argument 'rescale.p'. It is now possible
to simulate (slowly) the P value also in the 1D case
(contributed by Rolf Turner).
o choose(n,k) and lchoose(.) now also work for arbitrary (real) n
in accordance with the general binomial theorem. choose(*,k)
is more accurate (and faster) for small k.
o Added colorRamp() and colorRampPalette() functions for color
interpolation.
o colSums()/rowSums() now allow arrays with a zero-length extent
(requested by PR#7775).
o confint() has stub methods for classes "glm" and "nls" that
invoke those in package MASS. This avoids using the "lm"
method for "glm" objects if MASS is not attached.
confint() has a default method using asymptotic normality.
o contr.SAS() has been moved from the 'nlme' package to the
'stats' package.
o New function convertColors() maps between color spaces.
colorRamp() uses it.
o The cov() function in the non-Pearson cases now ranks data after
removal of missing values, not before. The pairwise-complete
method should now be consistent with cor.test. (Code
contributed by Shigenobu Aoki.)
o Added delayedAssign() function to replace delay(), which is now
deprecated.
o dir.create() has a new argument 'recursive' serving the same
purpose as Unix's mkdir -p.
o do.call() now takes either a function or a character string as
its first argument. The supplied arguments can optionally be
quoted.
o duplicated() and unique() now accept "list" objects, but are
fast only for simple list objects.
o ecdf() now has jumps of the correct size (a multiple of 1/n)
if there are ties. (Wished by PR#7292).
o eff.aovlist() assumed orthogonal contrasts for any term
with more than one degree of freedom: this is now documented
and checked for. Where each term only occurs in only one
stratum the efficiencies are all one: this is detected and
orthogonal contrasts are not required.
o New function encodeString() to encode character strings in the
same way that printing does.
o file("clipboard") now work for reading the primary selection on
Unix-alikes with an active X11 display. (It has long worked
for reading and writing under Windows.) The secondary
selection can also be read: see ?file.
file() now allows mode "w+b" as well as "w+".
o file.append() has been tuned, including for the case of
appending many files to a single file.
o Functions flush.console() and select.list() are now available
on all platforms. There is a Tcl/Tk-based version of
select.list() called tk_select.list() in package tcltk.
o gc() now reports maximum as well as current memory use.
o A new function getGraphicsEvent() has been added which will allow
mouse or keyboard input from a graphics device. (NB: currently
only the Windows screen device supports this function. This
should improve before the 2.1.0 release.)
o New functions gray.colors()/grey.colors() for gray color
palettes.
o grep(), gsub(), sub() and regexpr() now always attempt to
coerce their 'pattern', 'x', 'replacement' and 'text'
arguments to character. Previously this was undocumented but
done by [g]sub() and regexpr() for some values of their
other arguments. (Wish of PR#7742.)
o gsub/sub() have a new 'fixed' method.
o New function hcl() for creating colors for a given hue,
chroma and luminance (i.e. perceptual hsv).
o isTRUE() convenience function to be used for programming.
o kmeans() now returns an object of class "kmeans" which has a
print() method.
Two alternative algorithms have been implemented.
If the number of centres is supplied, it has a new option of
multiple random starts.
o The limits on the grid size in layout() are now documented, and
have been raised somewhat by using more efficient internal
structures.
o legend() now accepts positioning by keyword, e.g. "topleft",
and can put a title within the legend. (Suggested by Elizabeth
Purdom in PR#7400.)
o mahalanobis() now has a '...' argument which is passed to solve()
for computing the inverse of the covariance matrix, this replaces
the former 'tol.inv' argument.
o menu() uses a multi-column layout if possible for more than
10 choices.
menu(graphics = TRUE) is implemented on most platforms via
select.list() or tk_select.list().
o New function message() in 'base' for generating "simple"
diagnostic messages, replacing such a function in the
'methods' package.
o na.contiguous() is now (S3) generic with first argument
renamed to 'object'.
o New function normalizePath() to find canonical paths (and on
Windows, canonical names of components).
o The default in options("expressions") has been increased to 5000,
and the maximal settable value to 500000.
o p.adjust() has a new method "BY".
o pbeta() now uses a different algorithm for large values of at
least one of the shape parameters, which is much faster and is
accurate and reliable for very large values. (This affects
pbinom(), pf(), qbeta() and other functions using pbeta at C
level.)
o pch="." now by default produces a rectangle at least 0.01" per
side on high-resolution devices. (It used to be one-pixel
square even on high-resolution screens and Windows printers,
but 1/72" on postscript() and pdf() devices.) Additionally,
the size is now scalable by 'cex'; see ?points and note that
the details are subject to change.
o pdf() now responds to the 'paper' and 'pagecentre'
arguments. The default value of 'paper' is "special"
for backward-compatibility (this is different from the
default for postscript()).
o plot.data.frame() tries harder to produce sensible plots for
non-numeric data frames with one or two columns.
o The predict() methods for "prcomp" and "princomp" now match
the columns of 'newdata' to the original fit using column
names if these are available.
o New function recordGraphics() to encapsulate calculations
and graphics output together on graphics engine display list.
