From Hadley.Wickham at r-project.org Fri Jan 3 18:57:59 2014 From: Hadley.Wickham at r-project.org (Hadley Wickham) Date: Fri, 3 Jan 2014 11:57:59 -0600 Subject: The R Journal, Volume 5, Issue 2 Message-ID: Dear all, The latest issue of The R Journal is now available at http://journal.r-project.org/archive/2013-2/ Many thanks to all contributors. Hadley -- Editor-in-chief, The R Journal From pd.mes at cbs.dk Thu Mar 6 09:35:38 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 6 Mar 2014 09:35:38 +0100 Subject: R 3.0.3 is released Message-ID: The build system rolled up R-3.0.3.tar.gz (codename "Warm Puppy") 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-3.0.3.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. 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) = 84f8d8f310c4b6d7bd49c76c222ee0af MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 47fb73654407b2ccd61168105bb0eb9c MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = e840d32b7ef7a7603455d30d6d54fda7 MD5 (NEWS.html) = 4b349b74bbc762df22a32a707f1fc29c MD5 (R-latest.tar.gz) = f9025976863847f2d0502254d0f0dbf2 MD5 (README) = e259ae5dd943b8547f0b7719664e815b MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4 MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649 MD5 (R-3/R-3.0.3.tar.gz) = f9025976863847f2d0502254d0f0dbf2 This is the relevant part of the NEWS file CHANGES IN R 3.0.3: NEW FEATURES: * On Windows there is support for making .texi manuals using texinfo 5.0 or later: the setting is in file src/gnuwin32/MkRules.dist. A packaging of the Perl script and modules for texinfo 5.2 has been made available at . * write.table() now handles matrices of 2^31 or more elements, for those with large amounts of patience and disc space. * There is a new function, La_version(), to report the version of LAPACK in use. * The HTML version of 'An Introduction to R' now has links to PNG versions of the figures. * There is some support to produce manuals in ebook formats. (See doc/manual/Makefile. Suggested by Mauro Cavalcanti.) * On a Unix-alike Sys.timezone() returns NA if the environment variable TZ is unset, to distinguish it from an empty string which on some OSes means the UTC time zone. * The backtick may now be escaped in strings, to allow names containing them to be constructed, e.g. `\``. (PR#15621) * read.table(), readLines() and scan() now warn when an embedded nul is found in the input. (Related to PR#15625 which was puzzled by the behaviour in this unsupported case.) * (Windows only.) file.symlink() works around the undocumented restriction of the Windows system call to backslashes. (Wish of PR#15631.) * KalmanForecast(fast = FALSE) is now the default, and the help contains an example of how fast = TRUE can be used in this version. (The usage will change in 3.1.0.) * strptime() now checks the locale only when locale-specific formats are used and caches the locale in use: this can halve the time taken on OSes with slow system functions (e.g. OS X). * strptime() and the format() methods for classes "POSIXct", "POSIXlt" and "Date" recognize strings with marked encodings: this allows, for example, UTF-8 French month names to be read on (French) Windows. * iconv(to = "utf8") is now accepted on all platforms (some implementations did already, but GNU libiconv did not: however converted strings were not marked as being in UTF-8). The official name, "UTF-8" is still preferred. * available.packages() is better protected against corrupt metadata files. (A recurring problem with Debian package shogun-r: PR#14713.) * Finalizers are marked to be run at garbage collection, but run only at a somewhat safer later time (when interrupts are checked). This circumvents some problems with finalizers running arbitrary code during garbage collection (the known instances being running options() and (C-level) path.expand() re-entrantly). INSTALLATION and INCLUDED SOFTWARE: * The included version of PCRE has been updated to 8.34. This fixes bugs and makes the behaviour closer to Perl 5.18. In particular, the concept of 'space' includes VT and hence agrees with POSIX's. PACKAGE INSTALLATION: * The new field SysDataCompression in the DESCRIPTION file allows user control over the compression used for sysdata.rda objects in the lazy-load database. * install.packages(dependencies = value) for value = NA (the default) or value = TRUE omits packages only in LinkingTo for binary package installs. C-LEVEL FACILITIES: * The long undocumented remapping of rround() to Rf_fround() in header Rmath.h is now formally deprecated: use fround() directly. * Remapping of prec() and trunc() in the Rmath.h header has been disabled in C++ code (it has caused breakage with libc++ headers). BUG FIXES: * getParseData() truncated the imaginary part of complex number constants. (Reported by Yihui Xie.) * dbeta(x, a, b) with a or b within a factor of 2 of the largest representable number could infinite-loop. (Reported by Ioannis Kosmidis.) * provideDimnames() failed for arrays with a 0 dimension. (PR#15465) * rbind() and cbind() did not handle list objects correctly. (PR#15468) * replayPlot() now checks if it is replaying a plot from the same session. * rasterImage() and grid.raster() now give error on an empty (zero-length) raster. (Reported by Ben North.) * plot.lm() would sometimes scramble the labels in plot type 5. (PR#15458 and PR#14837) * min() did not handle NA_character_ values properly. (Reported by Magnus Thor Torfason.) * (Windows only.) readRegistry() would duplicate default values for keys. (PR#15455) * str(..., strict.width = "cut") did not handle it properly when more than one line needed to be cut. (Reported by Gerrit Eichner.) * Removing subclass back-references when S4 classes were removed or their namespace unloaded had several bugs (e.g., PR#15481). * aggregate() could fail when there were too many levels present in the by argument. (PR#15004) * namespaceImportFrom() needed to detect primitive functions when checking for duplicated imports (reported by Karl Forner). * getGraphicsEvent() did not exit when a user closed the graphics window. (PR#15208) * Errors in vignettes were not always captured and displayed properly. (PR#15495) * contour() could fail when dealing with extremely small z values. (PR#15454) * Several functions did not handle zero-length vectors properly, including browseEnv(), format(), gl(), relist() and summary.data.frame(). (E.g., PR#15499) * Sweave() did not restore the R output to the console if it was interrupted by a user in the middle of evaluating a code chunk. (Reported by Michael Sumner.) * Fake installs of packages with vignettes work again. * Illegal characters in the input caused parse() (and thus source()) to segfault. (PR#15518) * The nonsensical use of nmax = 1 in duplicated() or unique() is now silently ignored. * qcauchy(p, *) is now fully accurate even when p is very close to 1. (PR#15521) * The validmu() and valideta() functions in the standard glm() families now also report non-finite values, rather than failing. * Saved vignette results (in a .Rout.save file) were not being compared to the new ones during R CMD check. * Double-clicking outside of the list box (e.g. on the scrollbar) of a Tk listbox widget generated by tk_select.list() no longer causes the window to close. (PR#15407) * Improved handling of edge cases in parallel::splitindices(). (PR#15552) * HTML display of results from help.search() and ?? sometimes contained badly constructed links. * c() and related functions such as unlist() converted raw vectors to invalid logical vectors. (PR#15535) * (Windows only) When a call to system2() specified one of stdin, stdout or stderr to be a file, but the command was not found (e.g. it contained its arguments, or the program was not on the PATH), it left the file open and unusable until R terminated. (Reported by Mathew McLean.) * The bmp() device was not recording res = NA correctly: it is now recorded as 72 ppi. * Several potential problems with compiler-specific behaviour have been identified using the 'Undefined Behaviour Sanitizer' in conjunction with the clang compiler. * hcl() now honours NA inputs (previously they were mapped to black). * Some translations in base packages were being looked up in the main catalog rather than that for the package. * As a result of the 3.0.2 change about 'the last second before the epoch', most conversions which should have given NA returned that time. (The platforms affected include Linux and OS X, but not Windows nor Solaris.) * rowsum() has more support for matrices and dataframes with 2^31 or more elements. (PR#15587) * predict(, interval = "confidence", scale = ) now works. (PR#15564) * The bug fix in 3.0.2 for PR#15411 was too aggressive, and sometimes removed spaces that should