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NEWS for Microsoft R Open and R

logo.jpgMicrosoft R Open 3.3.2

  • Microsoft R Open 3.3.2 is based on R-3.3.2.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from November 1, 2016.

  • Microsoft R Open 3.3.2 is supported on the following platforms. Please post issues or suggestions on our Microsoft R Open User Forum.

    • Windows® 7.0 SP1, 8.1, 10, Windows Server® 2008 R2 SP1 and 2012
    • Ubuntu 14.04, 16.04
    • CentOS / Red Hat Enterprise Linux 6.5, 7.1
    • SUSE Linux Enterprise Server 11
    • Mac OS X Mavericks (10.9), Yosemite (10.10), El Capitan (10.11), Sierra (10.12)
  • A number of new packages have been bundled and/or updated with this release. Learn more...

  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgMicrosoft R Open 3.3.1

  • Microsoft R Open 3.3.1 is based on R-3.3.1.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from July 1, 2016. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • Microsoft R Open 3.3.1 is supported on the following platforms. Please post issues or suggestions on our Microsoft R Open User Forum.

    • Windows® 7.0 SP1, 8.1, 10, Windows Server® 2008 R2 SP1 and 2012
    • Ubuntu 14.04, 15.04
    • CentOS / Red Hat Enterprise Linux 6.5, 7.1
    • SUSE Linux Enterprise Server 11
    • Mac OS X Mavericks (10.9), Yosemite (10.10), El Capitan (10.11)
  • In addition to the checkpoint package, the following packages are now bundled with Microsoft R Open: deployrRserve (Windows & Linux only), doParallel, foreach, iterators, MicrosoftR, RevoIOQ, RevoMods, RevoUtils, RODBC (Windows only), and RUnit. Learn more...

  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgMicrosoft R Open 3.3.0

  • Microsoft R Open 3.3.0 is based on R-3.3.0.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from June 1, 2016. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • Microsoft R Open 3.3.0 is supported on the following platforms. Please post issues or suggestions on our Microsoft R Open User Forum.

    • Windows® 7.0 SP1, 8.1, 10, Windows Server® 2008 R2 SP1 and 2012
    • Ubuntu 14.04, 15.04
    • CentOS / Red Hat Enterprise Linux 6.5, 7.1
    • SUSE Linux Enterprise Server 11
    • Mac OS X Mavericks (10.9), Yosemite (10.10), El Capitan (10.11)
  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgMicrosoft R Open 3.2.5

  • Microsoft R Open 3.2.5 is based on R-3.2.5.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from May 1, 2016. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • Microsoft R Open 3.2.5 is supported on the following platforms. Please post issues or suggestions on our Microsoft R Open User Forum.

    • Windows® 7.0 SP1, 8.1, 10, Windows Server® 2008 R2 SP1 and 2012
    • Ubuntu 14.04, 15.04
    • CentOS / Red Hat Enterprise Linux 6.5, 7.1
    • SLES 11
  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgMicrosoft R Open 3.2.4

  • Microsoft R Open 3.2.4 is based on R-3.2.4-Revised, which has since been re-released as R-3.2.5.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from April 1, 2016. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • Microsoft R Open 3.2.4 is supported on the following platforms. Please post issues or suggestions on our Microsoft R Open User Forum.

  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgMicrosoft R Open 3.2.3

  • With this release, Revolution R Open was rebranded as Microsoft R Open.

  • Microsoft R Open 3.2.3 is based on R 3.2.3. See R 3.2.3 News for new features added to R since R 3.2.2.

  • Microsoft R Open is now supported on Mac OS X 10.11 (El Capitan) and Red Hat / CentOS 7.1.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from Jan 1, 2016. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • Microsoft R Open 3.2.3 is supported on the following platforms. Please post issues or suggestions on our Microsoft R Open User Forum.

  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgRRO 3.2.2

  • Revolution R Open (RRO) 3.2.2 is based on R 3.2.2. See R 3.2.2 News for new features added to R since R 3.2.1.

  • RRO is now supported on Windows 10.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from Aug 27, 2015. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • RRO 3.2.2 has https enabled by default to download packages (see https://www.r-consortium.org/news/blogs/2015/08/best-practices-using-r-securely).

  • The checkpoint package is now bundled with RRO 3.2.2.

  • RRO 3.2.2 is supported on the following platforms. Please post issues or suggestions on our RRO Google Group.

