From deepayan.sarkar at r-project.org Sat Jan 31 19:57:52 2015 From: deepayan.sarkar at r-project.org (Deepayan Sarkar) Date: Sun, 1 Feb 2015 00:27:52 +0530 Subject: The R Journal, Volume 6, Issue 2 Message-ID: Dear All, The latest issue of The R Journal is now available at http://journal.r-project.org/archive/2014-2/ Many thanks to all contributors. Regards, -Deepayan From maechler at stat.math.ethz.ch Wed Mar 4 23:13:14 2015 From: maechler at stat.math.ethz.ch (Martin Maechler) Date: Wed, 4 Mar 2015 23:13:14 +0100 Subject: format( "www.R-project.org" , year = 2015) Message-ID: The R Foundation is pleased to announce that our website http://www.r-project.org/ has under gone a nice retouch (and thus arrived in the 21st century :-) Thanks to a working group of Dirk Eddelbuettel, Simon Urbanek and Hadley Wickham., the current page sources are in markdown, and the html is auto produced using pandoc (and IT infrastructure in Vienna and Zurich). Martin Maechler, as secretary of the R Foundation From pd.mes at cbs.dk Mon Mar 9 10:04:28 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 9 Mar 2015 10:04:28 +0100 Subject: R 3.1.3 is released Message-ID: <4EE2768D-1C4B-487F-A72C-2AA8EEE50D05@cbs.dk> The build system rolled up R-3.1.3.tar.gz (codename "Smooth Sidewalk") 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-3.1.3.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) = cebbdd1eb8cd620bf2a6ac84c9e731c2 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = a699fa0eeef280b78134f0abe0b1c1b0 MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 8790db3a8000910f0bf00fb1ee039634 MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (R-latest.tar.gz) = 53a85b884925aa6b5811dfc361d73fc4 MD5 (R.css) = 444535b9cb76ddff1bab1e1865a3fb14 MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914 MD5 (THANKS) = 1989ce89fb3891420c9964dc418ab71c MD5 (R-3/R-3.1.3.tar.gz) = 53a85b884925aa6b5811dfc361d73fc4 This is the relevant part of the NEWS file CHANGES IN R 3.1.3: NEW FEATURES: * The internal method of download.file() can now handle files larger than 2GB on 32-bit builds which support such files (tested on 32-bit R running on 64-bit Windows). * kruskal.test() warns on more types of suspicious input. * The as.dendrogram() method for "hclust" objects gains a check argument protecting against memory explosion for invalid inputs. * capabilities() has a new item long.double which indicates if the build uses a long double type which is longer than double. * nlm() no longer modifies the callback argument in place (a new vector is allocated for each invocation, which mimics the implicit duplication that occurred in R < 3.1.0); note that this is a change from the previously documented behavior. (PR#15958) * icuSetCollate() now accepts locale = "ASCII" which uses the basic C function strcmp and so collates strings byte-by-byte in numerical order. * sessionInfo() tries to report the OS version in use (not just that compiled under, and including details of Linux distributions). * model.frame() (used by lm() and many other modelling functions) now warns when it drops contrasts from factors. (Wish of PR#16119) * install.packages() and friends now accept the value type = "binary" as a synonym for the native binary type on the platform (if it has one). * Single source or binary files can be supplied for install.packages(type = "both") and the appropriate type and repos = NULL will be inferred. * New function pcre_config() to report on some of the configuration options of the version of PCRE in use. In particular, this reports if regular expressions using \p{xx} are supported. * (Windows.) download.file(cacheOK = FALSE) is now supported when internet2.dll is used. * browseURL() has been updated to work with Firefox 36.0 which has dropped support for the -remote interface. INSTALLATION and INCLUDED SOFTWARE: * The included version of PCRE has been updated to 8.36. * configure accepts MAKEINFO=texi2any as another way to ensure texinfo 5.x is used when both 5.x and 4.x are installed. UTILITIES: * R CMD check now checks the packages used in \donttest sections of the examples are specified in the DESCRIPTION file. (These are needed to run the examples interactively.) * R CMD check checks for the undeclared use of GNU extensions in Makefiles, and for Makefiles with a missing final linefeed. R CMD build will correct line endings in all Makefiles, not just those in the src directory. * R CMD check notes uses of library() and require() in package code: see the section 'Suggested packages' of 'Writing R Extensions' for good practice. DEPRECATED AND DEFUNCT: * The configure option --with-valgrind-instrumentation=3 is deprecated and will be removed in R 3.2.0. BUG FIXES: * (Windows.) Rscript.exe was missing a manifest specifying the modern style for common controls (e.g., the download progress bar). * If a package had extra documentation files but no vignette, the HTML help system produced an empty index page. * The parser now gives an error if a null character is included in a string using Unicode escapes. (PR#16046) * qr.Q() failed on complex arguments due to pre-3.0(!) typo. (PR#16054) * abs() failed with named arguments when the argument was complex. (PR#16047) * "noquote" objects may now be used as columns in dataframes. (PR#15997) * Some values with extremely long names were printed incorrectly. (PR#15999) * Extremely large exponents on zero expressed in scientific notation (e.g. 0.0e50000) could give NaN. (PR#15976) * download.file() reported downloaded sizes as 0KB if less than 1MB, only for R 3.1.2 and only on big-endian platforms. * prompt() did not escape percent signs in the automatically generated usage section of help files. * drop.terms() dropped some of the attributes of the object it was working with. (PR#16029) * (Windows.) The command completion in Rgui.exe messed up the console. (PR#15791) * (Windows.) The choose.files() command returned a blank string when the user asked for a single file but cancelled the request. (PR#16074) * Math2 S4 group generics failed to correctly dispatch "structure"- and "nonStructure"-derived classes. * loadNamespace() imposed undocumented restrictions on the versionCheck parameter. (Reported by Geoff Lee.) * Rare over-runs detected by AddressSanitizer in substr() and its replacement version have been avoided. _Inter alia_ that fix gives the documented behaviour for substr(x, 1, 2) <- "" (subsequently reported as PR#16214). * Loading packages incorrectly defining an S4 generic followed by a function