not have been removed. (PR#15583) * Running R code in a tcltk callback failed to set the busy flag, which will be needed to tell OS X not to 'App Nap'. * The code for date-times before 1902 assumed that the offset from GMT in 1902 was a whole number of minutes: that was not true of Paris (as recorded on some platforms). * Using Sys.setlocale to set LC_NUMERIC to "C" (to restore the sane behavior) no longer gives a warning. * deparse() now deparses complex vectors in a way that re-parses to the original values. (PR#15534, patch based on code submitted by Alex Bertram.) * In some extreme cases (more than 10^15) integer inputs to dpqrxxx() functions might have been rounded up by one (with a warning about being non-integer). (PR#15624) * Plotting symbol pch = 14 had the triangle upside down on some devices (typically screen devices). The triangle is supposed to be point up. (Reported by Bill Venables.) * getSrcref() did not work on method definitions if rematchDefinition() had been used. * KalmanForecast(fast = FALSE) reported a (harmless) stack imbalance. * The count of observations used by KalmanRun() did not take missing values into account. * In locales where the abbreviated name of one month is a partial match for the full name of a later one, the %B format in strptime() could fail. An example was French on OS X, where juin is abbreviated to jui and partially matches juillet. Similarly for weekday names. * pbeta(x, a, b, log.p = TRUE) sometimes underflowed to zero for very small and very differently sized a, b. (PR#15641) * approx() and approxfun() now handle infinite values with the "constant" method. (PR#15655) * stripchart() again respects reversed limits in xlim and ylim. (PR#15664) -- 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 From pd.mes at cbs.dk Mon Mar 10 15:54:50 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 10 Mar 2014 15:54:50 +0100 Subject: 3.1.0 on April 10 Message-ID: We intend to release R 3.1.0 on April 10. Prerelease versions will appear starting March 13 (for the source version, binaries may come a little later). See developer.r-project.org for details. -- 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 From pd.mes at cbs.dk Thu Apr 10 12:05:40 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 10 Apr 2014 12:05:40 +0200 Subject: [R] R 3.0.3 is released Message-ID: <532362AE-0B84-4B24-AFA0-9F5CAD222EC4@cbs.dk> The build system rolled up R-3.1.0.tar.gz (codename "Spring Dance") 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-3.1.0.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 seems to be a minor mishap with the NEWS file not getting copied to CRAN. I'll attend to that shortly.) 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) = 2978039f3d69bde1d31c5a3699dbe88a MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS.html) = d88192d6e47eec39df1fe6ba3d673ae0 MD5 (R-latest.tar.gz) = a1ee52446bee81820409661e6d114ab1 MD5 (README) = e259ae5dd943b8547f0b7719664e815b MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4 MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649 MD5 (R-3/R-3.1.0.tar.gz) = a1ee52446bee81820409661e6d114ab1 This is the relevant part of the NEWS file CHANGES IN R 3.1.0: NEW FEATURES: * type.convert() (and hence by default read.table()) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs. If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify colClasses in read.table() to be "numeric". * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition of diff -b (as distinct from the description in the man pages of most systems). * New function anyNA(), a version of any(is.na(.)) which is fast for atomic vectors, based on a proposal by Tim Hesterberg. (Wish of PR#15239.) * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind = TRUE) now make use of names(.dimnames) when available. * is.unsorted() now also works for raw vectors. * The "table" method for as.data.frame() (also useful as as.data.frame.table()) now passes sep and base arguments to provideDimnames(). * uniroot() gets new optional arguments, notably extendInt, allowing to auto-extend the search interval when needed. The return value has an extra component, init.it. * switch(f, ...) now warns when f is a factor, as this typically happens accidentally where the useR meant to pass a character string, but f is treated as integer (as always documented). * The parser has been modified to use less memory. * The way the unary operators (+ - !) handle attributes is now more consistent. If there is no coercion, all attributes (including class) are copied from the input to the result: otherwise only names, dims and dimnames are. * colorRamp() and colorRampPalette() now allow non-opaque colours and a ramp in opacity via the new argument alpha = TRUE. (Suggested by Alberto Krone-Martins, but optionally as there are existing uses which expect only RGB values.) * grid.show.layout() and grid.show.viewport() get an optional vp.ex argument. * There is a new function find_gs_cmd() in the tools package to locate a GhostScript executable. (This is an enhanced version of a previously internal function there.) * object.size() gains a format() method. * There is a new family, "ArialMT", for the pdf() and postscript() devices. This will only be rendered correctly on viewers which have access to Monotype TrueType fonts (which are sometimes requested by journals). * The text and PDF news files, including NEWS and NEWS.2, have been moved to the doc directory. * combn(x, simplify = TRUE) now gives a factor result for factor input x (previously user error). (Related to PR#15442.) * Added utils::fileSnapshot() and utils::changedFiles() functions to allow snapshots and comparison of directories of files. * make.names(names, unique=TRUE) now tries to preserve existing names. (Suggestion of PR#15452.) * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate computation of cos(pi*x), etc, both in R and the C API. Using these gains accuracy in some cases, e.g., inside lgamma() or besselI(). (Suggested by Morten Welinder in PR#15529.) * print.table(x, zero.print = ".") now also has an effect when x is not integer-valued. * There is more support to explore the system's idea of time-zone names. Sys.timezone() tries to give the current system setting by name (and succeeds at least on Linux, OS X, Solaris and Windows), and OlsonNames() lists the names in the system's Olson database. Sys.timezone(location = FALSE) gives the previous behaviour. * Platforms with a 64-bit time_t type are allowed to handle conversions between the "POSIXct" and "POSIXlt" classes for date-times outside the 32-bit range (before 1902 or after 2037): the existing workarounds are used on other platforms. (Note that time-zone information for post-2037 is speculative at best, and the OS services are tested for known errors and so not used on OS X.) Currently time_t is usually long and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On R for Windows it is 64-bit (for both architectures as from this version). * The "save.defaults" option can include a value for compression_level. (Wish of PR#15579.) * colSums() and friends now have support for arrays and data-frame columns with 2^31 or more elements. * as.factor() is faster when f is an unclassed integer vector (for example, when called from tapply()). * fft() now works with longer inputs, from the 12 million previously supported up to 2 billion. (PR#15593) * Complex svd() now uses LAPACK subroutine ZGESDD, the complex analogue of the routine used for the real case. * Sweave now outputs .tex files in UTF-8 if the input encoding is declared to be UTF-8, regardless of the local encoding. The UTF-8 encoding may now be declared using a LaTeX comment containing the string %\SweaveUTF8 on a line by itself. * file.copy() gains a copy.date argument. * Printing of date-times will make use of the time-zone abbreviation in use at the time, if known. For example, for Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable this, the "POSIXlt" class has an optional component "zone" recording the abbreviation for each element. For platforms which support it, there is also a component "gmtoff" recording the offset from GMT where known. * (On Windows, by default on OS X and optionally elsewhere.) The system C function strftime has been replaced by a more comprehensive version with closer conformance to the POSIX 2008 standard. * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for |x| > 5; as suggested in PR#15620. * Some versions of the tiff() device have further compression options. * read.table(), readLines() and scan() have a new argument to influence the treatment of embedded nuls. * Avoid duplicating the right hand side values in complex assignments when possible. This reduces copying of replacement values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some package code has relied on there being copies. Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence. * The fast argument of KalmanLike(), KalmanRun() and KalmanForecast() has been replaced by update, which instead of updating mod in place, optionally returns the updated model in an attribute "mod" of the return value. * arima() and makeARIMA() get a new optional argument SSinit, allowing the choice of a different *s*tate *s*pace initialization which has been observed to be more reliable close to non-stationarity: see PR#14682. * warning() has a new argument noBreaks., to simplify post-processing of output with options(warn = 1). * pushBack() gains an argument encoding, to support reading of UTF-8 characters using scan(), read.table() and related functions in a non-UTF-8 locale. * all.equal.list() gets a new argument use.names which by default labels differing components by names (if they match) rather than by integer index. Saved R output in packages may need to be updated. * The methods for all.equal() and attr.all.equal() now have argument check.attributes after ... so it cannot be partially nor positionally matched (as it has been, unintentionally). A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to all.equal() are detected and reported. There are explicit checks that check.attributes is logical, tolerance is numeric and scale is NULL or numeric. This catches some unintended positional matching. The message for all.equal.numeric() reports a "scaled difference" only for scale != 1. * all.equal() now has a "POSIXt" method replacing the "POSIXct" method. * The "Date" and "POSIXt" methods of seq() allows by = "quarter" for completeness (by = "3 months" always worked). * file.path() removes any trailing separator on Windows, where they are invalid (although sometimes accepted). This is intended to enhance the portability of code written by those using POSIX file systems (where a trailing / can be used to confine path matching to directories). * New function agrepl() which like grepl() returns a logical vector. * fifo() is now supported on Windows. (PR#15600) * sort.list(method = "radix") now allows negative integers (wish of PR#15644). * Some functionality of print.ts() is now available in .preformat.ts() for more modularity. * mcparallel() gains an option detach = TRUE which allows execution of code independently of the current session. It is based on a new estranged = TRUE argument to mcfork() which forks child processes such that they become independent of the parent process. * The pdf() device omits circles and text at extremely small sizes, since some viewers were failing on such files. * The rightmost break for the "months", "quarters" and "years" cases of hist.POSIXlt() has been increased by a day. (Inter alia, fixes PR#15717.) * The handling of DF[i,] <- a where i is of length 0 is improved. (Inter alia, fixes PR#15718.) * hclust() gains a new method "ward.D2" which implements Ward's method correctly. The previous "ward" method is "ward.D" now, with the old name still working. Thanks to research and proposals by Pierre Legendre. * The sunspot.month dataset has been amended and updated from the official source, whereas the sunspots and sunspot.year datasets will remain immutable. The documentation and source links have been updated correspondingly. * The summary() method for "lm" fits warns if the fit is essentially perfect, as most of the summary may be computed inaccurately (and with platform-dependent values). Programmers who use summary() in order to extract just a component which will be reliable (e.g. $cov.unscaled) should wrap their calls in suppressWarnings(). INSTALLATION and INCLUDED SOFTWARE: * The included version of LAPACK has been updated to 3.5.0. * There is some support for parallel testing of an installation, by setting TEST_MC_CORES to an integer greater than one to indicate the maximum number of cores to be used in parallel. (It is worth specifying at least 8 cores if available.) Most of these require a make program (such as GNU make and dmake) which supports the $MAKE -j nproc syntax. Except on Windows: the tests of standard package examples in make check are done in parallel. This also applies to running tools::testInstalledPackages(). The more time-consuming regression tests are done in parallel. The package checks in make check-devel and make check-recommended are done in parallel. * More of make check will work if recommended packages are not installed: but recommended packages remain needed for thorough checking of an R build. * The version of tzcode included in src/extra/tzone has been updated. (Formerly used only on Windows.) * The included (64-bit) time-zone conversion code and Olson time-zone database can be used instead of the system version: use configure option --with-internal-tzcode. This is the default on Windows and OS X. (Note that this does not currently work if a non-default rsharedir configure variable is used.) (It might be necessary to set environment variable TZ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.) This option also switches to the version of strftime included in directory src/extra/tzone. * configure now tests for a C++11-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by CXX, but an alternative compiler, options and standard can be specified by variables CXX1X, CXX1XFLAGS and CXX1XSTD (e.g. -std=gnu++11). * R can now optionally be compiled to use reference counting instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in Rinternals.h. This may become the default in the future. * There is a new option --use-system-tre to use a suitable system tre library: at present this means a version from their git repository, after corrections. (Wish of PR#15660.) PACKAGE INSTALLATION: * The CRANextra repository is no longer a default repository on Windows: all the binary versions of packages from CRAN are now on CRAN, although CRANextra contains packages from Omegahat and elsewhere used by CRAN packages. * Only vignettes sources in directory vignettes are considered to be vignettes and hence indexed as such. * In the DESCRIPTION file, License: X11 is no longer recognized as valid. Use MIT or BSD_2_clause instead, both of which need + file LICENSE. * For consistency, entries in .Rinstignore are now matched case-insensitively on all platforms. * Help for S4 methods with very long signatures now tries harder to split the description in the Usage field to no more than 80 characters per line (some packages had over 120 characters). * R CMD INSTALL --build (not Windows) now defaults to the internal tar() unless R_INSTALL_TAR is set. * There is support for compiling C++11 code in packages on suitable platforms: see 'Writing R Extensions'. * Fake installs now install the contents of directory inst: some packages use this to install e.g. C++ headers for use by other packages that are independent of the package itself. Option --no-inst can be used to get the previous behaviour. DEBUGGING: * The behaviour of the code browser has been made more consistent, in part following the suggestions in PR#14985. * Calls to browser() are now consistent with calls to the browser triggered by debug(), in that Enter will default to n rather than c. * A new browser command s has been added, to "step into" function calls. * A new browser command f has been added, to "finish" the current loop or function. * Within the browser, the command help will display a short list of available commands. UTILITIES: * Only vignettes sources in directory vignettes are considered to be vignettes by R CMD check. That has been the preferred location since R 2.14.0 and is now obligatory. * For consistency, R CMD build now matches entries in .Rbuildignore and vignettes/.install_extras case-insensitively on all platforms (not just on Windows). * checkFF() (called by R CMD check by default) can optionally check foreign function calls for consistency with the registered type and argument count. This is the default for R CMD check --as-cran or can be enabled by setting environment variable _R_CHECK_FF_CALLS_ to registration (but is in any case suppressed by --install=no). Because this checks calls in which .NAME is an R object and not just a literal character string, some other problems are detected for such calls. Functions suppressForeignCheck() and dontCheck() have been added to allow package authors to suppress false positive reports. * R CMD check --as-cran warns about a false value of the DESCRIPTION field BuildVignettes for Open Source packages, and ignores it. (An Open Source package needs to have complete sources for its vignettes which should be usable on a suitably well-equipped system). * R CMD check --no-rebuild-vignettes