[R] R 3.0.2 is released
Peter Dalgaard
pd.mes at cbs.dk
Wed Sep 25 13:16:24 CEST 2013
The build system rolled up R-3.0.2.tar.gz (codename "Frisbee Sailing") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.0.2.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.
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:
MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 77da68a9d0abfa9121d54f6ff0bced33
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = e01b5a01aade71ccef967d39f3738e0a
MD5 (NEWS.html) = 1925b57c75bd51373adb33a04e2c18f8
MD5 (R-latest.tar.gz) = f9a8374736e7650e4848f33e2e3bbee3
MD5 (README) = e259ae5dd943b8547f0b7719664e815b
MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4
MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649
MD5 (R-3/R-3.0.2.tar.gz) = f9a8374736e7650e4848f33e2e3bbee3
This is the relevant part of the NEWS file
CHANGES IN R 3.0.2:
NEW FEATURES:
* The NEWS files have been re-organized.
This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The
latter files are now installed when R is installed. An HTML
version of news from 2.10.0 to 2.15.3 is available as
doc/html/NEWS.2.html.
* sum() for integer arguments now uses an integer accumulator of at
least 64 bits and so will be more accurate in the very rare case
that a cumulative sum exceeds 2^53 (necessarily summing more than
4 million elements).
* The example() and tools::Rd2ex() functions now have parameters to
allow them to ignore \dontrun markup in examples. (Suggested by
Peter Solymos.)
* str(x) is considerably faster for very large lists, or factors
with 100,000 levels, the latter as in PR#15337.
* col2rgb() now converts factors to character strings not integer
codes (suggested by Bryan Hanson).
* tail(warnings()) now works, via the new `[` method.
* There is now support for the LaTeX style file zi4.sty which has
in some distributions replaced inconsolata.sty.
* unlist(x) now typically returns all non-list xs unchanged, not
just the "vector" ones. Consequently, format(lst) now also works
when the list lst has non-vector elements.
* The tools::getVignetteInfo() function has been added to give
information about installed vignettes.
* New assertCondition(), etc. utilities in tools, useful for
testing.
* Profiling now records non-inlined calls from byte-compiled code
to BUILTIN functions.
* Various functions in stats and elsewhere that use non-standard
evaluation are now more careful to follow the namespace scoping
rules. E.g. stats::lm() can now find stats::model.frame() even
if stats is not on the search path or if some package defines a
function of that name.
* If an invalid/corrupt .Random.seed object is encountered in the
workspace it is ignored with a warning rather than giving an
error. (This allows R itself to rely on a working RNG, e.g. to
choose a random port.)
* seq() and seq.int() give more explicit error messages if called
with invalid (e.g. NaN) inputs.
* When parse() finds a syntax error, it now makes partial parse
information available up to the location of the error. (Request
of Reijo Sund.)
* Methods invoked by NextMethod() had a different dynamic parent to
the generic. This was causing trouble where S3 methods invoked
via lazy evaluation could lose track of their generic.
(PR#15267)
* Code for the negative binomial distribution now treats the case
size == 0 as a one-point distribution at zero.
* abbreviate() handles without warning non-ASCII input strings
which require no abbreviation.
* read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
PR#15250.)
* formatC(x) no longer copies the class of x to the result, to
avoid misuse creating invalid objects as in PR#15303. A warning
is given if a class is discarded.
* Dataset npk has been copied from MASS to allow more tests to be
run without recommended packages being installed.
* The initialization of the regression coefficients for
non-degenerate differenced models in arima() has been changed and
in some examples avoids a local maximum. (PR#15396)
* termplot() now has an argument transform.x to control the display
of individual terms in the plot. (PR#15329)
* format() now supports digits = 0, to display nsmall decimal
places.
* There is a new read-only par() parameter called "page", which
returns a logical value indicating whether the next plot.new()
call will start a new page.
* Processing Sweave and Rd documents to PDF now renders backticks
and single quotes better in several instances, including in \code
and \samp expressions.
* utils::modifyList() gets a new argument keep.null allowing NULL
components in the replacement to be retained, instead of causing
corresponding components to be deleted.
* tools::pkgVignettes() gains argument check; if set to TRUE, it
will warn when it appears a vignette requests a non-existent
vignette engine.
UTILITIES:
* R CMD check --as-cran checks the line widths in usage and
examples sections of the package Rd files.
* R CMD check --as-cran now implies --timings.
* R CMD check looks for command gfile if a suitable file is not
found. (Although file is not from GNU, OpenCSW on Solaris
installs it as gfile.)
* R CMD build (with the internal tar) checks the permissions of
configure and cleanup files and adds execute permission to the
recorded permissions for these files if needed, with a warning.
This is useful on OSes and file systems which do not support
execute permissions (notably, on Windows).
* R CMD build now weaves and tangles all vignettes, so suggested
packages are not required during package installation if the
source tarball was prepared with current R CMD build.
* checkFF() (used by R CMD check) does a better job of detecting
calls from other packages, including not reporting those where a
function has been copied from another namespace (e.g. as a
default method). It now reports calls where .NAME is a symbol
registered in another package.