of the same name caused an erroneous cyclic namespace dependency error. * Declared vignette encodings are now always passed to the vignette engine. * Port Tomas Kalibera's fix from R-devel that restores the loadMethod() fast path, effectively doubling the speed of S4 dispatch. * power.t.test() and power.prop.test() now make use of the extendInt option of uniroot() and hence work in more extreme cases. (PR#15792) * If a package was updated and attached when its namespace was already loaded, it could end up with parts from one version and parts from the other. (PR#16120) * tools:::.Rdconv() didn't accept --encoding= due to a typo. (PR#16121) * Unix-alike builds without a suitable makeinfo were documented to link the missing HTML manuals to CRAN, but did not. * save(*, ascii=TRUE) and load() now correctly deal with NaN's. (PR#16137) * split.Date() retains fractional representations while avoiding incomplete class propagation. * R_ext/Lapack.h had not been updated for changes made by LAPACK to the argument lists of its (largely internal) functions dlaed2 and dlaed3. (PR#16157) * RShowDoc("NEWS", "txt") had not been updated for the layout changes of R 3.1.0. * The xtfrm() method for class "Surv" has been corrected and its description expanded. * mode(x) <- y would incorrectly evaluate x before changing its mode. (PR#16215) * besselJ(1, 2^64) and besselY(..) now signal a warning, returning NaN instead of typically segfaulting. (Issue 3 of PR#15554) * HTML conversion of \href markup in .Rd files did not remove the backslash from \% and so gave an invalid URL. In a related change, the \ escape is now required in such URLs. -- 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 16 11:29:41 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 16 Apr 2015 11:29:41 +0200 Subject: [R] R 3.2.0 is released Message-ID: <4EAB40EE-2C15-4886-A593-EF8D34E932EA@cbs.dk> The build system rolled up R-3.2.0.tar.gz (codename "Full of Ingredients") 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-3.2.0.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. 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) = eb97a5cd38acb1cfc6408988bffef765 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = a699fa0eeef280b78134f0abe0b1c1b0 MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 99876f56fc07a7eb20825b85add9b66e MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (R-latest.tar.gz) = 66fa17ad457d7e618191aa0f52fc402e MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914 MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb MD5 (R-3/R-3.2.0.tar.gz) = 66fa17ad457d7e618191aa0f52fc402e This is the relevant part of the NEWS file CHANGES IN 3.2.0: NEW FEATURES: * anyNA() gains a recursive argument. * When x is missing and names is not false (including the default value), Sys.getenv(x, names) returns an object of class "Dlist" and hence prints tidily. * (Windows.) shell() no longer consults the environment variable SHELL: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). R_SHELL, the preferred way to select a non-default shell, can be used instead. * Some unusual arguments to embedFonts() can now be specified as character vectors, and the defaults have been changed accordingly. * Functions in the Summary group duplicate less. (PR#15798) * (Unix-alikes.) system(cmd, input = ) now uses 'shell-execution-environment' redirection, which will be more natural if cmd is not a single command (but requires a POSIX-compliant shell). (Wish of PR#15508) * read.fwf() and read.DIF() gain a fileEncoding argument, for convenience. * Graphics devices can add attributes to their description in .Device and .Devices. Several of those included with R use a "filepath" attribute. * pmatch() uses hashing in more cases and so is faster at the expense of using more memory. (PR#15697) * pairs() gains new arguments to select sets of variables to be plotted against each other. * file.info(, extra_cols = FALSE) allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists. * New function dir.exists() in package base to test efficiently whether one or more paths exist and are directories. * dput() and friends gain new controls hexNumeric and digits17 which output double and complex quantities as, respectively, binary fractions (exactly, see sprintf("%a")) and as decimals with up to 17 significant digits. * save(), saveRDS() and serialize() now support ascii = NA which writes ASCII files using sprintf("%a") for double/complex quantities. This is read-compatible with ascii = TRUE but avoids binary->decimal->binary conversions with potential loss of precision. Unfortunately the Windows C runtime's lack of C99 compliance means that the format cannot be read correctly there in R before 3.1.2. * The default for formatC(decimal.mark =) has been changed to be getOption("OutDec"); this makes it more consistent with format() and suitable for use in print methods, e.g. those for classes "density", "ecdf", "stepfun" and "summary.lm". getOption("OutDec") is now consulted by the print method for class "kmeans", by cut(), dendrogram(), plot.ts() and quantile() when constructing labels and for the report from legend(trace = TRUE). (In part, wish of PR#15819.) * printNum() and hence format() and formatC() give a warning if big.mark and decimal.mark are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed). * merge() can create a result which uses long vectors on 64-bit platforms. * dget() gains a new argument keep.source which defaults to FALSE for speed (dput() and dget() are most often used for data objects where this can make dget() many times faster). * Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages. * A number of macros have been added in the new share/Rd directory for use in package overview help pages, and promptPackage() now makes use of them. * tools::parse_Rd() gains a new permissive argument which converts unrecognized macros into text. This is used by utils:::format.bibentry to allow LaTeX markup to be ignored. * options(OutDec =) can now specify a multi-byte character, e.g., options(OutDec = "\u00b7") in a UTF-8 locale. * is.recursive(x) is no longer true when x is an external pointer, a weak reference or byte code; the first enables all.equal(x, x) when x <- getClass(.). * ls() (aka objects()) and as.list.environment() gain a new argument sorted. * The "source" attribute (which has not been added to functions by R since before R version 2.14.0) is no longer treated as special. * Function returnValue() has been added to give on.exit() code access