    • Ubuntu 12.04, 14.04, 15.04
    • CentOS / Red Hat Enterprise Linux 5.8, 6.5, 7.0
    • SLES 10 & 11 and openSUSE 13.1
    • Mac OS X Mavericks (10.9) & Yosemite (10.10), hotfix release Oct 8, 2015
    • Windows® 7.0 SP1, 8.1, 10, Windows Server® 2008 R2 SP1 and 2012  
  • The release notes, available on GitHub, include a list of any known defects. Also available are the release notes for the RRO hotfix released October 8th (Mac OS X only).

logo.jpgRRO 3.2.1

  • Revolution R Open (RRO) 3.2.1 is based on R 3.2.1. See R 3.2.1 News for new features added to R since R 3.2.0.

  • RRO now uses secure HTTPS connections by default for package downloads.

  • RRO is now supported on SLES 10 & 11 and openSUSE 13.1.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from July 1, 2015. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • RRO 3.2.1 is supported on the following platforms. Please post issues or suggestions on our RRO Google Group.

    • Ubuntu 12.04, 14.04, 15.04
    • CentOS / Red Hat Enterprise Linux 5.8, 6.5, 7.0
    • SLES 10 & 11 and openSUSE 13.1
    • Mac OS X Mavericks (10.9) & Yosemite (10.10)
    • Windows® 7.0 SP1, 8.1, Windows Server® 2008 R2 SP1 and 2012  
  • The release notes, available on GitHub, include a list of any known defects.

logo.jpgRRO 3.2.0

  • Revolution R Open (RRO) version numbers now track their corresponding R engine versions. Revolution R Open 3.2.0 is more recent than Revolution R Open 8.0.3.
     
  • RRO 3.2.0 is based on R 3.2.0. See R 3.2.0 News for new features added to R since R 3.1.3.
     

  • RRO 3.2.0 is supported on the following platforms. Please report any problems or suggestions to the RRO Google Group.

     
  • RRO has not been fully tested on this experimental platform, but we expect it to work. Please report any issues to the RRO Google Group
    • OpenSUSE 13.1.
     
  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from May 1, 2015. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.
     
  • Release notes, which include a list of known defects, are available on GitHub.

logo.jpgRevolution R Open 8.0.3

  • Revolution R Open (RRO) 8.0.3 is based on R 3.1.3. See R 3.1.3 News for new features added to R since R 3.1.2.
     
  • RRO 8.0.3 is supported on the following platforms. Please report any problems or suggestions to the RRO Google Group.

     
  • RRO has not been fully tested on this experimental platform, but we expect it to work. Please report any issues to the RRO Google Group
    • OpenSUSE 13.1.
     
  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from April 1, 2015. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.
     
  • Release notes, which include a list of known defects, are available on GitHub.

logo.jpgRevolution R Open 8.0.2

Revolution R Open 8.0.2 is beta-test software. It has been tested and we expect it to work on all supported platforms, but will retain the "beta" label while we gather feedback from the community. Please report any problems or suggestions to the RRO Google Group.

  • Revolution R Open 8.0.2 is based on R 3.1.2.
  • Supported platforms include:

    • Ubuntu 12.04, 14.04   [See known issues]
    • CentOS / Red Hat Enterprise Linux 5.8, 6.5, 7.0   [See known issues]
    • Mac OS X Mavericks (10.9) & Yosemite (10.10)   [See known issues]
    • Windows® 7.0 SP1, 8.1, Windows Server® 2008 R2 SP1 and 2012   [See known issues]
    • Experimental platform: OpenSUSE 13.1. RRO has not been fully tested on this experimental platform, but we expect it to work. Report any issues to the RRO Google Group.

  • The default CRAN mirror has been updated to point to the fixed CRAN repository snapshot from March 1, 2015. Visit our Package Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • The MKL accelerated math library is now an optional download for Windows and Linux systems. After installing RRO, download the "Math Library" installer, and then install it to enable multi-threaded math on these platforms.