is defunct: R CMD check --no-build-vignettes has been preferred since R 3.0.0. * R CMD build --no-vignettes is defunct: R CMD build --no-build-vignettes has been preferred since R 3.0.0. * R CMD Sweave and R CMD Stangle now process both Sweave and non-Sweave vignettes. The tools::buildVignette() function has been added to do the same tasks from within R. * The flags returned by R CMD config --ldflags and (where installed) pkg-config --libs libR are now those needed to link a front-end against the (shared or static) R library. * Sweave.sty has a new option [inconsolata]. * R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make available packages only in LinkingTo only for installation, and not for loading/runtime tests. * tools::checkFF() reports on .C and .Fortran calls with DUP = FALSE if argument check_DUP is true. This is selected by R CMD check by default. * R CMD check --use-gct can be tuned to garbage-collect less frequently using gctorture2() _via_ the setting of environment variable _R_CHECK_GCT_N_. * Where supported, tools::texi2dvi() limits the number of passes tried to 20. C-LEVEL FACILITIES: * (Windows only) A function R_WaitEvent() has been added (with declaration in headerR.h) to block execution until the next event is received by R. * Remapping in the Rmath.h header can be suppressed by defining R_NO_REMAP_RMATH. * The remapping of rround() in header Rmath.h has been removed: use fround() instead. * ftrunc() in header Rmath.h is now a wrapper for the C99 function trunc(), which might as well be used in C code: ftrunc() is still needed for portable C++ code. * The never-documented remapping of prec() to fprec() in header Rmath.h has been removed. * The included LAPACK subset now contains ZGESDD and ZGELSD. * The function LENGTH() now checks that it is only applied to vector arguments. However, in packages length() should be used. (In R itself LENGTH() is a macro without the function overhead of length().) * Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked for indices which are in-range: several packages were writing one element beyond the allocated length. * allocVector3 has been added which allows custom allocators to be used for individual vector allocations. DEPRECATED AND DEFUNCT: * chol(pivot = TRUE, LINPACK = TRUE) is defunct. Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(), solve() and svd() are ignored: LAPACK is always used. * .find.package() and .path.package() are defunct: only the versions without the initial dot introduced in R 2.13.0 have ever been in the API. * Partial matching when using the $ operator _on data frames_ now throws a warning and may become defunct in the future. If partial matching is intended, replace foo$bar by foo[["bar", exact = FALSE]]. * The long-deprecated use of \synopsis in the Usage section of .Rd files has been removed: such sections are now ignored (with a warning). * package.skeleton()'s deprecated argument namespace has been removed. * Many methods are no longer exported by package stats. They are all registered on their generic, which should be called rather than calling a method directly. * Functions readNEWS() and checkNEWS() in package tools are defunct. * download.file(method = "lynx") is deprecated. * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and may be disabled in future versions of R. As their help has long said, .Call() is much preferred. R CMD check notes such usages (by default). * The workaround of setting R_OSX_VALGRIND has been removed: it is not needed in current valgrind. BUG FIXES: * Calling lm.wfit() with no non-zero weights gave an array-overrun in the Fortran code and a not very sensible answer. It is now special-cased with a simpler answer (no qr component). * Error messages involving non-syntactic names (e.g. as produced by `\r` when that object does not exist) now encode the control characters. (Reported by Hadley Wickham.) * getGraphicsEvent() caused 100% usage of one CPU in Windows. (PR#15500) * nls() with no start argument may now work inside another function (scoping issue). * pbeta() and similar work better for very large (billions) ncp. * Where time zones have changed abbreviations over the years, the software tries to more consistently use the abbreviation appropriate to the time or if that is unknown, the current abbreviation. On some platforms where the C function localtime changed the tzname variables the reported abbreviation could have been that of the last time converted. * all.equal(list(1), identity) now works. * Bug fix for pushing viewports in grid (reported by JJ Allaire and Kevin Ushey). NOTE for anyone poking around within the graphics engine display list (despite the warnings not to) that this changes what is recorded by grid on the graphics engine display list. * Extra checks have been added for unit resolution and conversion in grid, to catch instances of division-by-zero. This may introduce error messages in existing code and/or produce a different result in existing code (but only where a non-finite location or dimension may now become zero). * Some bugs in TRE have been corrected by updating from the git repository. This allows R to be installed on some platforms for which this was a blocker (PR#15087 suggests Linux on ARM and HP-UX). * ? applied to a call to an S4 generic failed in several cases. (PR#15680) which this was a blocker (PR#15087 suggests Linux on ARM and HP-UX). * ? applied to a call to an S4 generic failed in several cases. (PR#15680) * The implicit S4 generics for primitives with ... in their argument list were incorrect. (PR#15690) * Bug fixes to methods::callGeneric(). (PR#15691) * The bug fix to aggregrate() in PR#15004 introduced a new bug in the case of no grouping variables. (PR#15699) * In rare cases printing deeply nested lists overran a buffer by one byte and on a few platforms segfaulted. (PR#15679) * The dendrogram method of as.dendrogram() was hidden accidentally, (PR#15703), and order.dendrogram(d) gave too much for a leaf d. (PR#15702) * R would try to kill processes on exit that have pids ever used by a child process spawned by mcparallel even though the current process with that pid was not actually its child. * cophenetic() applied to a "dendrogram" object sometimes incorrectly returned a "Labels" attribute with dimensions. (PR#15706) * printCoefmat() called from quite a few print() methods now obeys small getOption("width") settings, line wrapping the "signif. codes" legend appropriately. (PR#15708) * model.matrix() assumed that the stored dimnames for a matrix was NULL or length 2, but length 1 occurred. * The clipping region for a device was sometimes used in base graphics before it was set. -- 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 From pd.mes at cbs.dk Thu Apr 10 12:07:38 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 10 Apr 2014 12:07:38 +0200 Subject: [R] R 3.1.0 is released Message-ID: <4415F313-1667-4A20-9005-CB3518BCA43E@cbs.dk> (Resend with correct Subject field.) The build system rolled up R-3.1.0.tar.gz (codename "Spring Dance") 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-3.1.0.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 seems to be a minor mishap with the NEWS file not getting copied to CRAN. I'll attend to that shortly.) 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) = 2978039f3d69bde1d31c5a3699dbe88a MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS.html) = d88192d6e47eec39df1fe6ba3d673ae0 MD5 (R-latest.tar.gz) = a1ee52446bee81820409661e6d114ab1 MD5 (README) = e259ae5dd943b8547f0b7719664e815b MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4 MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649 MD5 (R-3/R-3.1.0.tar.gz) = a1ee52446bee81820409661e6d114ab1 This is the relevant part of the NEWS file CHANGES IN R 3.1.0: NEW FEATURES: * type.convert() (and hence by default read.table()) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs. If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify colClasses in read.table() to be "numeric". * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition of diff -b (as distinct from the description in the man pages of most systems). * New function anyNA(), a version of any(is.na(.)) which is fast for atomic vectors, based on a proposal by Tim Hesterberg. (Wish of PR#15239.) * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind = TRUE) now make use of names(.dimnames) when available. * is.unsorted() now also works for raw vectors. * The "table" method for as.data.frame() (also useful as as.data.frame.table()) now passes sep and base arguments to provideDimnames(). * uniroot() gets new optional arguments, notably extendInt, allowing to auto-extend the search interval when needed. The return value has an extra