To be used with care.
o New function RSiteSearch() to query R-related resources
on-line (contributed by Jonathan Baron and Andy Liaw).
o scan() arranges to share storage of duplicated character
strings read in: this can dramatically reduce the memory
requirements for large character vectors which will
subsequently be turned into factors with relatively few
levels. For a million items this halved the time and reduced
storage by a factor of 20.
scan() has a new argument 'allowEscapes' (default TRUE) that
controls when C-style escapes in the input are interpreted.
Previously only \n and \r were interpreted, and then only
within quoted strings when no separator was supplied.
scan() used on an open connection now pushes back on the
connection its private `ungetc' and so is safer to use to
read partial lines.
o scatter.smooth() and loess.smooth() now handle missing values
in their inputs.
o seq.Date() and seq.POSIXt() now allow 'to' to be before 'from'
if 'by' is negative.
o sprintf() has been enhanced to allow the POSIX/XSI specifiers
like "%2$6d", and also accepts "%x" and "%X".
sprintf() does limited coercion of its arguments.
sprintf() accepts vector arguments and operates on them in
parallel (after re-cycling if needed).
o New function strtrim() to trim character vectors to a display
width, allowing for double-width characters in multi-byte
character sets.
o subset() now has a method for matrices, similar to that for
data frames.
o Faster algorithm in summaryRprof().
o sunflowerplot() has new arguments 'col' and 'bg'.
o sys.function() now has argument 'which' (as has long been
presaged on its help page).
o Sys.setlocale("LC_ALL", ) now only sets the locale categories
which R uses, and Sys.setlocale("LC_NUMERIC", ) now gives a
warning (as it can cause R to malfunction).
o unclass() is no longer allowed for environments and external
pointers (since these cannot be copied and so unclass() was
destructive of its argument). You can still change the
"class" attribute.
o File-name matching is no longer case-insensitive with unz()
connections, even on Windows.
o New argument 'immediate.' to warning() to send an immediate
warning.
o New convenience wrappers write.csv() and write.csv2().
o There is a new version for write.table() which is implemented in C.
For simple matrices and data frames this is several times
faster than before, and uses negligible memory compared to the
object size.
The old version (which no longer coerces a matrix to a data
frame and then back to a matrix) is available for now as
write.table0().
o The functions xinch(), yinch(), and xyinch() have been moved
from package 'grDevices' into package 'graphics'.
o Plotmath now allows underline in expressions. (PR#7286,
contributed by Uwe Ligges.)
o BATCH on Unix no longer sets --gui="none" as the X11 module
is only loaded if needed.
o The X11 module (and the hence X11(), jpeg() and png() devices
and the X-based dataentry editor) is now in principle
available under all Unix GUIs except --gui="none", and this is
reflected in capabilities().
capabilities("X11") determines if an X server can be accessed,
and so is more likely to be accurate.
o Printing of arrays now honours the 'right' argument if there
are more than two dimensions.
o Tabular printing of numbers now has headers right-justified, as
they were prior to version 1.7.0 (spotted by Rob Baer).
o Lazy-loading databases are now cached in memory at first use:
this enables R to run much faster from slow file systems such
as USB flash drives. There is a small (less than 2Mb)
increase in default memory usage.
o The implicit class structure for numeric vectors has been
changed, so that integer/real vectors try first methods for
class "integer"/"double" and then those for class "numeric".
The implicit classes for matrices and arrays have been changed
to be "matrix"/"array" followed by the class(es) of the
underlying vector.
o splines::splineDesign() now allows the evaluation of a B-spline
basis everywhere instead of just inside the "inner" knots, by
setting the new argument `outer.ok = TRUE'.
o Hashing has been tweaked to use half as much memory as before.
o Readline is not used for tilde expansion when R is run with
--no-readline, nor from embedded applications. Then "~name"
is no longer expanded, but "~" still is.
o The regular expression code is now based on that in glibc 2.3.3.
It has stricter conformance to POSIX, so metachars such as
{ } + * may need to be escaped where before they did not
(but could have been).
o New encoding 'TeXtext.enc' improves the way postscript() works
with Computer Modern fonts.
o Replacement in a non-existent column of a data frame tries
harder to create a column of the correct length and so avoid a
corrupt data frame.
o For Windows and readline-based history, the saved file size is
re-read from R_HISTSIZE immediately before saving.
o Collected warnings during start-up are now printed before the
initial prompt rather than after the first command.
o Changes to package 'grid':
- preDrawDetails(), drawDetails(), and postDrawDetails()
methods are now recorded on the graphics engine
display list. This means that calculations within these
methods are now run when a device is resized or
when output is copied from one device to another.
- Fixed bug in grid.text() when 'rot' argument has length 0.
(privately reported by Emmanuel Paradis)
- New getNames() function to return just the names of all top-level
grobs on the display list.
- Recording on the grid display list is turned off within
preDrawDetails(), drawDetails(), and postDrawDetails() methods.
- Grid should recover better from errors or user-interrupts
during drawing (i.e., not leave you in a strange viewport
or with strange graphical parameter settings).
- New function grid.refresh() to redraw the grid display list.
- New function grid.record() to capture calculations
with grid graphics output.
