[R] R 3.1.1 is released
Peter Dalgaard
pd.mes at cbs.dk
Thu Jul 10 10:51:52 CEST 2014
The build system rolled up R-3.1.1.tar.gz (codename "Sock it to Me") 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-3.1.1.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. Perhaps with some delays due to vacations. In particular, the Mac OS X maintainer is traveling and may be without Internet access for some days yet.
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) = 19b98552686c3f3c95a6028596c533e9
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = bf2c79e7fd7e2dff621a3a8410c89bb4
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = e840d32b7ef7a7603455d30d6d54fda7
MD5 (NEWS.html) = 206dc0c4dc31004f245813b403ec6d6a
MD5 (R-latest.tar.gz) = 2598f5bbbedb00e463e0c1385e6fe999
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4
MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649
MD5 (R-3/R-3.1.1.tar.gz) = 2598f5bbbedb00e463e0c1385e6fe999
This is the relevant part of the NEWS file
NEW FEATURES:
* When attach() reports conflicts, it does so compatibly with
library() by using message().
* R CMD Sweave no longer cleans any files by default, compatibly
with versions of R prior to 3.1.0. There are new options
--clean, --clean=default and --clean=keepOuts.
* tools::buildVignette() and tools::buildVignettes() with clean =
FALSE no longer remove any created files. buildvignette() gains
a keep argument for more cleaning customization.
* The Bioconductor 'version' used by setRepositories() can now be
set by environment variable R_BIOC_VERSION at runtime, not just
when R is installed. (It has been stated that Bioconductor will
switch from 'version' 2.14 to 'version' 3.0 during the lifetime
of the R 3.1 series.)
* Error messages from bugs in embedded Sexpr code in Sweave
documents now report the source location.
* type.convert(), read.table() and similar read.*() functions get a
new numerals argument, specifying how numeric input is converted
when its conversion to double precision loses accuracy. The
default value, "allow.loss" allows accuracy loss, as in R
versions before 3.1.0.
* For some compilers, integer addition could overflow without a
warning. R's internal code for both integer addition and
subtraction is more robust now. (PR#15774)
* The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().
* dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
for a = 0, b = 0, or infinite a and b (where they typically
returned NaN before).
* Many package authors report that the RStudio graphics device does
not work correctly with their package's use of dev.new(). The
new option dev.new(noRStudioGD = TRUE) replaces the RStudio
override by the default device as selected by R itself, still
respecting environment variables R_INTERACTIVE_DEVICE and
R_DEFAULT_DEVICE.
* readRDS() now returns visibly.
* Modifying internal logical scalar constants now results in an
error instead of a warning.
* install.packages(repos = NULL) now accepts http:// or ftp:// URLs
of package archives as well as file paths, and will download as
required. In most cases repos = NULL can be deduced from the
extension of the URL.
* The warning when using partial matching with the $ operator on
data frames is now only given when
options("warnPartialMatchDollar") is TRUE.
* Package help requests like package?foo now try the package foo
whether loaded or not.
* General help requests now default to trying all loaded packages,
not just those on the search path.
* Added a new function promptImport(), to generate a help page for
a function that was imported from another package (and presumably
re-exported, or help would not be needed).
INSTALLATION and INCLUDED SOFTWARE:
* configure option --with-internal-tzcode can now be used with
variable rsharedir.
* The included version of PCRE has been updated to 8.35.
* There is a new target make uninstall-libR to remove an installed
shared/static libR.
make install-libR now works if a sub-architecture is used,
although the user will need to specify libdir differently for
different sub-architectures.
* There is more extensive advice on which LaTeX packages are
required to install R or to make package manuals (as done by R
CMD check) in the 'Writing R Extensions' manual.
* Compilers/linkers were handling the visibility controls in
src/extra/xz inconsistently (and apparently in some cases
incorrectly), so it has been simplified. (PR#15327)
* (Windows) There is updated support for the use of ICU for
collation: see the 'R Installation and Administration Manual'.
BUG FIXES:
* dbinom(x, n), pbinom(), dpois(), etc, are slightly less
restrictive in checking if n is integer-valued. (Wish of
PR#15734.)
* pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
100, ncp = 1, log = TRUE). (Based on PR#15635 and a suggestion
by Roby Joehanes.)