to a function's return value for debugging purposes. * crossprod(x, y) allows more matrix coercions when x or y are vectors, now equalling t(x) %*% y in these cases (also reported by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in more cases with vector arguments. * Utility function dynGet() useful for detecting cycles, aka infinite recursions. * The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code. * apply(m, 2, identity) is now the same as the matrix m when it has _named_ row names. * A new function debuggingState() has been added, allowing to temporarily turn off debugging. * example() gets a new optional argument run.donttest and tools::Rd2ex() a corresponding commentDonttest, with a default such that example(..) in help examples will run \donttest code only if used interactively (a change in behaviour). * rbind.data.frame() gains an optional argument make.row.names, for potential speedup. * New function extSoftVersion() to report on the versions of third-party software in use in this session. Currently reports versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and the iconv implementation. A similar function grSoftVersion() in package grDevices reports on third-party graphics software. Function tcltk::tclVersion() reports the Tcl/Tk version. * Calling callGeneric() without arguments now works with primitive generics to some extent. * vapply(x, FUN, FUN.VALUE) is more efficient notably for large length(FUN.VALUE); as extension of PR#16061. * as.table() now allows tables with one or more dimensions of length 0 (such as as.table(integer())). * names(x) <- NULL now clears the names of call and ... objects. * library() will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path. * A new plot() method for class "raster" has been added. * New check_packages_in_dir_changes() function in package tools for conveniently analyzing how changing sources impacts the check results of their reverse dependencies. * Speed-up from Peter Haverty for ls() and methods:::.requirePackage() speeding up package loading. (PR#16133) * New get0() function, combining exists() and get() in one call, for efficiency. * match.call() gains an envir argument for specifying the environment from which to retrieve the ... in the call, if any; this environment was wrong (or at least undesirable) when the definition argument was a function. * topenv() has been made .Internal() for speedup, based on Peter Haverty's proposal in PR#16140. * getOption() no longer calls options() in the main case. * Optional use of libcurl (version 7.28.0 from Oct 2012 or later) for Internet access: * capabilities("libcurl") reports if this is available. * libcurlVersion() reports the version in use, and other details of the "libcurl" build including which URL schemes it supports. * curlGetHeaders() retrieves the headers for http://, https://, ftp:// and ftps:// URLs: analysis of these headers can provide insights into the `existence' of a URL (it might for example be permanently redirected) and is so used in R CMD check --as-cran. * download.file() has a new optional method "libcurl" which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs. * url() has a new method "libcurl" which handles more URL schemes and follows redirections. The default method is controlled by a new option url.method, which applies also to the opening of URLs _via_ file() (which happens implicitly in functions such as read.table.) * When file() or url() is invoked with a https:// or ftps:// URL which the current method cannot handle, it switches to a suitable method if one is available. * (Windows.) The DLLs internet.dll and internet2.dll have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an R session. The Windows internet functions are still selected by flag --internet2 or setInternet2(). This can be overridden for an url() connection _via_ its new method argument. download.file() has new method "wininet", selected as the default by --internet2 or setInternet2(). * parent.env<- can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar. * New function isLoadedNamespace() for readability and speed. * names(env) now returns all the object names of an environment env, equivalently to ls(env, all.names = TRUE, sorted = FALSE) and also to the names of the corresponding list, names(as.list(env, all.names = TRUE)). Note that although names() returns a character vector, the names have no particular ordering. * The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint. * New function trimws() for removing leading/trailing whitespace. * cbind() and rbind() now consider S4 inheritance during S3 dispatch and also obey deparse.level. * cbind() and rbind() will delegate recursively to methods::cbind2 (methods::rbind2) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity). * (Windows.) download.file(quiet = FALSE) now uses text rather than Windows progress bars in non-interactive use. * New function hsearch_db() in package utils for building and retrieving the help search database used by help.search(), along with functions for inspecting the concepts and keywords in the help search database. * New function .getNamespaceInfo(), a no-check version of getNamespaceInfo() mostly for internal speedups. * The help search system now takes \keyword entries in Rd files which are not standard keywords (as given in KEYWORDS in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts. * New lengths() function for getting the lengths of all elements in a list. * New function toTitleCase() in package tools, tailored to package titles. * The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elements. (For cbind(), wish of PR#16198.) * The default method of image() has an explicit check for a numeric or logical matrix (which was always required). * URLencode() will not by default encode further URLs which appear to be already encoded. * BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima() fitted models, as nobs(mod) now gives the number of "used" observations for such models. This fixes PR#16198, quite differently than proposed there. * The print() methods for "htest", "pairwise.htest" and "power.htest" objects now have a digits argument defaulting to (a function of) getOption("digits"), and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases. * Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached. * The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate. * unzip() will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to PR#16243). * methods() reports S4 in addition