- grobWidth and grobHeight ("grobwidth" and "grobheight" units)
for primitives (text, rects, etc, ...) are now
calculated based on a bounding box for the relevant grob.
NOTE: this has changed the calculation of the size of a scalar
rect (or circle or lines).
- New arguments 'warn' and 'wrap' for function grid.grab()
- New function grid.grabExpr() which captures the output from
an expression (i.e., not from the current scene) without
doing any drawing (i.e., no impact on the current scene).
- upViewport() now (invisibly) returns the path that it goes up
(suggested by Ross Ihaka).
- The 'gamma' gpar has been deprecated (this is a device property
not a property of graphical objects; suggested by Ross Ihaka).
- New 'lex' gpar; a line width multiplier.
- grid.text() now handles any language object as mathematical
annotation (instead of just expressions).
- plotViewport() has default value for 'margins' argument (that match
the default value for par(mar)).
- The 'extension' argument to dataViewport() can now be vector,
in which case the first value is used to extend the xscale and
the second value is used to extend the y scale.
(suggested by Ross Ihaka).
- All 'just' arguments (for viewports, layouts, rectangles, text)
can now be numeric values (typically between 0 [left] and 1 [right])
as well as character values ("left", "right", ...).
For rectangles and text, there are additional 'hjust' and 'vjust'
arguments which allow numeric vectors of justification in
each direction (e.g., so that several pieces of text can have
different justifications).
(suggested by Ross Ihaka)
- New 'edits' argument for grid.xaxis() and grid.yaxis() to
allow specification of on-the-fly edits to axis children.
- applyEdit(x, edit) returns x if target of edit (i.e., child
specified by a gPath) cannot be found.
- Fix for calculation of length of max/min/sum unit. Length is
now (correctly) reported as 1 (was reported as length of first arg).
- Viewport names can now be any string (they used to have to be a
valid R symbol).
- The 'label' argument for grid.xaxis() and grid.yaxis() can now
also be a language object or string vector, in which case it
specifies custom labels for the tick marks.
INTERNATIONALIZATION
o Unix-alike versions of R can now be used in UTF-8 and other
multi-byte locales on suitably equipped OSes if configured
with option --enable-mbcs (which is the default). [The
changes to font handling in the X11 module are based on the
Japanization patches of Ei-ji Nakama.]
Windows versions of R can be used in `East Asian' locales on
suitable versions of Windows.
See the 'Internationalization' chapter in the 'Installation
and Administration' manual.
o New command-line flag --encoding to specify the encoding to
be assumed for stdin (but not for a console).
o New function iconv() to convert character vectors between
encodings, on those OSes which support this. See the new
capabilities("iconv").
o The meaning of 'encoding' for a connection has changed: it now
allows any charset encoding supported by iconv on the
platform, and can re-encode output as well as input.
As the new specification is a character string and the old was
numeric, this should not cause incorrect operation.
o New function localeToCharset() to find/guess encoding(s) from
the locale name.
o nchar() returns the true number of bytes stored (including any
embedded nuls), this being 2 for missing values. It has an
optional argument 'type' with possible non-default values
"chars" and "width" to give the number of characters or the
display width in columns.
o Characters can be entered in hexadecimal as e.g. \x9c, and in
UTF-8 and other multibyte locales as \uxxxx, \u{xxxx},
\Uxxxxxxxx or \U{xxxxxxxx}. Non-printable Unicode characters
are displayed C-style as \uxxxx or \Uxxxxxxxx.
o LC_MONETARY is set to the locale, which affects the result of
Sys.localeconv(), but nothing else in R itself. (It could
affect add-on packages.)
o source() now has an 'encoding' argument which can be used to
make it try out various possible encodings. This is made use
of by example() which will convert (non-UTF-8) Latin-1 example
files in a UTF-8 locale.
o read/writeChar() work in units of characters, not bytes.
o .C() now accepts an ENCODING= argument where re-encoding is
supported by the OS. See `Writing R Extensions'.
o delimMatch (tools) now reports match positions and lengths in
units of characters, not bytes. The delimiters can be
strings, not just single ASCII characters.
o .Rd files can indicate via a \encoding{} argument the encoding
that should be assumed for non-ASCII characters they contain.
o Phrases in .Rd files can be marked by \enc{}{} to show a
transliteration to ASCII for use in e.g. text help.
o The use of 'pch' in points() now allows for multi-byte character
sets: in such a locale a glyph can either be specified as a
multi-byte single character or as a number, the Unicode point.
o New function l10n_info() reports on aspects of the
locale/charset currently in use.
o scan() is now aware of double-byte locales such as Shift-JIS
in which ASCII characters can occur as the second ('trail')
byte.
o Functions sQuote() and dQuote() use the Unicode directional
quotes if in a UTF-8 locale.
o The infrastructure is now in place for C-level error and warning
messages to be translated and used on systems with Native
Language Support. This has been used for the startup message
in English and to translate Americanisms such as 'color' into
English: translations to several other languages are under
way, and some are included in this release.