  • Revolution R Open 8.0.2 Beta now includes checkpoint v0.3.9 by default. The version contains the following changes:

    • You can now specify any folder location as the checkpoint library location. Previously, checkpoint always installed packages in the location ~/.checkpoint. This is still the default, but now you can change this, for example to store your checkpoint packages on a USB drive.
    • You can now run checkpoint() without it scanning for packages. This option addresses the use case where you run code in a production environment for which you are already certain that all package dependencies are installed in the .checkpoint folder. In this special case, not scanning for packages leads to lower latency and better performance.
    • You can now specify that your checkpoint project depends on a specific version of R.
    • The dependency on the knitr package has been removed. If the knitr package is available on your machine, then checkpoint will scan all rmarkdown script files in the project for package dependencies.

logo.jpgRevolution R Open 8.0.1

RRO 8.0.1 GENERAL

  • Revolution R Open 8.0.1 is beta-test software. It has been tested and we expect it to work on all supported platforms, but will retain the "beta" label while we gather feedback from the community. Please report any problems or suggestions to the RRO Google Group.

  • Supported platforms include:

  • Experimental platform: OpenSUSE 13.1
    RRO has not been fully tested on this experimental platform, but we expect it to work. Please report any issues to the RRO Google Group.

  • The default CRAN mirror was updated to the fixed CRAN repository snapshot from December 1, 2014. Visit our Spotlight page to read more about some of the new and updated packages available using that snapshot date as the default repository for this release.

  • The Mac build has been reconfigured to use the Mac Accelerate Framework for multi-threaded computations. This provides comparable performance to the Intel MKL. (Windows and Linux platforms continue to use Intel MKL.)

RRO 8.0.1 NEW FEATURES

  • Revolution R Open 8.0.1 Beta is based on R 3.1.2. See R 3.1.2 News.

RRO 8.0.1 BUGS FIXED

  • A problem that caused RRO on the Mac to default to building packages from source has been resolved. [Issue #32]

  • Fixed some installation issues on CentOS. [Issue #36 and #9]

  • The RPM package name now includes the RRO version number. [Issue #10]


logo.jpgRevolution R Open 8.0.0

  • Revolution R Open 8.0.0 is beta-test software. It has been tested and we expect it to work on all supported platforms, but will retain the "beta" label while we gather feedback from the community.
    Please report any problems or suggestions to the RRO Google Group.

  • Revolution R Open 8.0.0 Beta is based on R 3.1.1. See R 3.1.1 News.

  • Supported platforms include:

    • Ubuntu 12.04, 14.04; CentOS / Red Hat Enterprise Linux 5.8, 6.5, 7.0
    • Mac OS X Mavericks (10.9)
    • Windows® 7.0 (SP 1), 8.1, Windows Server® 2008 R2 (SP1) and 2012

  • Experimental platforms include: OpenSUSE 13.1 and Mac OS X Yosemite (10.10)
    RRO has not been fully tested on these experimental platforms, but we expect it to work. Please report any issues to the RRO Google Group.

  • Revolution R Open is built with the Intel MKL libraries to enable multi-threaded computation.

  • The default CRAN mirror is a fixed CRAN repository snapshot from October 1, 2014.

  • The checkpoint package is automatically installed with Revolution R Open.


logo.jpgR 3.3.2

NEW FEATURES

  • extSoftVersion() now reports the version (if any) of the readline library in use.

  • The version of LAPACK included in the sources has been updated to 3.6.1, a bug-fix release including a speedup for the non-symmetric case of eigen().

  • Use options(deparse.max.lines=) to limit the number of lines recorded in .Traceback and other deparsing activities.

  • format(<AsIs>) looks more regular, also for non-character atomic matrices.

  • abbreviate() gains an option named = TRUE.

  • The online documentation for package methods is extensively rewritten. The goals are to simplify documentation for basic use, to note old features not recommended and to correct out-of-date information.

  • Calls to setMethod() no longer print a message when creating a generic function in those cases where that is natural: S3 generics and primitives.

INSTALLATION and INCLUDED SOFTWARE

  • Versions of the readline library >= 6.3 had been changed so that terminal window resizes were not signalled to readline: code has been added using a explicit signal handler to work around that (when R is compiled against readline >= 6.3). (PR#16604)

  • configure works better with Oracle Developer Studio 12.5.

UTILITIES

  • R CMD check reports more dubious flags in files ‘src/Makevars[.in]’, including -w and -g.

  • R CMD check has been set up to filter important warnings from recent versions of gfortran with -Wall -pedantic: this now reports non-portable GNU extensions such as out-of-order declarations.

  • R CMD config works better with paths containing spaces, even those of home directories (as reported by Ken Beath).