to S3 methods; output is simplified when the class argument is used. .S3methods() and methods::.S4methods() report S3 and S4 methods separately. * Higher order functions such as the apply functions and Reduce() now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves PR#16093. INSTALLATION and INCLUDED SOFTWARE: * The \donttest sections of R's help files can be tested by make check TEST_DONTTEST=TRUE . * It is possible to request the use of system valgrind headers _via_ configure option --with-system-valgrind-headers: note the possible future incompatibility of such headers discussed in the 'R Installation and Administration' manual. (Wish of PR#16068.) * The included version of liblzma has been updated to xz-utils 5.0.7 (minor bug fixes from 5.0.5). * configure options --with-system-zlib, --with-system-bzlib and --with-system-pcre are now the default. For the time being there is fallback to the versions included in the R sources if no system versions are found or (unlikely) if they are too old. Linux users should check that the -devel or -dev versions of packages zlib, bzip2/libbz2 and pcre as well as xz-devel/liblzma-dev (or similar names) are installed. * configure by default looks for the texi2any script from texinfo 5.1 or later, rather than the makeinfo program. (makeinfo is a link to the Perl script texi2any in texinfo 5.x.) * R CMD INSTALL gains an option --built-timestamp=STAMP allowing 100% reproducible package building, thanks to Dirk Eddelbuettel. UTILITIES: * There is support for testing the \dontrun and \donttest parts of examples in packages. tools::testInstalledPackage() accepts new arguments commentDontrun = FALSE and commentDonttest = FALSE. R CMD check gains options --run-dontrun and --run-donttest. * The HTML generated by tools::Rd2HTML() and tools::toHTML() methods is now 'XHTML 1.0 Strict'. * The compiler package's utility function setCompilerOptions() now returns the old values invisibly. The initial optimization level can also be set with the environment variable R_COMPILER_OPTIMIZE. * R CMD build adds a NeedsCompilation field if one is not already present in the DESCRIPTION file. * R CMD check gains option --test-dir to specify an alternative set of tests to run. * R CMD check will now by default continue with testing after many types of errors, and will output a summary count of errors at the end if any have occurred. * R CMD check now checks that the Title and Description fields are correctly terminated. * R CMD check --as-cran now: * checks a README.md file can be processed: this needs pandoc installed. * checks the existence and accessibility of URLs in the DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the help files (provided the build has libcurl support). * reports non-ASCII characters in R source files when there is no package encoding declared in the DESCRIPTION file. * reports (apparent) S3 methods exported but not registered. * reports overwriting registered S3 methods from base/recommended packages. (Such methods are replaced in the affected package for the rest of the session, even if the replacing namespace is unloaded.) * reports if the Title field does not appear to be in title case (see 'Writing R Extensions': there may be false positives, but note that technical words should be single-quoted and will then be accepted). Most of these checks can also be selected by environment variables: see the 'R Internals' manual. C-LEVEL FACILITIES: * New C API utility logspace_sum(logx[], n). * Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by default) to Rf_rbinom_mu etc. This requires packages using them to be re-installed. * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so arguments are duplicated if DUP = TRUE would do so. As their help has long said, .Call() is much preferred. * New entry point R_allocLD, like R_alloc but guaranteed to have sufficient alignment for long double pointers. * isPairList() now returns TRUE for DOTSXP. WINDOWS BUILD CHANGES: A number of changes to the Windows build system are in development. The following are currently in place. * Installation using external binary distributions of zlib, bzip2, liblzma, pcre, libpng, jpeglib and libtiff is now required, and the build instructions have been revised. * A new make target rsync-extsoft has been added to obtain copies of the external libraries from CRAN. * Building the manuals now requires texi2any from texinfo 5.1 or later. CRAN binary builds include the manuals, but by default builds from source will not, and they will be accessed from CRAN. See the comments in src/gnuwin32/MkRules.dist for how to specify the location of texi2any. * (Windows) Changes have been made to support an experimental Windows toolchain based on GCC 4.9.2. The default toolchain continues to be based on GCC 4.6.3, as the new toolchain is not yet stable enough. A change to a new toolchain is expected during the R 3.2.x lifetime. PACKAGE INSTALLATION: * (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win (which has not been documented for a long time) now requires an external libz.a to be available (it is part of the 'goodies' used to compile Windows binary packages). It would be simpler to use -lz instead. * The default for option pkgType on platforms using binary packages is now "both", so source packages will be tried if binary versions are not available or not up to date. There are options for what install.packages(type = "both") (possibly called _via_ update.packages()) will do if compilation of a source package is desirable: see ?options (under utils). If you intend not to accept updates as source packages, you should use update.packages(type = "binary"). DEPRECATED AND DEFUNCT: * download.file(method = "lynx") is defunct. * Building R using the included versions of zlib, bzip2, xz and PCRE is deprecated: these are frozen (bar essential bug-fixes) and will be removed for R 3.3.0. * The configure option --with-valgrind-instrumentation=3 has been withdrawn, as it did not work with recent valgrind headers: it is now treated as level 2. * The MethodsList class in package methods had been deprecated in R 2.11.0 and is defunct now. Functions using it are defunct if they had been deprecated in R 2.11.0, and are deprecated now, otherwise. BUG FIXES: * Fixed two obscure bugs in pairlist subassignment, reported by Radford Neal as part of pqR issue 16. * Fixes for bugs in handling empty arguments and argument matching by name in log(). * all.equal() gains methods for environments and refClasses. * [<- and [[<- gain S4 data.frame methods to avoid corruption of S4 class information by the S3 methods. * callNextMethod() should now work within a .local call when ... is absent from formals(.local). * dput(pairlist(x)) generates a call to the pairlist constructor instead of the list constructor. * Fix missing() when arguments are propagated through ... . (PR#15707) * eigen(m) now defaults to symmetric = TRUE even when the dimnames are asymmetric if the matrix is otherwise symmetric. (PR#16151) * Fix issues with forwarding ... through callGeneric() and callNextMethod(). (PR#16141) * callGeneric() now works after a callNextMethod(). * Subclass information is kept consistent when replacing an ordinary S4 class with an "old class" _via_ the S4Class argument to setOldClass(). Thus, for example, a data.frame is valid for a list argument in the signature, and a factor is valid for vector arguments. * In qbeta() the inversion of pbeta() is much more sophisticated. This works better in corner cases some of which failed completely previously (PR#15755), or were using too many iterations. * Auto-printing no longer duplicates objects when printing is dispatched to a method. * kmeans(x, k) would fail when nrow(x) >= 42949673. (Comment 6 of PR#15364) * 'Abbreviated' locale-specific day and month names could have been truncated in those rare locales where there are the same as the full names. * An irrelevant warning message from updating subclass information was silenced (the namespace would not be writable in this case). From pd.mes at cbs.dk Mon May 18 09:30:11 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 18 May 2015 09:30:11 +0200 Subject: Release of R 3.2.1 scheduled for June 18 Message-ID: <127E408C-FBBE-41D1-B6D6-2D53B8D8B208@cbs.dk> We intend to have a patch release on June 18, nickname will be "World-Famous Astronaut". The detailed schedule will be made available via developer.r-project.org as usual. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From maechler at lynne.stat.math.ethz.ch Thu May 21 11:01:46 2015 From: maechler at lynne.stat.math.ethz.ch (Martin Maechler) Date: Thu, 21 May 2015 11:01:46 +0200 Subject: The R Foundation announces new mailing list 'R-package-devel' Message-ID: <21853.40698.326587.61371@stat.math.ethz.ch> New Mailing list: R-package-devel -- User R Packages Development At last week's monthly meeting, the R foundation has decided to create a new mailing list in order to help R package authors in their package development and testing. The idea is that some experienced R programmers (often those currently helping on R-devel or also R-help) will help package authors and thus unload some of the burden of the CRAN team members. Please read the detailed description of the mailing list here, https://stat.ethz.ch/mailman/listinfo/r-package-devel or also the more extended announcement of the list on R-devel, archived at https://stat.ethz.ch/pipermail/r-devel/2015-May/071208.html For the R foundation, Martin Maechler, Secretary General From pd.mes at cbs.dk Thu Jun 18 11:04:58 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 18 Jun 2015 11:04:58 +0200 Subject: R 3.2.1 liftoff Message-ID: <7442C2E6-39F7-4EF5-9670-245B096EEC05@cbs.dk> The build system sent R-3.2.1.tar.gz (codename "World-Famous Astronaut") in orbit 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-3.2.1.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. 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) = eb97a5cd38acb1cfc6408988bffef765 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 181370b39076e34f64b842257076cd5c MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 6342bc1164e9f8e17713f47cff1910b4 MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (R-latest.tar.gz) = c2aac8b40f84e08e7f8c9068de9239a3 MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914 MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb MD5 (R-3/R-3.2.1.tar.gz) = c2aac8b40f84e08e7f8c9068de9239a3 This is the relevant part of the NEWS file CHANGES IN R 3.2.1: NEW FEATURES: * utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not. * install.packages() now allows type = "both" with repos = NULL if it can infer the type of file. * nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability. * news() more flexibly extracts dates from package NEWS.Rd files. * lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar. * The included version of PCRE has been updated to 8.37, a bug-fix release. * diag() no longer duplicates a matrix when extracting its diagonal. * as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted. BUG FIXES: * acf() and ccf() now guarantee values strictly in [-1,1] (instead of sometimes very slightly outside). PR#15832. * as.integer("111111111111") now gives NA (with a warning) as it does for the corresponding numeric or negative number coercions. Further, as.integer(M + 0.1) now gives M (instead of NA) when M is the maximal representable integer. * On some platforms nchar(x, "c") and nchar(x, "w") would return values (possibly NA) for inputs which were declared to be UTF-8 but were not, or for invalid strings without a marked encoding in a multi-byte locale, rather than give an error. Additional checks have been added to mitigate this. * apply(a, M, function(u) c(X = ., Y = .)) again has dimnames containing "X" and "Y" (as in R < 3.2.0). * (Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178) * (Windows only) choose.files() would occasionally include characters from the result of an earlier call in the result of a later one. (PR#16270) * A change in RSiteSearch() in R 3.2.0 caused it to submit invalid URLs. (PR#16329) * Rscript and command line R silently ignored incomplete statements at the end of a script; now they are reported as parse errors. (PR#16350) * Parse data for very long strings was not stored. (PR#16354) * plotNode(), the workhorse of the plot method for "dendrogram"s is no longer recursive, thanks to Suharto Anggono, and hence also works for deeply nested dendrograms. (PR#15215) * The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358) * If the CRAN mirror was not set, install.packages(type = "both") and related functions could repeatedly query the user for it. (Part of PR#16362) * The low-level functions .rowSums() etc. did not check the length of their argument, so could segfault. (PR#16367) * The quietly argument of library() is now correctly propagated from .getRequiredPackages2(). * Under some circumstances using the internal PCRE when building R fron source would cause external libs such as -llzma to be omitted from the main link. * The .Primitive default methods of the logic operators, i.e., !, & and |, now give correct error messages when appropriate, e.g., for `&`(TRUE) or `!