See 'Writing R Extensions' for how to make use of this in a
package: all the standard packages have been set up to do
translation, and the 'language' 'en@quot' is implemented to
allow Unicode directional quotes in a UTF-8 locale.
o R-level stop(), warning() and message() messages can be
translated, as can other messages via the new function
gettext(). Tools xgettext() and xgettext2pot() are provided in
package tools to help manage error messages.
gettextf() is a new wrapper to call sprintf() using
gettext() on the format string.
o Function ngettext() allows the management of singular and
plural forms of messages.
UTILITIES
o New functions mirror2html() and checkCRAN().
o R CMD check has a new option '--use-valgrind'.
o R CMD check now checks that Fortran and C++ files have LF
line endings, as well as C files. It also checks Makevars[.in]
files for portable compilation flags.
o R CMD check will now work on a source tarball and prints out
information about the version of R and the package.
o tools:::.install_package_code_files() (used to collate R files
when installing packages) ensures files are separated by a
line feed.
o vignette() now returns an object of class "vignette" whose
print() method opens the corresponding PDF file. The edit()
method can be used to open the code of the vignette in an
editor.
o R CMD INSTALL on Unix has a new option '--build' matching
that on Windows, to package as tarball the installed package.
o R CMD INSTALL on Unix can now install binary bundles.
o R CMD build now changes src files to LF line endings if necessary.
o R CMD build now behaves consistently between source and binary
builds: in each case it prepares a source directory and then
either packages that directory as a tarball or calls R CMD
INSTALL --build on the prepared sources.
This means that R CMD build --binary now respects
.Rbuildignore and will rebuild vignettes (unless the option
--no-vignettes is used). For the latter, it now installs the
current sources into a temporary library and uses that version
of the package/bundle to rebuild the vignettes.
o R CMD build now reports empty directories in the source tree.
o New function write_PACKAGES() in package 'tools' to help with
preparing local package repositories. (Based on a contribution
by Uwe Ligges.) How to prepare such repositories is
documented in the 'R Installation and Administration' manual.
o package.skeleton() adds a bit more to DESCRIPTION.
o Sweave changes:
- \usepackage[nogin]{Sweave} in the header of an Sweave file
supresses auto-setting of the graphical parameter like width
of graphics.
- The new \SweaveInput{} command works similar to LaTeX's
\input{} command.
- Option value strip.white=all strips all blank lines from the
output of a code chunk.
- Code chunks with eval=false are commented out by Stangle() and
hence no longer tested by R CMD check.
DOCUMENTATION
o File doc/html/faq.html no longer exists, and doc/manual/R-FAQ.html
(which has active links to other manuals) is used instead.
(If makeinfo >= 4.7 is not available, the version on CRAN is
linked to.)
o Manual 'Writing R Extensions' has further details on writing
new front-ends for R using the new public header files.
o There are no longer any restrictions on characters in the
\name{} field of a .Rd file: in particular _ is supported.
C-LEVEL FACILITIES
o There are new public C/C++ header files Rinterface.h and
R_ext/RStartup.h for use with external GUIs.
o Added an onExit() function to graphics devices, to be executed
upon user break if non-NULL.
o ISNAN now works even in C++ code that undefines the 'isnan' macro.
o R_alloc's limit on 64-bit systems has been raised from just
under 2^31 bytes (2Gb) to just under 2^34 (16Gb), and is now checked.
o New math utility functions log1pmx(x), lgamma1p(x),
logspace_add(logx, logy), and logspace_sub(logx, logy).
DEPRECATED & DEFUNCT
o The aqua module for MacOS X has been removed: --with-aqua now
refers to the unbundled Cocoa GUI.
o Capabilities "bzip2", "GNOME", "libz" and "PCRE" are defunct.
o The undocumented use of UseMethod() with no argument was
deprecated in 2.0.1 and is now regarded as an error.
o Capability "IEEE754" is deprecated.
o The 'CRAN' argument to update.packages(), old.packages(),
new.packages(), download.packages() and install.packages() is
deprecated in favour of 'repos', which replaces it as a
positional argument (so this is only relevant for calls with
named args).
o The S3 methods for getting and setting names of "dist" objects
have been removed (as they provided names with a different
length from the "dist" object itself).
o Option "repositories" is no longer used and so not set.
o loadURL() is deprecated in favour of load(url()).
o delay() is deprecated. Use delayedAssign() instead.
INSTALLATION CHANGES
o New configure option --enable-mbcs to enable support for
UTF-8 locales, on by default.
o R_XTRA_[CF]FLAGS are now used during the configuration tests,
and [CF]PICFLAGS if --enable-R-shlib was specified. This
ensures that features such as inlining are only used if the
compilation flags specified support them. (PR#7257)
o Files FAQ, RESOURCES, doc/html/resources.html are no longer in
the SVN sources but are made by 'make dist'.
o The GNOME GUI is unbundled, now provided as a package on CRAN.
o Configuring without having the recommended packages is now an
error unless --with-recommended-packages=no (or equivalent) is used.
o Configuring without having the X11 headers and libraries is now
an error unless --with-x=no (or equivalent) is used.
o Configure tries harder to find a minimal set of FLIBS. Under
some circumstances this may remove from R_LD_LIBRARY_PATH
path elements that ought to have specified in LDFLAGS (but
were not).
o The C code for most of the graphics device drivers and their
afm files are now in package grDevices.
o R is now linked against ncurses/termlib/termcap only if
readline is specified (now the default) and that requires it.
o Makeinfo 4.7 or later is now required for building the HTML and
Info versions of the manuals.