* The s ("step into") command in the debugger would cause R to step
into expressions evaluated there, not just into functions being
debugged. (PR#15770)
* The C code used by strptime() rejected time-zone offsets of more
than +1200 (+1245, +1300 and +1400 can occur). (PR#15768)
* (Windows only.) png(type = "cairo", antialias = "gray") was not
accepted. (PR#15760)
* Use of save(..., envir=) with named objects could fail.
(PR#15758)
* Sweave() mis-parsed Sexpr expressions that contained backslashes.
(PR#15779)
* The return value from options(foo = NULL) was not the previous
value of the option. (PR#15781)
* enc2utf8() and enc2native() did not always mark the encoding of
the return values when it was known.
* dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
to -Inf for large mu, thanks to a suggestion from Alessandro
Mammana (MPI MolGen, Berlin).
* pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
a small x-region) because of denormalized numbers. Also,
pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
time".
* The "CRAN" filter (see available.packages()) no longer removes
duplicates other than of packages on CRAN, and does not fail if
there is no CRAN repository in getOption("repos").
* The device listing from dev2bitmap() and bitmap() was truncated
to 1000 characters: modern versions of GhostScript on most
platforms have many more devices.
* (Windows.) Commands such as Sys.which() and pipe() which needed
to find the full path to a command could segfault if the 'long'
path name was much longer than the 'short' path name (which
Sys.which() returns), as the behaviour of the Windows API call
had changed.
* R CMD build will fail with an error if one of the packages
specified in the VignetteBuilder field is not installed.
(Without loading those packages it cannot be ascertained which
files are intended to be vignettes. This means that the
VignetteBuilder packages have to be installed for package
checking too.) (Wish of PR#15775.)
* Misguided attempts to use chull() with non-finite points now give
an error (related to PR#15777).
* For a formula with exactly 32 variables the 32nd variable was
aliased to the intercept in some C-level computations of terms,
so that for example attempting to remove it would remove the
intercept instead (and leave a corrupt internal structure).
(PR#15735)
* anyDuplicated() silently returned wrong values when the first
duplicate was at an index which was too large to be stored in an
integer vector (although a lot of RAM and patience would have
been needed to encounter this).
* tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
one line.
* Hexadecimal constants such as 0x110p-5L which were incorrectly
qualified by L were parsed incorrectly since R 3.0.0, with a
slightly garbled warning. (PR#15753)
* system() returned success on some platforms even if the system
was unable to launch a process. (PR#15796)
* (Windows Rgui console.) Unbuffered output was sometimes not
output immediately if the prompt was not on the last line of the
console.
* The built-in help server did not declare the encoding for the
DESCRIPTION or other text files to be the package encoding, so
non-ASCII characters could be displayed incorrectly.
* R is now trying harder to not cleanup child processes that were
not spawned by mcparallel() on platforms that provide information
about the source process of the SIGCHLD signal. This allows 3rd
party libraries to manage the exit status of children that they
spawn without R interfering.
* mcmapply() was only parallelizing if the number of jobs was
bigger than the number of cores. It now parallelizes if the
number of jobs is more than one.
* Auto-printing would re-evaluate its argument when trying to
dispatch to a print method. This is now avoided when possible.
* Unserializing (including load() and readRDS()) could silently
return incorrect numeric values from ASCII saves if there was a
read error.
* getParseData() could return incorrect values for the parents of
some elements. (Reported by Andrew Redd.)
* Attempting to use data frames of 2^31 or more rows with merge()
or to create a merged data frame of that size now gives a clearer
error message.
* parse() did not check its file argument was a connection if it
was not a character string, so e.g. parse(FALSE) attempted to
read from stdin.
Nor did dump() and dput().
* The "help.try.all.packages" option was ignored when the shortcut
syntax for help was used, e.g. ?foo.
* A potential segfault in string allocation has been fixed. (Found
by Radford Neal.)
* Potential memory protection errors in sort() and D() have been
fixed. (Found by Radford Neal.)
* Fixed a lack of error checking in graphics event functions.
(Found by Radford Neal; a different patch used here than the one
in pqR.)
* numericDeriv() sometimes miscalculated the gradient. (PR#15849,
reported originally by Radford Neal)
--
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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