* On Unix-alike systems, R CMD INSTALL now installs packages group
writably whenever the library (lib.loc) is group writable.
Hence, update.packages() works for other group members (suggested
originally and from a patch by Dirk Eddelbuettel).
* R CMD javareconf now supports the use of symbolic links for
JAVA_HOME on platforms which have realpath. So it is now
possible to use
R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0
on a Linux system and record that value rather than the
frequently-changing full path such as
/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64.
* (Windows only.) Rscript -e requires a non-empty argument for
consistency with Unix versions of R. (Also Rterm -e and R -e.)
* R CMD check does more thorough checking of declared packages and
namespaces. It reports
* packages declared in more than one of the Depends, Imports,
Suggests and Enhances fields of the DESCRIPTION file.
* namespaces declared in Imports but not imported from, neither
in the NAMESPACE file nor using the :: nor ::: operators.
* packages which are used in library() or requires() calls in
the R code but were already put on the search path _via_
Depends.
* packages declared in Depends not imported _via_ the NAMESPACE
file (except the standard packages). Objects used from
Depends packages should be imported to avoid conflicts and to
allow correct operation when the namespace is loaded but not
attached.
* objects imported _via_ ::: calls where :: would do.
* objects imported by :: which are not exported.
* objects imported by ::: calls which do not exist.
See 'Writing R Extensions' for good practice.
* R CMD check optionally checks for non-standard top-level files
and directories (which are often mistakes): this is enabled for
--as-cran.
* LaTeX style file upquote.sty is no longer included (the version
was several years old): it is no longer used in R. A much later
version is commonly included in LaTeX distributions but does not
play well with the ae fonts which are the default for Sweave
vignettes.
* R CMD build makes more use of the build sub-directory of package
sources, for example to record information about the vignettes.
INSTALLATION and INCLUDED SOFTWARE:
* The macros used for the texinfo manuals have been changed to work
better with the incompatible changes made in texinfo 5.x.
* The minimum version for a system xz library is now 5.0.3 (was
4.999). This is in part to avoid 5.0.2, which can compress in
ways other versions cannot decompress.
* The included version of PCRE has been updated to 8.33.
* The included version of zlib has been updated to 1.2.8, a bug-fix
release.
* The included version of xz utils's liblzma has been updated to
5.0.5.
* Since javareconf (see above) is used when R is installed, a
stable link for JAVA_HOME can be supplied then.
* Configuring with --disable-byte-compilation will override the
DESCRIPTION files of recommended packages, which typically
require byte-compilation.
* More of the installation and checking process will work even when
TMPDIR is set to a path containing spaces, but this is not
recommended and external software (such as texi2dvi) may fail.
PACKAGE INSTALLATION:
* Installation is aborted immediately if a LinkingTo package is not
installed.
* R CMD INSTALL has a new option --no-byte-compile which will
override a ByteCompile field in the package's DESCRIPTION file.
* License BSD is deprecated: use BSD_3_clause or BSD_2_clause
instead.
License X11 is deprecated: use MIT or BSD_2_clause instead.
* Version requirements for LinkingTo packages are now recognized:
they are checked at installation. (Fields with version
requirements were previously silently ignored.)
* The limit of 500 S3method entries in a NAMESPACE file has been
removed.
* The default 'version' of Bioconductor for its packages has been
changed to the upcoming 2.13, but this can be set by the
environment variable R_BIOC_VERSION, e.g. in file Renviron.site.
C-LEVEL FACILITIES:
* Rdefines.h has been tweaked so it can be included in C++ code
after R_ext/Boolean.h (which is included by R.h).
Note that Rdefines.h is not kept up-to-date, and Rinternals.h is
preferred for new code.
* eval and applyClosure are now protected against package code
supplying an invalid rho.
DEPRECATED AND DEFUNCT:
* The unused namespace argument to package.skeleton() is now
formally deprecated and will be removed in R 3.1.0.
* plclust() is deprecated: use the plot() method for class "hclust"
instead.
* Functions readNEWS() and checkNEWS() in package tools are
deprecated (and they have not worked with current NEWS files for
a long time).
DOCUMENTATION:
* 'An Introduction to R' has a new chapter on using R as a
scripting language including interacting with the OS.
BUG FIXES:
* help.request() could not determine the current version of R on
CRAN. (PR#15241)
* On Windows, file.info() failed on root directories unless the
path was terminated with an explicit ".". (PR#15302)
* The regmatches<-() replacement function mishandled results coming
from regexpr(). (PR#15311)
* The help for setClass() and representation() still suggested the
deprecated argument representation=. (PR#15312)
* R CMD config failed in an installed build of R 3.0.1 (only) when
a sub-architecture was used. (Reported by Berwin Turlach.)
* On Windows, the installer modified the etc/Rconsole and
etc/Rprofile.site files even when default options were chosen, so
the MD5 sums did not refer to the installed versions. (Reported
by Tal Galili.)
* plot(hclust(), cex =) respects cex again (and possibly others
similarly). (Reported by Peter Langfelder.)
* If multiple packages were checked by R CMD check, and one was
written for a different OS, it would set --no-install for all
following packages as well as itself.
