R 2.15.3 is released

Follows is the announcement today from Peter Dalgaard, for the R Core Team: The build system rolled up R-2.15.3.tar.gz (codename “Security Blanket”) at 9:00 this morning. This is intended to be the final round-up release of the 2.15 series, and in fact of the entire 2.x.y series which started 2004-10-04. The list below details the changes in this release. You can get the source code from http://cran.r-project.org/src/base/R-2/R-2.15.3.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. This is the relevant part of the NEWS file CHANGES IN R VERSION 2.15.3:


o lgamma(x) for very small x (in the denormalized range) is no longer Inf with a warning. o image() now sorts an unsorted breaks vector, with a warning. o The internal methods for tar() and untar() do a slightly more general job for ‘ustar’-style handling of paths of more than 100 bytes. o Packages compiler and parallel have been added to the reference index (refman.pdf). o 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. o sQuote() and dQuote() now handle 0-length inputs. (Suggestion of Ben Bolker.) o summaryRprof() returns zero-row data frames rather than throw an error if no events are recorded, for consistency. o The included version of PCRE has been updated to 8.32. o 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()). o 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.


o 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).


o On a 64-bit Windows platform with enough RAM, R_alloc can now allocate up to just under 32GB like other 64-bit platforms.


o Use of col2rgb(0) is deprecated (see the help page for its limitations). o The deprecated intensities component returned by hist() is no longer recognized by the plot() method and will be removed in R 3.0.0. o real(), as.real() and is.real() are now formally deprecated and give a warning. o This is formal notice that the non-API EISPACK entry points in R will be removed shortly.


o The configure tests for Objective C and Objective C++ now work on Mac OS 10.8 with Xcode 4.5.2 (PR#15107). o 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”). o 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.


o beta(a, b) could overflow to infinity in its calculations when one of a and b was less than one. (PR#15075) o lbeta(a, b) no longer gives NaN if a or b is very small (in the denormalized range). o bquote() is now able to substitute default arguments in single-argument functions. (PR#15077) o browseEnv(html = FALSE) would segfault if called from R (not R.app) on a CRAN-style Mac OS X build of R. o [[when RHS is used more than once. (PR#15098) o 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. o The call() function did not duplicate its arguments. (PR#15115) o TukeyHSD() could give NA results with some na.action methods such as na.exclude(). (Hinted at on R-help by John Fox.) o The deprecated svd(X, LINPACK = TRUE) could alter X in R 2.15.[12]. (Reported by Bill Dunlap.) o Under Windows, file.link() and file.symlink() used the link name twice, so would always fail. (Reported by Rui Barradas/Oliver Soong). o summaryRprof(memory = “both”) mixed up the units of Vcells and Ncells: it now works in bytes. (PR#15138) o tools::Rd2HTML() would sometimes delete text. (PR#15134) o plot() failed for “table” objects containing just one entry. (PR#15118) o embedFonts() needed to quote some filepaths. (PR#15149) o parallel::mccollect() handled NULL returns incorrectly (removing the element rather than setting it to NULL). o The full reference index (fullrefman.pdf) was missing packages compiler and parallel. o 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) o qt(1e-12, 1.2) no longer gives NaN. o dt(1e160, 1.2, log=TRUE) no longer gives -Inf. o 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. o The version for Windows 8 and Windows Server 2012 is now displayed by win.version(). (Reported by Gabor Grothendieck.) o The custom Windows installer target myR in the installer Makefile did not work in 2.15.2. (Reported by Erich Neuwirth.) o aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), “A”) no longer segfaults. o Expressions involving user defined operators were not always deparsed faithfully. (PR#15179) o The enc2utf8() function converted NA_character_ to “NA” in non-UTF-8 locales. (PR#15201) o The exclude argument to xtabs() was ignored for “factor” arguments. o 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.) o 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.   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) = c82ec3aa971272312ca6f3f28c58d329 MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e MD5 (NEWS) = 09e5c175b09d33e28023c655a11e9b8d MD5 (NEWS.html) = c7dccfe18e943427b85e9ddd1c7ba46b MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = b2f1a5d701f1f90679be0c60e1931a5c MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4 MD5 (THANKS) = 7a87321ccf0ecd2bece697e39dce5e67 MD5 (R-2/R-2.15.3.tar.gz) = b2f1a5d701f1f90679be0c60e1931a5c   — Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School    

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