DEPRECATED AND DEFUNCT

  • Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers are included by R headers from C++ as from R 3.3.0, so it should no longer be needed).

BUG FIXES

  • The check for non-portable flags in R CMD check could be stymied by ‘src/Makevars’ files which contained targets.

  • (Windows only) When using certain desktop themes in Windows 7 or higher, Alt-Tab could cause Rterm to stop accepting input. (PR#14406; patch submitted by Jan Gleixner.)

  • pretty(d, ..) behaves better for date-time d (PR#16923).

  • When an S4 class name matches multiple classes in the S4 cache, perform a dynamic search in order to obey namespace imports. This should eliminate annoying messages about multiple hits in the class cache. Also, pass along the package from the ClassExtends object when looking up superclasses in the cache.

  • sample(NAreal) now works.

  • Packages using non-ASCII encodings in their code did not install data properly on systems using different encodings.

  • merge(df1, df2) now also works for data frames with column names "na.last", "decreasing", or "method". (PR#17119)

  • contour() caused a segfault if the labels argument had length zero. (Reported by Bill Dunlap.)

  • unique(warnings()) works more correctly, thanks to a new duplicated.warnings() method.

  • findInterval(x, vec = numeric(), all.inside = TRUE) now returns 0s as documented. (Reported by Bill Dunlap.)

  • (Windows only) R CMD SHLIB failed when a symbol in the resulting library had the same name as a keyword in the ‘.def’ file. (PR#17130)

  • pmax() and pmin() now work with (more ?) classed objects, such as "Matrix" from the Matrix package, as documented for a long time.

  • axis(side, x = D) and hence Axis() and plot() now work correctly for "Date" and time objects D, even when “time goes backward”, e.g., with decreasing xlim. (Reported by William May.)

  • str(I(matrix(..))) now looks as always intended.

  • plot.ts(), the plot() method for time series, now respects cex, lwd and lty. (Reported by Greg Werbin.)

  • parallel::mccollect() now returns a named list (as documented) when called with wait = FALSE. (Reported by Michel Lang.)

  • If a package added a class to a class union in another package, loading the first package gave erroneous warnings about “undefined subclass”.

  • c()'s argument use.names is documented now, as belonging to the (C internal) default method. In “parallel”, argument recursive is also moved from the generic to the default method, such that the formal argument list of base generic c() is just (...).

  • rbeta(4, NA) and similarly rgamma() and rnbinom() now return NaN's with a warning, as other r<dist>(), and as documented. (PR#17155)

  • Using options(checkPackageLicense = TRUE) no longer requires acceptance of the licence for non-default standard packages such as compiler. (Reported by Mikko Korpela.)

  • split(<very_long>, ) now works even when the split off parts are long. (PR#17139)

  • min() and max() now also work correctly when the argument list starts with character(0). (PR#17160)

  • Subsetting very large matrices (prod(dim(.)) >= 2^31) now works thanks to Michael Schubmehl's PR#17158.

  • bartlett.test() used residual sums of squares instead of variances, when the argument was a list of lm objects. (Reported by Jens Ledet Jensen).

  • plot(<lm>, which = ) now correctly labels the contour lines for the standardized residuals for which = 6. It also takes the correct p in case of singularities (also for which = 5). (PR#17161)

  • xtabs(~ exclude) no longer fails from wrong scope, thanks to Suharto Anggono's PR#17147.

  • Reference class calls to methods() did not re-analyse previously defined methods, meaning that calls to methods defined later would fail. (Reported by Charles Tilford).

  • findInterval(x, vec, left.open = TRUE) misbehaved in some cases. (Reported by Dmitriy Chernykh.)

logo.jpgR 3.3.1

BUG FIXES

  • R CMD INSTALL and hence install.packages() gave an internal error installing a package called description from a tarball on a case-insensitive file system.

  • match(x, t) (and hence x %in% t) failed when x was of length one, and either character and x and t only differed in their Encoding or when x and t where complex with NAs or NaNs. (PR#16885.)

  • unloadNamespace(ns) also works again when ns is a ‘namespace’, as from getNamespace().

  • rgamma(1,Inf) or rgamma(1, 0,0) no longer give NaN but the correct limit.

  • length(baseenv()) is correct now.

  • pretty(d, ..) for date-time d rarely failed when "halfmonth" time steps were tried (PR#16923) and on ‘inaccurate’ platforms such as 32-bit windows or a configuration with --disable-long-double; see comment #15 of PR#16761.