PACKAGE INSTALLATION CHANGES
o There are new types of packages, identified by the Type field
in the DESCRIPTION file. For example the GNOME console is now
a separate package (on CRAN), and translations can be
distributed as packages.
o There is now support of installing from within R both source and
binary packages on MacOS X and Windows. Most of the R
functions now have a 'type' argument defaulting to
getOption("pkgType") and with possible values "source",
"win.binary" and "mac.binary". The default is "source" except
under Windows and the CRAN GUI build for MacOS X.
o install.packages() and friends now accept a vector of URLs for
'repos' or 'contriburl' and get the newest available version of
a package from the first repository on the list in which it is
found. The argument 'CRAN' is still accepted, but deprecated.
install.packages() on Unix can now install from local .tar.gz
files via repos = NULL (as has long been done on Windows).
install.packages() no longer asks if downloaded packages
should be deleted: they will be deleted at the end of the
session anyway (and can be deleted by the user at any time).
If the repository provides the information, install.packages()
will now accept the name of a package in a bundle.
If 'pkgs' is omitted install.packages() will use a listbox to
display the available packages, on suitable systems.
'dependencies' can be a character vector to allow only some
levels of dependencies (e.g. not "Suggests") to be requested.
o There is a new possible value update.packages(ask="graphics")
that uses a widget to (de)select packages, on suitable systems.
o The option used is now getOption("repos") not getOption("CRAN")
and it is initially set to a dummy value. Its value can be a
character vector (preferably named) giving one or several
repositories.
A new function chooseCRANmirror() will select a CRAN mirror.
This is called automatically if the contrib.url() encounters
the initial dummy value of getOption("repos")
A new function setRepositories() can be used to create
getOption("repos") from a (platform-specific) list of known
repositories.
o New function new.packages() to report uninstalled packages
available at the requested repositories. This also reports
incomplete bundles. It will optionally install new packages.
o New function available.packages(), similar to CRAN.packages()
but for use with multiple repositories. Both now only report
packages whose R version requirements are met.
o update.packages() and old.packages() have a new option
'checkBuilt' to allow packages installed under earlier
versions of R to be updated.
o remove.packages() can now remove bundles.
o The Contains: field of the DESCRIPTION file of package bundles
is now installed, so later checks can find out if the bundle
is complete.
o packageStatus() is now built on top of *.packages, and gains a
'method' argument. It defaults to the same repositories as
the other tools, those specified by getOption("repos").
BUG FIXES
o Configuring for Tcl/Tk makes use of ${TK_LIB_SPEC} ${TK_LIBS}
not ${TK_LIB_SPEC} ${TK_XLIBSW}, which is correct for
recent versions of Tk, but conceivably not for old
tkConfig.sh files.
o detach() was not recomputing the S4 methods for primitives
correctly.
o Methods package now has class "expression" partly fixed in basic
classes, so S4 classes can extend these (but "expression" is
pretty broken as a vector class in R).
o Collected warnings had messages with unneeded trailing space.
o S4 methods for primitive functions must be exported from
name spaces; this is now done automatically.
Note that is.primitive() is now in "base", not "methods".
o Package grid:
- Fixed bug in grid.text() when "rot" argument has length 0.
(reported by Emmanuel Paradis)
o .install_package_vignette_index() created an index even in an
empty 'doc' directory.
o The print() method for factors now escapes characters in the
levels in the same way as they are printed.
o str() removed any class from environment objects.
str() no longer interprets control characters in character
strings and factor levels; also no longer truncates factor
levels unless they are longer than 'nchar.max'.
Truncation of such long strings is now indicated ''outside''
the string.
str(<S4.object>) was misleading for the case of a single slot.
str() now also properly displays S4 class definitions (such as
returned by getClass().
o print.factor(quote=TRUE) was not quoting levels, causing
ambiguity when the levels contained spaces or quotes.
o R CMD check was confused by a trailing / on a package name.
o write.table() was writing incorrect column names if the data
frame contained any matrix-like columns.
o write.table() was not quoting row names for a 0-column x.
o t(x)'s default method now also preserves names(dimnames(x)) for
1D arrays 'x'.
o r <- a %*% b no longer produces names(dimnames(r)) == c("", "")
unless one of a or b has named dimnames.
o Some .Internal functions that were supposed to return invisibly
did not. This was behind PR#7397 and PR#7466.
o eval(expr, NULL, encl) now looks up variables in encl, as
eval(expr, list(), encl) always did
o Coercing as.data.frame(NULL) to a pairlist caused an error.
o p.adjust(p, ..) now correctly works when `p' contains NAs (or when
it is of length 0 or length 2 for method = "hommel").
o 'methods' initialization was calling a function intended for
.Call() with .C().
o optim() needed a check that the objective function returns a
value of length 1 (spotted by Ben Bolker).
o X11() was only scaling its fonts to pointsize if the dpi
was within 0.5 of 100dpi.