component, init.it. * switch(f, ...) now warns when f is a factor, as this typically happens accidentally where the useR meant to pass a character string, but f is treated as integer (as always documented). * The parser has been modified to use less memory. * The way the unary operators (+ - !) handle attributes is now more consistent. If there is no coercion, all attributes (including class) are copied from the input to the result: otherwise only names, dims and dimnames are. * colorRamp() and colorRampPalette() now allow non-opaque colours and a ramp in opacity via the new argument alpha = TRUE. (Suggested by Alberto Krone-Martins, but optionally as there are existing uses which expect only RGB values.) * grid.show.layout() and grid.show.viewport() get an optional vp.ex argument. * There is a new function find_gs_cmd() in the tools package to locate a GhostScript executable. (This is an enhanced version of a previously internal function there.) * object.size() gains a format() method. * There is a new family, "ArialMT", for the pdf() and postscript() devices. This will only be rendered correctly on viewers which have access to Monotype TrueType fonts (which are sometimes requested by journals). * The text and PDF news files, including NEWS and NEWS.2, have been moved to the doc directory. * combn(x, simplify = TRUE) now gives a factor result for factor input x (previously user error). (Related to PR#15442.) * Added utils::fileSnapshot() and utils::changedFiles() functions to allow snapshots and comparison of directories of files. * make.names(names, unique=TRUE) now tries to preserve existing names. (Suggestion of PR#15452.) * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate computation of cos(pi*x), etc, both in R and the C API. Using these gains accuracy in some cases, e.g., inside lgamma() or besselI(). (Suggested by Morten Welinder in PR#15529.) * print.table(x, zero.print = ".") now also has an effect when x is not integer-valued. * There is more support to explore the system's idea of time-zone names. Sys.timezone() tries to give the current system setting by name (and succeeds at least on Linux, OS X, Solaris and Windows), and OlsonNames() lists the names in the system's Olson database. Sys.timezone(location = FALSE) gives the previous behaviour. * Platforms with a 64-bit time_t type are allowed to handle conversions between the "POSIXct" and "POSIXlt" classes for date-times outside the 32-bit range (before 1902 or after 2037): the existing workarounds are used on other platforms. (Note that time-zone information for post-2037 is speculative at best, and the OS services are tested for known errors and so not used on OS X.) Currently time_t is usually long and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On R for Windows it is 64-bit (for both architectures as from this version). * The "save.defaults" option can include a value for compression_level. (Wish of PR#15579.) * colSums() and friends now have support for arrays and data-frame columns with 2^31 or more elements. * as.factor() is faster when f is an unclassed integer vector (for example, when called from tapply()). * fft() now works with longer inputs, from the 12 million previously supported up to 2 billion. (PR#15593) * Complex svd() now uses LAPACK subroutine ZGESDD, the complex analogue of the routine used for the real case. * Sweave now outputs .tex files in UTF-8 if the input encoding is declared to be UTF-8, regardless of the local encoding. The UTF-8 encoding may now be declared using a LaTeX comment containing the string %\SweaveUTF8 on a line by itself. * file.copy() gains a copy.date argument. * Printing of date-times will make use of the time-zone abbreviation in use at the time, if known. For example, for Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable this, the "POSIXlt" class has an optional component "zone" recording the abbreviation for each element. For platforms which support it, there is also a component "gmtoff" recording the offset from GMT where known. * (On Windows, by default on OS X and optionally elsewhere.) The system C function strftime has been replaced by a more comprehensive version with closer conformance to the POSIX 2008 standard. * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for |x| > 5; as suggested in PR#15620. * Some versions of the tiff() device have further compression options. * read.table(), readLines() and scan() have a new argument to influence the treatment of embedded nuls. * Avoid duplicating the right hand side values in complex assignments when possible. This reduces copying of replacement values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some package code has relied on there being copies. Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence. * The fast argument of KalmanLike(), KalmanRun() and KalmanForecast() has been replaced by update, which instead of updating mod in place, optionally returns the updated model in an attribute "mod" of the return value. * arima() and makeARIMA() get a new optional argument SSinit, allowing the choice of a different *s*tate *s*pace initialization which has been observed to be more reliable close to non-stationarity: see PR#14682. * warning() has a new argument noBreaks., to simplify post-processing of output with options(warn = 1). * pushBack() gains an argument encoding, to support reading of UTF-8 characters using scan(), read.table() and related functions in a non-UTF-8 locale. * all.equal.list() gets a new argument use.names which by default labels differing components by names (if they match) rather than by integer index. Saved R output in packages may need to be updated. * The methods for all.equal() and attr.all.equal() now have argument check.attributes after ... so it cannot be partially nor positionally matched (as it has been, unintentionally). A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to all.equal() are detected and reported. There are explicit checks that check.attributes is logical, tolerance is numeric and scale is NULL or numeric. This catches some unintended positional matching. The message for all.equal.numeric() reports a "scaled difference" only for scale != 1. * all.equal() now has a "POSIXt" method replacing the "POSIXct" method. * The "Date" and "POSIXt" methods of seq() allows by = "quarter" for completeness (by = "3 months" always worked). * file.path() removes any trailing separator on Windows, where they are invalid (although sometimes accepted). This is intended to enhance the portability of code written by those using POSIX file systems (where a trailing / can be used to confine path matching to directories). * New function agrepl() which like grepl() returns a logical vector. * fifo() is now supported on Windows. (PR#15600) * sort.list(method = "radix") now allows negative integers (wish of PR#15644). * Some functionality of print.ts() is now available in .preformat.ts() for more modularity. * mcparallel() gains an option detach = TRUE which allows execution of code independently of the current session. It is based on a new estranged = TRUE argument to mcfork() which forks child processes such that they become independent of the parent process. * The pdf() device omits circles and text at extremely small sizes, since some viewers were failing on such files. * The rightmost break for the "months", "quarters" and "years" cases of hist.POSIXlt() has been increased by a day. (Inter alia, fixes PR#15717.) * The handling of DF[i,] <- a where i is of length 0 is improved. (Inter alia, fixes PR#15718.) * hclust() gains a new method "ward.D2" which implements Ward's method correctly. The previous "ward" method is "ward.D" now, with the old name still working. Thanks to research and proposals by Pierre Legendre. * The sunspot.month dataset has been amended and updated from the official source, whereas the sunspots and sunspot.year datasets will remain immutable. The documentation and source links have been updated correspondingly. * The summary() method for "lm" fits warns if the fit is essentially perfect, as most of the summary may be computed inaccurately (and with platform-dependent values). Programmers who use summary() in order to extract just a component which will be reliable (e.g. $cov.unscaled) should wrap their calls in suppressWarnings(). INSTALLATION and INCLUDED SOFTWARE: * The included version of LAPACK has been updated to 3.5.0. * There is some support for parallel testing of an installation, by setting TEST_MC_CORES to an integer greater than one to indicate the maximum number of cores to be used in parallel. (It is worth specifying at least 8 cores if available.) Most of these require a make program (such as GNU make and dmake) which supports the $MAKE -j nproc syntax. Except on Windows: the tests of standard package examples in make check are done in parallel. This also applies to running tools::testInstalledPackages(). The more time-consuming regression tests are done in parallel. The package checks in make check-devel and make check-recommended are done in parallel. * More of make check will work if recommended packages are not installed: but recommended packages remain needed for thorough checking of an R build. * The version of tzcode included in src/extra/tzone has been updated. (Formerly used only on Windows.) * The included (64-bit) time-zone conversion code and Olson time-zone database can be used instead of the system version: use configure option --with-internal-tzcode. This is the default on Windows and OS X. (Note that this does not currently work if a non-default rsharedir configure variable is used.) (It might be necessary to set environment variable TZ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.) This option also switches to the version of strftime included in directory src/extra/tzone. * configure now tests for a C++11-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by CXX, but an alternative compiler, options and standard can be specified by variables CXX1X, CXX1XFLAGS and CXX1XSTD (e.g. -std=gnu++11). * R can now optionally be compiled to use reference counting instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in Rinternals.h. This may become the default in the future. * There is a new option --use-system-tre to use a suitable system tre library: at present this means a version from their git repository, after corrections. (Wish of PR#15660.) PACKAGE INSTALLATION: * The CRANextra repository is no longer a default repository on Windows: all the binary versions of packages from CRAN are now on CRAN, although CRANextra contains packages from Omegahat and elsewhere used by CRAN packages. * Only vignettes sources in directory vignettes are considered to be vignettes and hence indexed as such. * In the DESCRIPTION file, License: X11 is no longer recognized as valid. Use MIT or BSD_2_clause instead, both of which need + file LICENSE. * For consistency, entries in .Rinstignore are now matched case-insensitively on all platforms. * Help for S4 methods with very long signatures now tries harder to split the description in the Usage field to no more than 80 characters per line (some packages had over 120 characters). * R CMD INSTALL --build (not Windows) now defaults to the internal tar() unless R_INSTALL_TAR is set. * There is support for compiling C++11 code in packages on suitable platforms: see 'Writing R Extensions'. * Fake installs now install the contents of directory inst: some packages use this to install e.g. C++ headers for use by other packages that are independent of the package itself. Option --no-inst can be used to get the previous behaviour. DEBUGGING: * The behaviour of the code browser has been made more consistent, in part following the suggestions in PR#14985. * Calls to browser() are now consistent with calls to the browser triggered by debug(), in that Enter will default to n rather than c. * A new browser command s has been added, to "step into" function calls. * A new browser command f has been added, to "finish" the current loop or function. * Within the browser, the command help will display a short list of available commands. UTILITIES: * Only vignettes sources in directory vignettes are considered to be vignettes by R CMD check. That has been the preferred location since R 2.14.0 and is now obligatory. * For consistency, R CMD build now matches entries in .Rbuildignore and vignettes/.install_extras case-insensitively on all platforms (not just on Windows). * checkFF() (called by R CMD check by default) can optionally check foreign function calls for consistency with the registered type and argument count. This is the default for R CMD check --as-cran or can be enabled by setting environment variable _R_CHECK_FF_CALLS_ to registration (but is in any case suppressed by --install=no). Because this checks calls in which .NAME is an R object and not just a literal character string, some other problems are detected for such calls. Functions suppressForeignCheck() and dontCheck() have been added to allow package authors to suppress false positive reports. * R CMD check --as-cran warns about a false value of the DESCRIPTION field BuildVignettes for Open Source packages, and ignores it. (An Open Source package needs to have complete sources for its vignettes which should be usable on a suitably well-equipped system). * R CMD check --no-rebuild-vignettes is defunct: R CMD check --no-build-vignettes has been preferred since R 3.0.0. * R CMD build --no-vignettes is defunct: R CMD build --no-build-vignettes has been preferred since R 3.0.0. * R CMD Sweave and R CMD Stangle now process both Sweave and non-Sweave vignettes. The tools::buildVignette() function has been added to do the same tasks from within R. * The flags returned by R CMD config --ldflags and (where installed) pkg-config --libs libR are now those needed to link a front-end against the (shared or static) R library. * Sweave.sty has a new option [inconsolata]. * R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make available packages only in LinkingTo only for installation, and not for loading/runtime tests. * tools::checkFF() reports on .C and .Fortran calls with DUP = FALSE if argument check_DUP is true. This is selected by R CMD check by default. * R CMD check --use-gct can be tuned to garbage-collect less frequently using gctorture2() _via_ the setting of environment variable _R_CHECK_GCT_N_. * Where supported, tools::texi2dvi() limits the number of passes tried to 20. C-LEVEL FACILITIES: * (Windows only) A function R_WaitEvent() has been added (with declaration in headerR.h) to block execution until the next event is received by R. * Remapping in the Rmath.h header can be suppressed by defining R_NO_REMAP_RMATH. * The remapping of rround() in header Rmath.h has been removed: use fround() instead. * ftrunc() in header Rmath.h is now a wrapper for the C99 function trunc(), which might as well be used in C code: ftrunc() is still needed for portable C++ code. * The never-documented remapping of prec() to fprec() in header Rmath.h has been removed. * The included LAPACK subset now contains ZGESDD and ZGELSD. * The function LENGTH() now checks that it is only applied to vector arguments. However, in packages length() should be used. (In R itself LENGTH() is a macro without the function overhead of length().) * Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked for indices which are in-range: several packages were writing one element beyond the allocated length. * allocVector3 has been added which allows custom allocators to be used for individual vector allocations. DEPRECATED AND DEFUNCT: * chol(pivot = TRUE, LINPACK = TRUE) is defunct. Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(), solve() and svd() are ignored: LAPACK is always used. * .find.package() and .path.package() are defunct: only the versions without the initial dot introduced in R 2.13.0 have ever been in the API. * Partial matching when using the $ operator _on data frames_ now throws a warning and may become defunct in the future. If partial matching is intended, replace foo$bar by foo[["bar", exact = FALSE]]. * The long-deprecated use of \synopsis in the Usage section of .Rd files has been removed: such sections are now ignored (with a warning). * package.skeleton()'s deprecated argument namespace has been removed. * Many methods are no longer exported by package stats. They are all registered on their generic, which should be called rather than calling a method directly. * Functions readNEWS() and checkNEWS() in package tools are defunct. * download.file(method = "lynx") is deprecated. * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and may be disabled in future versions of R. As their help has long said, .Call() is much preferred. R CMD check notes such usages (by default). * The workaround of setting R_OSX_VALGRIND has been removed: it is not needed in current valgrind. BUG FIXES: * Calling lm.wfit() with no non-zero weights gave an array-overrun in the Fortran code and a not very sensible answer. It is now special-cased with a simpler answer (no qr component). * Error messages involving non-syntactic names (e.g. as produced by `\r` when that object does not exist) now encode the control characters. (Reported by Hadley Wickham.) * getGraphicsEvent() caused 100% usage of one CPU in Windows. (PR#15500) * nls() with no start argument may now work inside another function (scoping issue). * pbeta() and similar work better for very large (billions) ncp. * Where time zones have changed abbreviations over the