[R] R 3.1.1 is released

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