[R] R 2.3.0 is released
Peter Dalgaard
p.dalgaard at biostat.ku.dk
Mon Apr 24 13:32:37 CEST 2006
I've rolled up R-2.3.0.tar.gz a short while ago. This version contains
several changes and additions, mostly incremental. See the full list
of changes below.
You can get it (in a short while) from
http://cran.r-project.org/src/base/R-2/R-2.3.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
There is also a version split for floppies.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
eb723b61539feef013de476e68b5c50a COPYING
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
152bf40b34f471387c623c724e112a58 FAQ
70447ae7f2c35233d3065b004aa4f331 INSTALL
fcb3488d9d8e95e439f4bde1b730a615 NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
11cc1e9df640ab52e608cf9e695f7354 R-2.3.0.tar.gz
2fb2766d3a35b1c4b525d61dec39f502 R-2.3.0.tar.gz-split.aa
51ac3cd512cbc0f265ca1c8318732c30 R-2.3.0.tar.gz-split.ab
0d5c03adcdc336e2881c1e5a080c8542 R-2.3.0.tar.gz-split.ac
d7a9431dff3a3a7fefd60ce0ac4b39aa R-2.3.0.tar.gz-split.ad
096386cbc903ea5c5af2a91415b3535b R-2.3.0.tar.gz-split.ae
7e05f409a33e08df384aa8ae8ec80f90 R-2.3.0.tar.gz-split.af
6b79a851552a70a491454be0cfdfa685 R-2.3.0.tar.gz-split.ag
474a171062b1ea432bfdcb68afd696b7 R-2.3.0.tar.gz-split.ah
08173075ecea19a8cc75a062bf3fa2ac R-2.3.0.tar.gz-split.ai
c9cdbbed7dce6b1d5a2af4dc4c495fc1 R-2.3.0.tar.gz-split.aj
11cc1e9df640ab52e608cf9e695f7354 R-latest.tar.gz
433182754c05c2cf7a04ad0da474a1d0 README
020479f381d5f9038dcb18708997f5da RESOURCES
Here is the relevant bit of the NEWS file:
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. (PR8529 and 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. [Experimental.]
On Windows access violations and illegal instructions are
caught with a simple error handler. [Experimental.]
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 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
namespace (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/namespace. (PR#8761)
o Added protection in configure against systems for which using
xmkmf fails to eport 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)
--
O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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