o X11() font selection was looking for any symbol font, and
sometimes got e.g. bold italic if the server has such a font.
o dpois(*, lambda=Inf) now returns 0 (or -Inf for log).
o Using pch="" gave a square (pch=0)! Now it is regarded as the
same as NA, which was also undocumented but omits the point.
o Base graphics now notices (ab)lines which have a zero
coordinate on log scale, and omits them. (PR#7559)
o stop() and warning() now accept NULL as they are documented
to do (although this seems of little use and is equivalent to "").
o weighted.mean() now checks the length of the weight vector w.
o getAnywhere() was confused by names with leading or trailing dots
(spotted by Robert McGehee)
o eval() was not handling values from return() correctly.
o par(omd) is now of the form c(x1, x2, y1, y2) to match the
documentation and for S-PLUS compatibility.
[Previously, par(omd) was of the form c(bottom, left, top, right)
like par(oma) and par(omi)]
o formatC() did not check its 'flag' argument, and could
segfault if it was incorrect. (PR#7686)
o Contrasts needed to be coerced to numeric (e.g. from integer)
inside model.matrix. (PR#7695)
o socketSelect() did not check for buffered input.
o Reads on a non-blocking socket with no available data were
not handled properly and could result in a segfault.
o The "aovlist" method for se.contrast() failed in some very
simple cases that were effectively not multistratum designs,
e.g. only one treatment occurring in only one stratum.
o pgamma() uses completely re-written algorithms, and should work
for all (even very extreme) arguments; this is based on Morten
Welinder's contribution related to PR#7307.
o dpois(10, 2e-308, log=TRUE) and similar cases gave -Inf.
o x <- 2^(0:1000); plot(x, x^.9, type="l", log="xy")# and
x <- 2^-(1070:170); plot(x, x^.9, type="l", log="xy")# now both work
o summary.lm() asked for a report on a reasonable occurrence, but
the check failed to take account of NAs.
o lm() was miscalculating 'df.residual' for empty models with a
matrix response.
o summary.lm() now behaves more sensibly for empty models.
o plot.window() was using the wrong sign when adjusting
xlim/ylim for positive 'asp' and a reversed axis.
o If malloc() fails when allocating a large object the allocator now
does a gc and tries the malloc() again.
o packageSlot() and getGroupMembers() are now exported from the
'methods' package as they should from documentation and the
Green Book.
o rhyper() was giving numbers slightly too small, due to a bug in the
original algorithm. (PR#7314)
o gsub() was sometimes incorrectly matching ^ inside a string,
e.g. gsub("^12", "x", "1212") was "xx".
o [g]sub(perl = TRUE) was giving random results for a 0-length
initial match. (PR#7742)
o [g]sub was ignoring most 0-length matches, including all initial
ones. Note that substitutions such as gsub("[[:space:]]*", "
", ...) now work as they do in 'sed' (whereas the effect was
previously the same as gsub("[[:space:]]+", " ", ...)).
(In part PR#7742)
o Promises are now evaluated when extracted from an environment
using '$' or '[[ ]]'.
o reshape(direction="wide") had some sorting problems when
guessing time points (PR#7669)
o par() set 'xaxp' before 'xlog' and 'yaxp' before 'ylog',
causing PR#831.
o The logic in tclRequire() to check the availability of a Tcl
package turned out to be fallible. It now uses a try()-and-see
mechanism instead.
o Opening a unz() connection on a non-existent file left a file
handle in use.
o "dist" objects of length 0 failed to print.
o INSTALL and the libR try harder to find a temporary directory
(since there might be one left over with the same PID).
o acf() could cause a segfault with some datasets. (PR#7771)
o tan(1+LARGEi) now gives 0+1i rather than 0+NaNi (PR#7781)
o summary(data.frame(mat = I(matrix(1:8, 4)))) does not go into
infinite recursion anymore.
o writeBin() performed byte-swapping incorrectly on complex
vectors, also swapping real and imaginary parts. (PR#7778)
o read.table() sometimes discarded as blank lines containing
only white space, even if sep=",".
**************************************************
* *
* 2.0 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.0.1 patched
NEW FEATURES
o warnings() now looks only in the workspace for `last.warning'
(suggested by PR#7363).
o The search for browsers now starts with firefox, and has mozilla
ahead of netscape.
PACKAGE INSTALLATION CHANGES
o A package DESCRIPTION file which contains a Built field (it
should not!) is now worked around, with loud warnings.