`(). (PR#16385) * cummax(x) now correctly propagates NAs also when x is of type integer and begins with an NA. * summaryRprof() could fail when the profile contained only two records. (PR#16395) * HTML vignettes opened using vignette() did not support links into the rest of the HTML help system. (Links worked properly when the vignette was opened using browseVignettes() or from within the help system.) * arima(*, xreg = .) (for d >= 1) computes estimated variances based on a the number of effective observations as in R version 3.0.1 and earlier. (PR#16278) * slotNames(.) is now correct for "signature" objects (mostly used internally in methods). * On some systems, the first string comparison after a locale change would result in NA. From Bettina.Gruen at jku.at Wed Jul 1 07:27:33 2015 From: Bettina.Gruen at jku.at (Bettina Gruen) Date: Wed, 01 Jul 2015 07:27:33 +0200 Subject: The R Journal, Volume 7, Issue 1 Message-ID: <55937A45.8060600@jku.at> Dear all, The latest issue of The R Journal is now available at http://journal.r-project.org/archive/2015-1/ Many thanks to all contributors. Regards, Bettina -- ------------------------------------------------------------------- Bettina Gr?n Institut f?r Angewandte Statistik / IFAS Johannes Kepler Universit?t Linz Altenbergerstra?e 69 4040 Linz, Austria Tel: +43 732 2468-6829 Fax: +43 732 2468-6800 E-Mail: Bettina.Gruen at jku.at www.ifas.jku.at From pd.mes at cbs.dk Fri Jul 17 18:23:56 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 17 Jul 2015 18:23:56 +0200 Subject: Release of R 3.2.2 scheduled for August 14 Message-ID: <1D0E985F-12DC-41DD-8BDF-F00DC3AA4C06@cbs.dk> We intend to have a patch release on August 14, nickname will be "Fire Safety". The detailed schedule will be made available via developer.r-project.org as usual. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Fri Aug 14 11:21:48 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 14 Aug 2015 11:21:48 +0200 Subject: R 3.2.2 is released Message-ID: <14CDC0C4-DE12-4742-897C-C30D0E78976A@cbs.dk> The build system rolled up R-3.2.2.tar.gz (codename "Fire Safety") this morning. The list below details the changes in this release. The main point of this release is to enable package installation via secure HTTP, since ordinary HTTP is increasingly being considered a security risk. You can get the source code from http://cran.r-project.org/src/base/R-3/R-3.2.2.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) = eb97a5cd38acb1cfc6408988bffef765 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = e74e64dde0f92181957d46a0f8538e8b MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 5ff829377f0de5cdb0ad30bb42977611 MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (R-latest.tar.gz) = 57cef5c2e210a5454da1979562a10e5b MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435 MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb MD5 (VERSION-INFO.dcf) = 55826f7f976cd9623577e5a9ac694c47 MD5 (R-3/R-3.2.2.tar.gz) = 57cef5c2e210a5454da1979562a10e5b This is the relevant part of the NEWS file CHANGES IN R 3.2.2: SIGNIFICANT USER-VISIBLE CHANGES: * It is now easier to use secure downloads from https:// URLs on builds which support them: no longer do non-default options need to be selected to do so. In particular, packages can be installed from repositories which offer https:// URLs, and those listed by setRepositories() now do so (for some of their mirrors). Support for https:// URLs is available on Windows, and on other platforms if support for libcurl was compiled in and if that supports the https protocol (system installations can be expected to do). So https:// support can be expected except on rather old OSes (an example being OS X 'Snow Leopard', where a non-system version of libcurl can be used). (Windows only) The default method for accessing URLs _via_ download.file() and url() has been changed to be "wininet" using Windows API calls. This changes the way proxies need to be set and security settings made: there have been some reports of sites being inaccessible under the new default method (but the previous methods remain available). NEW FEATURES: * cmdscale() gets new option list. for increased flexibility when a list should be returned. * configure now supports texinfo version 6.0, which (unlike the change from 4.x to 5.0) is a minor update. (Wish of PR#16456.) * (Non-Windows only) download.file() with default method = "auto" now chooses "libcurl" if that is available and a https:// or ftps:// URL is used. * (Windows only) setInternet2(TRUE) is now the default. The command-line option --internet2 and environment variable R_WIN_INTERNET2 are now ignored. Thus by default the "internal" method for download.file() and url() uses the "wininet" method: to revert to the previous default use setInternet2(FALSE). This means that https:// can be read by default by download.file() (they have been readable by file() and url() since R 3.2.0). There are implications for how proxies need to be set (see ?download.file): also, cacheOK = FALSE is not supported. * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors in preference to HTTP mirrors. This changes the interpretation of their ind arguments: see their help pages. * capture.output() gets optional arguments type and split to pass to sink(), and hence can be used to capture messages. C-LEVEL FACILITIES: * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has the alloca.h header (it is needed to define alloca on Solaris and AIX, at least: see 'Writing R Extensions' for how to use it). INSTALLATION and INCLUDED SOFTWARE: * The libtool script generated by configure has been modified to support FreeBSD >= 10 (PR#16410). BUG FIXES: * The HTML help page links to demo code failed due to a change in R 3.2.0. (PR#16432) * If the na.action argument was used in model.frame(), the original data could be modified. (PR#16436) * getGraphicsEvent() could cause a crash if a graphics window was closed while it was in use. (PR#16438) * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type "expression". * strptime() could overflow the allocated storage on the C stack when the timezone had a non-standard format much longer than the standard formats. (Part of PR#16328.) * options(OutDec = s) now signals a warning (which will become an error in the future) when s is