years, the software tries to more consistently use the abbreviation appropriate to the time or if that is unknown, the current abbreviation. On some platforms where the C function localtime changed the tzname variables the reported abbreviation could have been that of the last time converted. * all.equal(list(1), identity) now works. * Bug fix for pushing viewports in grid (reported by JJ Allaire and Kevin Ushey). NOTE for anyone poking around within the graphics engine display list (despite the warnings not to) that this changes what is recorded by grid on the graphics engine display list. * Extra checks have been added for unit resolution and conversion in grid, to catch instances of division-by-zero. This may introduce error messages in existing code and/or produce a different result in existing code (but only where a non-finite location or dimension may now become zero). * Some bugs in TRE have been corrected by updating from the git repository. This allows R to be installed on some platforms for which this was a blocker (PR#15087 suggests Linux on ARM and HP-UX). * ? applied to a call to an S4 generic failed in several cases. (PR#15680) which this was a blocker (PR#15087 suggests Linux on ARM and HP-UX). * ? applied to a call to an S4 generic failed in several cases. (PR#15680) * The implicit S4 generics for primitives with ... in their argument list were incorrect. (PR#15690) * Bug fixes to methods::callGeneric(). (PR#15691) * The bug fix to aggregrate() in PR#15004 introduced a new bug in the case of no grouping variables. (PR#15699) * In rare cases printing deeply nested lists overran a buffer by one byte and on a few platforms segfaulted. (PR#15679) * The dendrogram method of as.dendrogram() was hidden accidentally, (PR#15703), and order.dendrogram(d) gave too much for a leaf d. (PR#15702) * R would try to kill processes on exit that have pids ever used by a child process spawned by mcparallel even though the current process with that pid was not actually its child. * cophenetic() applied to a "dendrogram" object sometimes incorrectly returned a "Labels" attribute with dimensions. (PR#15706) * printCoefmat() called from quite a few print() methods now obeys small getOption("width") settings, line wrapping the "signif. codes" legend appropriately. (PR#15708) * model.matrix() assumed that the stored dimnames for a matrix was NULL or length 2, but length 1 occurred. * The clipping region for a device was sometimes used in base graphics before it was set. -- 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 From jeroen.ooms at stat.ucla.edu Mon Jun 2 06:31:07 2014 From: jeroen.ooms at stat.ucla.edu (Jeroen Ooms) Date: Sun, 1 Jun 2014 21:31:07 -0700 Subject: Updates from the useR! 2014 organizing committee Message-ID: Hi all, We are exactly one month away from the useR! 2014 conference [1]. Time for an update from the organizing committee. This weekend, registrations passed the 500 mark, which is a new record for useR! according to data collected by Gergely Dar?czi [2]. Yet, there is plenty of additional capacity, both for the conference itself, as well as the beautiful on-campus housing at UCLA. We hope to see many more registrations over the upcoming weeks and appreciate all help in spreading the word to friends and colleagues that (should) use R, but might not be actively following the blogs or mailing lists. To those who are unsure whether to attend, we want to emphasize that useR! is not just for seasoned professionals, but has lots to offer to any R user. Abstracts and (free) tutorials cover a great diversity of topics in both research and industry applications, ranging from introductory to very advanced. The conference provides a great opportunity to learn and mingle with the community, and is interesting for beginner as well as experienced R users. Tutorials this year are included with the conference ticket and no separate registration is required. All registrants will receive an email survey asking which tutorial they would like to attend, if any. This information will be used for scheduling purposes and to facilitate communication between presenters and participants (e.g. distribution of preparation material). Finally, we urge international guests to verify that their visa or visa-waiver documents are valid to enter the United States. Citizens from visa-waiver countries [3] that do not already have a US visa, must apply online for an ESTA travel authorization at least 72 hours prior to departure. Once approved, the ESTA is generally valid for a period of 2 years, so now would be a good time to complete this process. We look forward to seeing all of you in California! Please keep an eye on the conference website, which is continuously updated with most recent news and information as it becomes available. Best, Jeroen, on behalf of the organizing committee [1] http://user2014.stat.ucla.edu/ [2] http://rapporter.net/custom/R-activity/data/Rstats.csv [3] http://www.esta.us/visa_waiver_countries.html From pd.mes at cbs.dk Fri Jun 13 16:18:23 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 13 Jun 2014 16:18:23 +0200 Subject: Release of R 3.1.1 scheduled for July 10 Message-ID: <812FE86A-84B4-493E-9BDE-4A22F6339E93@cbs.dk> Just a quick notice that we intend to have a patch release on July 10. Nickname is still undecided. Due to calendar conflicts, the binaries for some platforms may be delayed by a week or so. -pd -- 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 From pd.mes at cbs.dk Thu Jul 10 10:51:52 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 10 Jul 2014 10:51:52 +0200 Subject: [R] R 3.1.1 is released Message-ID: <737AC669-98EA-41D4-9C83-ABB6F09C6724@cbs.dk> 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 = , 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 From deepayan.sarkar at r-project.org Tue Aug 5 09:31:03 2014 From: deepayan.sarkar at r-project.org (Deepayan Sarkar) Date: Tue, 5 Aug 2014 13:01:03 +0530 Subject: The R Journal, Volume 6, Issue 1 Message-ID: Dear All, The latest issue of The R Journal is now available at http://journal.r-project.org/archive/2014-1/ Many thanks to all contributors, and apologies for the delay. Regards, -Deepayan From rgentlem at gmail.com Mon Sep 15 18:36:17 2014 From: rgentlem at gmail.com (Robert Gentleman) Date: Mon, 15 Sep 2014 09:36:17 -0700 Subject: Updates to R Core and R Foundation Membership Message-ID: Hi all, It is my pleasure to announce new members to R Core and to the R Foundation whose efforts will be most appreciated as R continues to evolve and advance. There are 2 new R core members: Martin Morgan and Michael Lawrence. In addition Stefano Iacus has decided to step down from R Core. There are 7 new R foundation members: Dirk Eddelbuettel, Torsten Hothorn, Marc Schwartz, Hadley Wickham, and Achim Zeileis, Martin Morgan and Michael Lawrence. The R Foundation now has 29 ordinary members. Please join me in welcoming them to their new roles and especially in thanking Stefano for his many years of contributions. best wishes Robert for the R Foundation -- Robert Gentleman rgentlem at gmail.com [[alternative HTML version deleted]] From pd.mes at cbs.dk Fri Oct 31 11:13:24 2014 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 31 Oct 2014 11:13:24 +0100 Subject: [R] R 3.1.2 is released Message-ID: <97264A18-3A52-4B9B-B97F-A78923BE6818@cbs.dk> The build system rolled up R-3.1.2.tar.gz (codename "Pumpkin Helmet") 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-3.1.2.