BUG FIXES
o split() was accepting raw and list vectors as input, but
not populating the output correctly.
split() now handles vectors with names internally and so is
almost as fast as on vectors without names (and maybe 100x
faster than before).
o subset() now throws an error if its 'subset' argument is not
logical whereas it could appear to work and give wrong answers
with e.g. a numeric 'subset' argument.
o sum(), max(), min(), prod(), any() and all() were incorrectly
using partial matching for their na.rm argument.
o kmeans() now ensures that the initial cluster centers it chooses
are distinct.
o text()'s default method could segfault if passed 0-length coordinates.
o R CMD INSTALL (Unix) was sometimes leaving a temporary dir
behind. (PR#7230)
o read.table() could fail when the row.names were looking like numbers.
o seq(length= <n>) now always returns "integer" storage.
o labels.lm was broken. (PR#7417)
o The hashing used for character vectors in object.size() was
inefficient for vectors with thousands of identical values not
sharing the same storage (an unusual case).
o data.matrix() now warns if applied to a data frame with
classed columns.
o Plotting histograms where the expression used to deparse to
multiple lines now gives a sensible default title. (PR#7421)
o The print method for getDLLRegisteredRoutines() was badly
designed, and failed for all the standard packages' DLLs.
o getDLLRegisteredRoutines.character() was broken.
o write.table(x, row.names=FALSE) was incorrect for a 0-column x.
o write.table() assumed dec = "," if it was not ".".
o morley.tab used by R-intro was not installed on Unix since 2.0.0
(it was on Windows).
o gsub(perl=TRUE) returned a string which printed with trailing
garbage if there was a match at the beginning whose
replacement was shorter. (PR#7479)
Similarly, the result was truncated if a replacement at the
beginning was longer.
o Some PDF readers do not define PDFDocEncoding, so pdf()'s
ISOLatin1 encoding is now derived from WinAnsi rather than
PDFDocEncoding.
o xfig() had not been updated for the 2.0.0 alpha changes.
Using more than one plot with a non-white background and with
onefile=FALSE could segfault.
o sprintf() did not check for buffer overflow on character
strings. (PR#7554)
o The error message when evaluation depth was exceeded itself
caused an error in deparsing and so was not shown.
o The 'datalist' file was not being used during installation
(2.0.1 only).
o replications() was wrongly reporting lack of balance in
designs with interactions (and had since unique() gained a
matrix method).
CHANGES IN R VERSION 2.0.1
NEW FEATURES
o Platform equivalence in library() is tested by a new function
testPlatformEquivalence() which ignores the 'vendor' field and
can be customized by cognescenti.
o The assignment form of split() allows recycling of vectors
within the value list. In particular, things like
split(x, g) <- lapply(split(x, g), mean)
now work
DOCUMENTATION
o Manual `Writing R Extensions' has new sections on writing
portable packages and on writing new front-ends for R -- the
latter will be more comprehensive in R 2.1.0 which has new
public header files.
DEPRECATED & DEFUNCT
o The aqua module in MacOS X is deprecated.
o Capabilities "bzip2", "GNOME", "libz" and "PCRE" are deprecated.
o The GNOME GUI on Unix-alikes is deprecated as part of R;
it will be available in another form as from R 2.1.0.
o The undocumented use of UseMethod() with no argument is now
formally deprecated.
INSTALLATION CHANGES
o Building on Alpha OSF/1 no longer forces the C flag -std1,
which appears to be no longer needed. (PR#7257)
o The compiler flag -mieee-fp is no longer used on i386 Linux
(these days it is only passed to the linker and was only
invoked for compilation steps).
o -D__NO_MATH_INLINES is only used on older ix86 glibc-based
systems which need it (tested at configure time). This leads to
small improvements in speed and accuracy on modern systems.
o If makeinfo >= 4.5 is not available, warnings are given that
some of the HTML manuals will be missing, and the index page
given by help.start() will link to CRAN versions of those manuals.
o Files aclocal.m4 and acinclude.m4 used in maintainer builds
are not longer included in the distribution.
C-LEVEL FACILITIES
o It was not clear in 'Writing R Extensions' that some of the
entry points in the 'Utilities' section were not declared in
<R.h> (they were in <R_ext/Applic.h>). Now all the entry
points in that section are declared in <R_ext/Utils.h>,
included by <R.h>.
BUG FIXES
o The grid.grab() function in package grid would throw an error
if there were no viewports pushed (now returns NULL).
o model.frame.default() takes row names from the response
variable if that has suitable names and there is no 'data'
argument. (This follows S but was not previously implemented
in R.)
o write.table() was not respecting the 'dec' argument for complex
numbers.
o write.table() printed a mixture of numeric and complex numbers
as all complex. (PR#7260)
o R CMD INSTALL failed with versioned installs on packages which
save images (only).
o dlogis() gave NaN not 0 for large negative arguments.
o Importing from another name space was broken for versioned
installs, incorrectly reporting something like
"package 'imported_from' does not have a name space".
o The GNOME interface under Linux/Unix was broken. (PR#7276)
o For the jpeg/png devices under Linux/Unix, under certain rare
circumstances clipping needed to be cleared before starting a
new page. (PR#7270, which has been the case since the devices
were introduced in 1.1.0.)
o First lattice plot (first grid.newpage() call) did not start
a new page IF there had been a previous traditional graphics
plot (on the same device).
o Using install.packages() to install the same package to more
than one library gave an incorrect warning message. (If there
were two or more such packages it might give an error.)
o .packages(all.available=TRUE) returned packages with an invalid
version field in their DESCRIPTION whereas .find.packages() and
packageDescription() did not. Now all do not.
o packageDescription() now correctly reports that a package does
not exist, rather than that its DESCRIPTION file is 'missing
or broken'.
o 'make dist' from builddir != sourcedir was copying not linking
recommended packages to *.tgz.