not a string with exactly one character, as that has been a documented requirement. * prettyNum() gains a new option input.d.mark which together with other changes, e.g., the default for decimal.mark, fixes some format()ting variants with non-default getOption("OutDec") such as in PR#16411. * download.packages() failed for type equal to either "both" or "binary". (Reported by Dan Tenenbaum.) * The dendrogram method of labels() is much more efficient for large dendrograms, now using rapply(). (Comment #15 of PR#15215) * The "port" algorithm of nls() could give spurious errors. (Reported by Radford Neal.) * Reference classes that inherited from reference classes in another package could invalidate methods of the inherited class. Fixing this requires adding the ability for methods to be "external", with the object supplied explicitly as the first argument, named .self. See "Inter-Package Superclasses" in the documentation. * readBin() could fail on the SPARC architecture due to alignment issues. (Reported by Radford Neal.) * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead of returning NaN. (PR#16475) * Auto-printing of S3 and S4 values now searches for print() in the base namespace and show() in the methods namespace instead of searching the global environment. * polym() gains a coefs = NULL argument and returns class "poly" just like poly() which gets a new simple=FALSE option. They now lead to correct predict()ions, e.g., on subsets of the original data. * rhyper(nn, ) now works correctly. (PR#16489) * ttkimage() did not (and could not) work so was removed. Ditto for tkimage.cget() and tkimage.configure(). Added two Ttk widgets and missing subcommands for Tk's image command: ttkscale(), ttkspinbox(), tkimage.delete(), tkimage.height(), tkimage.inuse(), tkimage.type(), tkimage.types(), tkimage.width(). (PR#15372, PR#16450) * getClass("foo") now also returns a class definition when it is found in the cache more than once. From naras at stanford.edu Wed Sep 9 17:46:36 2015 From: naras at stanford.edu (Balasubramanian Narasimhan) Date: Wed, 9 Sep 2015 08:46:36 -0700 Subject: useR! 2016 Conference Announcement Message-ID: <55F0545C.6030602@stanford.edu> We are happy to announce that the R user conference useR! 2016 is scheduled for June 27-30, 2016, and will take place at the campus of Stanford University, Stanford California, USA. Following the formats of previous conferences, the program will consist of a day of tutorials followed by three days of invited lectures and user-contributed sessions. The program will cover topics such as * History of R and computing with data * Bayesian Statistics * Bioinformatics * Economics, Finance and Insurance * High Performance Computing * Industrial Applications * Statistical Learning with Big Data * Spatial Statistics * Teaching * Visualization & Graphics * and many more. CONFERENCE WEBPAGE The URL for the conference web page is: http://www.R-project.org/useR-2016 It is minimal at the moment but details of invited speakers, tutorial sessions, registration and abstract submission process will soon appear. A follow-up announcement will be posted to announce important details but please feel free to check the website periodically. CALL FOR TUTORIAL SUBMISSIONS We invite R users to submit proposals for three hour tutorials on special topics on R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before January 3, 2016 to useR-2016 at R-project.org. IMPORTANT DATES October 26, 2015 open submission of abstracts December 1, 2015 open registration January 3, 2016 tutorial submission deadline March 1, 2016 early registration deadline March 3, 2016 submission deadline for abstracts March 28, 2016 notification of abstract acceptance June 1, 2016 registration deadline June 20, 2016 late registration deadline (space permitting) June 27, 2016 tutorials June 28, 2016 conference start June 30, 2016 conference end We hope to meet you in Stanford! The organizing committee: John Chambers, Sandrine Dudoit, Trevor Hastie, Susan Holmes, Simon Jackman, Olivia Lau, Nicholas Lewin-Koh, Norman Matloff, Balasubramanian Narasimhan, Karthik Ram, Joseph Rickert, Duncan Temple Lang. From martyn.plummer at r-project.org Thu Oct 22 15:06:34 2015 From: martyn.plummer at r-project.org (Martyn Plummer) Date: Thu, 22 Oct 2015 15:06:34 +0200 Subject: Codes of Conduct at R Conferences Message-ID: <1445519194.6634.174.camel@r-project.org> The useR! conferences in 2014 and 2015 both had codes of conduct in order to ensure an experience free from harassment for all participants. After a request from some members of the R community, the R Foundation has decided to endorse this practice. Future conferences supported by the R Foundation must have a code of conduct. We encourage other R meetings not affiliated with the R Foundation to adopt the same policy. A code of conduct serves two important purposes. Firstly, it sends a clear message to those outside the community that an R conference is a professional and comfortable working environment for all participants. Secondly, it provides a mechanism for reporting and monitoring any incidents of harassment that may occur. We have decided not to require a particular formulation for the code of conduct, but suggest that conference organizers use the model of the useR! 2015 meeting ( http://user2015.math.aau.dk/behaviouR ). This will allow the code to be adapted to local circumstances and to evolve in the future. Conference organizers should ensure that any sanctions laid out in the code of conduct are legally and practically enforceable. Vigorous debate and lively exchange are important features of R conferences. We expect this to continue within the boundaries set by the code of conduct. For the R Foundation Martyn Plummer, Co-President ----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}} From pd.mes at cbs.dk Fri Nov 13 11:18:58 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 13 Nov 2015 11:18:58 +0100 Subject: [R] Release of R 3.2.3 scheduled for December 10 Message-ID: <46A477A2-1E2A-46ED-9BEE-CAF66B3F0345@cbs.dk> We intend to have a patch release on December 10, nickname will be "Wooden Christmas-Tree". The detailed schedule will be made available via developer.r-project.org as usual (later today). For the R Core Team, Peter D. From pd.mes at cbs.dk Thu Dec 10 13:07:57 2015 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 10 Dec 2015 13:07:57 +0100 Subject: R 3.2.3 is released Message-ID: <090FD1B2-509D-49B3-945A-822AE6C5E5CD@cbs.dk> The build system rolled up R-3.2.3.tar.gz (codename "Wooden Christmas-Tree") 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-3.2.3.