* qr.coef() and related functions did not properly coerce real
vectors to complex when necessary. (PR#15332)
* ftable(a) now fixes up empty dimnames such that the result is
printable.
* package.skeleton() was not starting its search for function
objects in the correct place if environment was supplied.
(Reported by Karl Forner.)
* Parsing code was changing the length field of vectors and
confusing the memory manager. (PR#15345)
* The Fortran routine ZHER2K in the reference BLAS had a
comment-out bug in two places. This caused trouble with eigen()
for Hermitian matrices. (PR#15345 and report from Robin Hankin)
* vignette() and browseVignettes() did not display non-Sweave
vignettes properly.
* Two warning/error messages have been corrected: the (optional)
warning produced by a partial name match with a pairlist, the
error message from a zero-length argument to the : operator.
(Found by Radford Neal; PR#15358, PR#15356)
* svd() returned NULL rather than omitting components as
documented. (Found by Radford Neal; PR#15360)
* mclapply() and mcparallel() with silent = TRUE could break a
process that uses stdout output unguarded against broken pipes
(e.g., zip will fail silently). To work around such issues, they
now replace stdout with a descriptor pointed to /dev/null
instead. For this purpose, internal closeStdout and closeStderr
functions have gained the to.null flag.
* log(), signif() and round() now raise an error if a single named
argument is not named x. (PR#15361)
* deparse() now deparses raw vectors in a form that is
syntactically correct. (PR#15369)
* The jpeg driver in Sweave created a JPEG file, but gave it a .png
extension. (PR#15370)
* Deparsing of infix operators with named arguments is improved.
(PR#15350)
* mget(), seq.int() and numericDeriv() did not duplicate arguments
properly. (PR#15352, PR#15353, PR#15354)
* kmeans(algorithm = "Hartigan-Wong") now always stops iterating in
the QTran stage. (PR#15364).
* read.dcf() re-allocated incorrectly and so could segfault when
called on a file with lines of more than 100 bytes.
* On systems where mktime() does not set errno, the last second
before the epoch could not be converted from POSIXlt to POSIXct.
(Reported by Bill Dunlap.)
* add1.glm() miscalculated F-statistics when df > 1. (Bill Dunlap,
PR#15386).
* stem() now discards infinite inputs rather than hanging.
(PR#15376)
* The parser now enforces C99 syntax for floating point hexadecimal
constants (e.g. 0x1.1p0), rather than returning unintended values
for malformed constants. (PR#15234)
* model.matrix() now works with very long LHS names (more than 500
bytes). (PR#15377)
* integrate() reverts to the pre-2.12.0 behaviour: from 2.12.0 to
3.0.1 it sometimes failed to achieve the requested tolerance and
reported error estimates that were exceeded. (PR#15219)
* strptime() now handles %W fields with value 0. (PR#15915)
* R is now better protected against people trying to interact with
the console in startup code. (PR#15325)
* Subsetting 1D arrays often lost dimnames (PR#15301).
* Unary + on a logical vector did not coerce to integer, although
unary - did.
* na.omit() and na.exclude() added a row to a zero-row data frame.
(PR#15399)
* All the (where necessary cut-down) vignettes are installed if R
was configured with --without-recommended-packages.
* source() did not display filenames when reporting syntax errors.
* Syntax error reports misplaced the caret pointing out the bad
token.
* (Windows only) Starting R with R (instead of Rterm or Rgui) would
lose any zero-length strings from the command line arguments.
(PR#15406)
* Errors in the encoding specified on the command line via
--encoding=foo were not handled properly. (PR#15405)
* If x is a symbol, is.vector(x, "name") now returns TRUE, since
"name" and "symbol" should be synonyms. (Reported by Herv'e
Pag`es.)
* R CMD rtags works on platforms (such as OS X) with a
XSI-conformant shell command echo. (PR#15231)
* is.unsorted(NA) returns false as documented (rather than NA).
* R CMD LINK did not know about sub-architectures.
* system() and system2() are better protected against users who
misguidedly have spaces in the temporary directory path.
* file.show() and edit() are now more likely to work on file paths
containing spaces. (Where external utilities are used, not the
norm on Windows nor in R.app which should previously have
worked.)
* Packages using the methods package are more likely to work when
they import it but it is not attached. (Several parts of its C
code were looking for its R functions on the search path rather
than in its namespace.)
* lgamma(-x) is no longer NaN for very small x.
* (Windows) system2() now respects specifying stdout and stderr as
files if called from Rgui. (PR#15393)
* Closing an x11() device whilst locator() or identify() is in
progress no longer hangs R. (PR#15253)
* list.dirs(full.names = FALSE) was not implemented. (PR#15170)
* format() sometimes added unnecessary spaces. (PR#15411)
* all.equal(check.names = FALSE) would ignore the request to ignore
the names and would check them as attributes.
* The symbol set by tools::Rd2txt_options(itemBullet=) was not
respected in some locales. (PR#15435)
* mcMap() was not exported by package parallel. (PR#15439)
* plot() for TukeyHSD objects did not balance dev.hold() and
dev.flush() calls on multi-page plots. (PR#15449)
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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