o Slots in prototype objects can inherit from locally defined
classes (which were not being found correctly before).
o Several fixes to the behavior of as() when there are either
coerce= or replace= methods supplied in a call to
setIs(). Related fixes to setIs() to handle correctly previous
methods, if there were any.
o splinefun(1[0], 1[0])(1) doesn't segfault anymore (PR#7290).
spline() and splinefun() now also work with missing values by
omiting them.
o ecdf() was failing on inputs containing NAs. (Part of PR#7292)
o tools:::.install_package_description was splitting the Built:
field across lines on platforms with very long names.
o capabilities() was wrong for the Aqua GUI on MacOS X.
o Using Rprof() with a non-writable 'file' argument is now a
non-fatal error and does not abort R.
o binom.test() did not deparse its arguments early enough such
that the reported data were ugly if x was a table.
o Systems based on glibc, including those using R's substitute for
strptime, were handling strptime("2001", "%Y") incorrectly, in
some cases crashing. R's substitute code has been corrected
(but problems may remain if glibc is used). See the ?strptime
for what should happen (which is system-specific).
o untrace() after trace() failed if package 'methods' was attached.
(PR#7301)
o summary.stepfun() was reporting for n > 6 summaries of the
knots and levels as the actual values. Both print() and
summary() methods called the constant values "step heights",
although they were not the heights of the steps.
o is.na/is.nan() were giving spurious warnings if applied to a
raw vector.
o is.atomic() gave incorrect result (false) for a raw vector.
o rank() and order() accepted raw and list inputs, but did not
give a sensible answer (always 1:n). Similarly, partial sorts
of a raw vector were accepted but did nothing.
o require() without a version argument tried for an unversioned
load of a package even though a versioned install was already
loaded. This often led to a message that a required package
was being loaded when it was not actually being loaded.
o str(<S4.object>) made use of attributes() instead of slot(),
and hence didn't properly print NULL slots.
o contrib.url() now handles URLs ending in '/' correctly.
o str() removed any class from externalptr objects.
o logLik() and hence AIC() failed or gave incorrect answers
on "lm" fits with na.action = na.exclude (and perhaps other
na.actions's except na.omit and na.fail).
o pmax() and pmin() sometimes used NAs in internal subassignments,
and sometimes these failed.
o Subassigning an expression, e.g. expr[2] <- 1, could leave an
invalid object and so cause a segfault. (PR#7326)
o download/install.packages() would misbehave if there was more
than one version of a package in a repository.
o sort(partial=) silently ignored some other arguments: using
'decreasing' or 'index.return' or supplying a factor are now
errors.
o The ave() function had trouble if the grouping contained
unused levels.
o read.fwf() got confused by skip > 0 and could infinite loop
under some circumstances. (PR#7350)
o upgrade(x, ask = FALSE) was broken for a "packageStatus" object.
o Class "raw" had been omitted from the list of basic classes in
the "methods" package and so could not be used in S4 classes.
o Function getGroupMembers(), part of the definition of S4
classes, had been promised for release 2.0, but slipped through.
o toLatex(sessionInfo()) produced incorrect LaTeX on some
platforms due to special characters in the platform
identifier.
CHANGES IN R VERSION 2.0.0
USER-VISIBLE CHANGES
o The stub packages from 1.9.x have been removed: the library()
function selects the new home for their code.
o `Lazy loading' of R code has been implemented, and is used for
the standard and recommended packages by default. Rather than
keep R objects in memory, they are kept in a database on disc
and only loaded on first use. This accelerates startup (down
to 40% of the time for 1.9.x) and reduces memory usage -- the
latter is probably unimportant of itself, but reduces
commensurately the time spent in garbage collection.
Packages are by default installed using lazy loading if they
have more than 25Kb of R code and did not use a saved image.
This can be overridden by INSTALL --[no-]lazy or via a field
in the DESCRIPTION file. Note that as with --save, any other
packages which are required must be already installed.
As the lazy-loading databases will be consulted often, R
will be slower if run from a slow network-mounted disc.
o All the datasets formerly in packages 'base' and 'stats' have
been moved to a new package 'datasets'. data() does the
appropriate substitution, with a warning. However, calls to
data() are not normally needed as the data objects are visible
in the 'datasets' package.
Packages can be installed to make their data objects visible
via R CMD INSTALL --lazy-data or via a field in the
DESCRIPTION file.
o Package 'graphics' has been split into 'grDevices' (the graphics
devices shared between base and grid graphics) and 'graphics'
(base graphics). Each of the 'graphics' and 'grid' packages
load 'grDevices' when they are attached. Note that
ps.options() has been moved to grDevices and user hooks may
need to be updated.
o The semantics of data() have changed (and were incorrectly
documented in recent releases) and the function has been moved
to package 'utils'. Please read the help page carefully if
you use the 'package' or 'lib.loc' arguments.
data() now lists datasets, and not just names which data() accepts.
o Dataset 'phones' has been renamed to 'WorldPhones'.
o Datasets 'sunspot.month' and 'sunspot.year' are available
*********************************************************
* *
* News of 1.x.y is in file 'NEWS.1' *
* *
*********************************************************
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