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) = eb97a5cd38acb1cfc6408988bffef765 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 3a15bad19f5031d05d1a4893f0fadb81 MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = e09aa00e906c9feb3f63838e4b4919c9 MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (R-latest.tar.gz) = 1ba3dac113efab69e706902810cc2970 MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435 MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb MD5 (VERSION-INFO.dcf) = a042818b70e88f7c5253ee533f45cd2f MD5 (R-3/R-3.2.3.tar.gz) = 1ba3dac113efab69e706902810cc2970 This is the relevant part of the NEWS file CHANGES IN R 3.2.3: NEW FEATURES: * Some recently-added Windows time zone names have been added to the conversion table used to convert these to Olson names. (Including those relating to changes for Russia in Oct 2014, as in PR#16503.) * (Windows) Compatibility information has been added to the manifests for Rgui.exe, Rterm.exe and Rscript.exe. This should allow win.version() and Sys.info() to report the actual Windows version up to Windows 10. * Windows "wininet" FTP first tries EPSV / PASV mode rather than only using active mode (reported by Dan Tenenbaum). * which.min(x) and which.max(x) may be much faster for logical and integer x and now also work for long vectors. * The 'emulation' part of tools::texi2dvi() has been somewhat enhanced, including supporting quiet = TRUE. It can be selected by texi2dvi = "emulation". (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015: tools::texi2dvi() tries texify.exe if it is not found. * (Windows only) Shortcuts for printing and saving have been added to menus in Rgui.exe. (Request of PR#16572.) * loess(..., iterTrace=TRUE) now provides diagnostics for robustness iterations, and the print() method for summary() shows slightly more. * The included version of PCRE has been updated to 8.38, a bug-fix release. * View() now displays nested data frames in a more friendly way. (Request with patch in PR#15915.) INSTALLATION and INCLUDED SOFTWARE: * The included configuration code for libintl has been updated to that from gettext version 0.19.5.1 - this should only affect how an external library is detected (and the only known instance is under OpenBSD). (Wish of PR#16464.) * configure has a new argument --disable-java to disable the checks for Java. * The configure default for MAIN_LDFLAGS has been changed for the FreeBSD, NetBSD and Hurd OSes to one more likely to work with compilers other than gcc (FreeBSD 10 defaults to clang). * configure now supports the OpenMP flags -fopenmp=libomp (clang) and -qopenmp (Intel C). * Various macros can be set to override the default behaviour of configure when detecting OpenMP: see file config.site. * Source installation on Windows has been modified to allow for MiKTeX installations without texi2dvi.exe. See file MkRules.dist. BUG FIXES: * regexpr(pat, x, perl = TRUE) with Python-style named capture did not work correctly when x contained NA strings. (PR#16484) * The description of dataset ToothGrowth has been improved/corrected. (PR#15953) * model.tables(type = "means") and hence TukeyHSD() now support "aov" fits without an intercept term. (PR#16437) * close() now reports the status of a pipe() connection opened with an explicit open argument. (PR#16481) * Coercing a list without names to a data frame is faster if the elements are very long. (PR#16467) * (Unix-only) Under some rare circumstances piping the output from Rscript or R -f could result in attempting to close the input file twice, possibly crashing the process. (PR#16500) * (Windows) Sys.info() was out of step with win.version() and did not report Windows 8. * topenv(baseenv()) returns baseenv() again as in R 3.1.0 and earlier. This also fixes compilerJIT(3) when used in .Rprofile. * detach()ing the methods package keeps .isMethodsDispatchOn() true, as long as the methods namespace is not unloaded. * Removed some spurious warnings from configure about the preprocessor not finding header files. (PR#15989) * rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases (where the limit is unique). (PR#16521) * pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for ncp > ~60). * nchar(x, "w") returned -1 for characters it did not know about (e.g. zero-width spaces): it now assumes 1. It now knows about most zero-width characters and a few more double-width characters. * Help for which.min() is now more precise about behavior with logical arguments. (PR#16532) * The print width of character strings marked as "latin1" or "bytes" was in some cases computed incorrectly. * abbreviate() did not give names to the return value if minlength was zero, unlike when it was positive. * (Windows only) dir.create() did not always warn when it failed to create a directory. (PR#16537) * When operating in a non-UTF-8 multibyte locale (e.g. an East Asian locale on Windows), grep() and related functions did not handle UTF-8 strings properly. (PR#16264) * read.dcf() sometimes misread lines longer than 8191 characters. (Reported by Herv'e Pag`es with a patch.) * within(df, ..) no longer drops columns whose name start with a ".". * The built-in HTTP server converted entire Content-Type to lowercase including parameters which can cause issues for multi-part form boundaries (PR#16541). * Modifying slots of S4 objects could fail when the methods package was not attached. (PR#16545) * splineDesign(*, outer.ok=TRUE) (splines) is better now (PR#16549), and interpSpline() now allows sparse=TRUE for speedup with non-small sizes. * If the expression in the traceback was too long, traceback() did not report the source line number. (Patch by Kirill M"uller.) * The browser did not truncate the display of the function when exiting with options("deparse.max.lines") set. (PR#16581) * When bs(*, Boundary.knots=) had boundary knots inside the data range, extrapolation was somewhat off. (Patch by Trevor Hastie.) * var() and hence sd() warn about factor arguments which are deprecated now. (PR#16564) * loess(*, weights = *) stored wrong weights and hence gave slightly wrong predictions for newdata. (PR#16587) * aperm(a, *) now preserves names(dim(a)). * poly(x, ..) now works when either raw=TRUE or coef is specified. (PR#16597) * data(package=*) is more careful in determining the path. * prettyNum(*, decimal.mark, big.mark): fixed bug introduced when fixing PR#16411.