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) = 23bbd5f6f8060f187cc02a7b84b342b5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = c1e4c113071453c7832e5d9ecea623eb MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 15cc434143e5e9a8ae3d34eead26521c MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (NEWS.html) = 561c491e3bf9554c86675b614c85d34c MD5 (R-latest.tar.gz) = 3af29ec06704cbd08d4ba8d69250ae74 MD5 (R.css) = 444535b9cb76ddff1bab1e1865a3fb14 MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914 MD5 (THANKS) = 1989ce89fb3891420c9964dc418ab71c MD5 (R-3/R-3.1.2.tar.gz) = 3af29ec06704cbd08d4ba8d69250ae74 This is the relevant part of the NEWS file CHANGES IN R 3.1.2: NEW FEATURES: * embedFonts() now defaults to format = "ps2write" for .ps and .eps files. This is available in Ghostscript 9.x (since 2010) whereas the previous default, format = "pswrite", was removed in Ghostscript 9.10. * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a point mass at exp(mulog) rather than return NaN (for an error). * capabilities() now reports if ICU is compiled in for use for collation (it is only actually used if a suitable locale is set for collation, and never for a C locale). * (OS X only.) Package tcltk checks when loaded if it is linked against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk component and the X11 libraries are installed. This allows more informative error messages to be given advising the installation of the missing component or of XQuartz. The X11() device and X11-based versions of the data editor and viewer (invoked by edit() and View() for data frames and matrices from command-line R) check that the X11 libraries are installed and if not advises installing XQuartz. * icuSetCollate() allows locale = "default", and locale = "none" to use OS services rather than ICU for collation. Environment variable R_ICU_LOCALE can be used to set the default ICU locale, in case the one derived from the OS locale is inappropriate (this is currently necessary on Windows). * New function icuGetCollate() to report on the ICU collation locale in use (if any). * utils::URLencode() was updated to use unreserved and reserved characters from RFC 3986, , instead of RFC 1738. * unique(warnings()) and c(warnings()) are now supported. * The Bioconductor 'version' used by setRepositories() now defaults to 3.0. (It can be set at runtime _via_ environment variable R_BIOC_VERSION.) INSTALLATION and INCLUDED SOFTWARE: * The configure script reports on the more important capabilities/options which will not be compiled in. More types of external BLAS are recognized by name in that report. * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH} flag is placed earlier in the link commands used during installation and when packages are installed: this helps ensure that the current build has priority if an R shared library has already been installed by e.g. install-libR in a library mentioned in LDFLAGS (and not in 'your system's library directory' as documented). (Wish of PR#15790.) * LaTeX package upquote is no longer required for R's use of inconsolata. * (Windows only) If both 32 and 64 bit versions of R are installed, the bin/R.exe and bin/Rscript.exe executables now run 64 bit R. (To run 32 bit R, overwrite these files with copies of bin/i386/Rfe.exe.) UTILITIES: * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes the VignetteBuilder packages available even if they are listed in Suggests, since they are needed to recognise and process non-Sweave vignettes. * R CMD check now reports empty importFrom declarations in a NAMESPACE file, as these are common errors (writing importFrom(Pkg) where import(Pkg) was intended). * R CMD check now by default checks code usage directly on the package namespace without loading and attaching the package and its suggests and enhances. For good practice with packages in the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'. For use of lazy-data objects in the package's own code, see ?data. BUG FIXES: * dmultinom() did not handle non-finite probabilities correctly. * prettyNum(x, zero.print=*) now also works when x contains NAs. * A longstanding bug exhibited by nlminb() on Windows was traced to a compiler bug in gcc 4.6.3; a workaround has been put in place. (PR#15244 and PR#15914). * Rendering of \command in HTML versions of help pages has been improved: this is particularly evident on the help page for INSTALL. * as.hexmode(x) and as.octmode(x) now behave correctly for some numeric x, e.g., c(NA, 1) or c(1, pi). * drop1() failed if the scope argument had no variables to drop. (PR#15935) * edit() (and hence fix()) failed if an object had a non-character attribute named "source" (an attribute that had been used in R prior to version 2.14.0). * callGeneric() could fail if the generic had ... as a formal argument. (PR#15937). * Forking in package parallel called C entry point exit in the child. This was unsafe (_exit should have been called), and could flush stdin of the main R process (seen most often on Solaris). As good practice, stdout is now flushed before forking a child. * R objects such as list(`a\b` = 1) now print correctly. * getAnywhere("C_pbinom") now returns correctly a single object (rather than unlisting it). * The confint() method for nls() fits failed it these has specified parameter limits despite using an algorithm other than "port". (PR#15960) * Subclassing an S4 class failed if the class required arguments to the generator, through its initialize() method. * removeSource() did not properly handle expressions containing arguments that were supplied as missing, e.g. x[i,]. (PR#15957) * as.environment(list()) now works, and as.list() of such an environment is now the same as list(). * Several tcltk functions failed when run in unusual environments. (PR#15970) * options(list()) now works (trivially). (PR#15979) * merge(, ..) now works correctly for two `independent' dendrograms (PR#15648), and still compatibly via adjust = "auto" e.g. for two branches of an existing dendrogram. * The plot method for "hclust" objects gets an optional argument check; When that is true (the default) it checks more carefully for valid input. * (Windows only) If a user chose to install 64 bit R but not 32 bit R, the bin/R and bin/Rscript executables failed to run. (PR#15981) * Various possible buffer overruns have been prevented, and missed memory protection added. (PR#15990) * Rscript no longer passes --args to R when there are no extra ("user") arguments. * objects like getClass("refClass")@prototype now print() and str() without error. * identical() now also looks at the S4 bit. * hist(x, breaks) is more robust in adding a small fuzz to few breaks when some are very large. (PR#15988) * sub() and gsub() did not handle regular expressions like "\s{2,}" properly if the text contained NA or non-ascii elements in a UTF-8 locale. Part of this was due to a bug in the TRE library. (PR#16009) * RShowDoc("NEWS") now displays the PDF version. * Matrices and arrays with last dimension zero did not print at all or incompletely. (PR#16012) * plot.histogram() and hence hist() now respect the xaxs, yaxs and lab graphics parameters. (PR#16021) * bw.SJ(x) and other bw.*() no longer segfault when x contains non-finite values. (PR#16024) * R CMD Rd2pdf unintentionally ignored its --os option. * The internal method of download.file() was not reporting file sizes and progress correctly on files larger than 2GB (inherited from libxml2). This is corrected for 64-bit builds (32-bit platforms may not support such files, but where possible will be supported in future versions of R). * Work around a bug in OS X Yosemite where key environment variables may be duplicated causing issues in subprocesses. The duplicates are now removed on R startup (via Rprofile). (PR#16042) * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize latest XQuartz. -- 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 From maechler at stat.math.ethz.ch Tue Dec 16 15:26:30 2014 From: maechler at stat.math.ethz.ch (Martin Maechler) Date: Tue, 16 Dec 2014 15:26:30 +0100 Subject: The R Foundation - New board Message-ID: <21648.16662.859007.156817@stat.math.ethz.ch> Dear R lovers and other useRs, notably benefactors, donors, supporting members and institutions of the R foundation http://www.r-project.org/foundation/ About 11.7 years ago, in April 2003, the R Foundation was announced by Fritz Leisch, https://stat.ethz.ch/pipermail/r-announce/2003/000385.html shortly after its foundation, and since then, its board has lead the foundation during years of phenomenal growth and success. Our thanks go to the *past* board members Presidents: Robert Gentleman, Ross Ihaka Secretary General: Friedrich Leisch Treasurer: Kurt Hornik Member at Large: John Chambers In addition, Peter Dalgaard and Martin M?chler had acted as auditors. After Summer meetings of the R Core and the R Foundation, we, i.e., Robert Gentleman, on Sep. 15 announced the new ("ordinary") memberships and the fact that the membership of the foundation has grown to 29 persons: https://stat.ethz.ch/pipermail/r-announce/2014/000577.html Subsequently (after a careful nomination and voting process), the election of a new *board* finalized on December 1, and the new board has started acting since. It consists of Presidents: Duncan Murdoch, Martyn Plummer Secretary General: Martin M?chler Treasurer: Kurt Hornik Members at Large: John Chambers Brian Ripley Dirk Eddelbuettel and the two auditors Peter Dalgaard and Roger Bivand. This is very soon to be reflected on http://www.r-project.org/foundation/board.html The foundation and its board aim to become considerably more active in the future. Details about this will be announced here in due time. Thank you all for supporting the R project, a Free Software (hence Open source) endeavor only made possible by the dedicated work of many thousands of volunteers and their contributions in several ways, including to become supporting (or ++) members of the R foundation! Martin Maechler