  • In text.default(x, y, labels), the rarely(?) used default for labels is now correct also for the case of a 2-column matrix x and missing y.

  • as.factor(c(a = 1L)) preserves names() again as in R < 3.1.0.

  • strtrim(""[0], 0[0]) now works.

  • Use of Ctrl-C to terminate a reverse incremental search started by Ctrl-R in the readline-based Unix terminal interface is now supported for readline >= 6.3 (Ctrl-G always worked). (PR#16603)

  • diff(<difftime>) now keeps the "units" attribute, as subtraction already did, PR#16940.

logo.jpgR 3.3.0

SIGNIFICANT USER-VISIBLE CHANGES

  • nchar(x, *)'s argument keepNA governing how the result for NAs in x is determined, gets a new default keepNA = NA which returns NA where x is NA, except for type = "width" which still returns 2, the formatting / printing width of NA.

  • All builds have support for https: URLs in the default methods for download.file(), url() and code making use of them.

    Unfortunately that cannot guarantee that any particular https: URL can be accessed. For example, server and client have to successfully negotiate a cryptographic protocol (TLS/SSL, ...) and the server's identity has to be verifiable via the available certificates. Different access methods may allow different protocols or use private certificate bundles: we encountered a https: CRAN mirror which could be accessed by one browser but not by another nor by download.file() on the same Linux machine.

NEW FEATURES

  • The print method for methods() gains a byclass argument.

  • New functions validEnc() and validUTF8() to give access to the validity checks for inputs used by grep() and friends.

  • Experimental new functionality for S3 method checking, notably isS3method().

    Also, the names of the R ‘language elements’ are exported as character vector tools::langElts.

  • str(x) now displays "Time-Series" also for matrix (multivariate) time-series, i.e. when is.ts(x) is true.

  • (Windows only) The GUI menu item to install local packages now accepts ‘.tar.gz’ files as well as ‘.zip’ files (but defaults to the latter).

  • New programmeR's utility function chkDots().

  • D() now signals an error when given invalid input, rather than silently returning NA. (Request of John Nash.)

  • formula objects are slightly more “first class”: e.g., formula() or new("formula", y ~ x) are now valid. Similarly, for "table", "ordered" and "summary.table". Packages defining S4 classes with the above S3/S4 classes as slots should be reinstalled.

  • New function strrep() for repeating the elements of a character vector.

  • rapply() preserves attributes on the list when how = "replace".

  • New S3 generic function sigma() with methods for extracting the estimated standard deviation aka “residual standard deviation” from a fitted model.

  • news() now displays R and package news files within the HTML help system if it is available. If no news file is found, a visible NULL is returned to the console.

  • as.raster(x) now also accepts raw arrays x assuming values in 0:255.

  • Subscripting of matrix/array objects of type "expression" is now supported.

  • type.convert("i") now returns a factor instead of a complex value with zero real part and missing imaginary part.

  • Graphics devices cairo_pdf() and cairo_ps() now allow non-default values of the cairographics ‘fallback resolution’ to be set.

    This now defaults to 300 on all platforms: that is the default documented by cairographics, but apparently was not used by all system installations.

  • file() gains an explicit method argument rather than implicitly using getOption("url.method", "default").

  • Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically faster than x[which(x != 0)] (in the case where x has no NAs, the two are equivalent).

  • read.table() now always uses the names for a named colClasses argument (previously names were only used when colClasses was too short). (In part, wish of PR#16478.)

  • (Windows only) download.file() with default method = "auto" and a ftps:// URL chooses "libcurl" if that is available.

  • The out-of-the box Bioconductor mirror has been changed to one using https://: use chooseBioCmirror() to choose a http:// mirror if required.

  • The data frame and formula methods for aggregate() gain a drop argument.

  • available.packages() gains a repos argument.

  • The undocumented switching of methods for url() on https: and ftps: URLs is confined to method = "default" (and documented).

  • smoothScatter() gains a ret.selection argument.

  • qr() no longer has a ... argument to pass additional arguments to methods.

  • [ has a method for class "table".

  • It is now possible (again) to replayPlot() a display list snapshot that was created by recordPlot() in a different R session.

    It is still not a good idea to use snapshots as a persistent storage format for R plots, but it is now not completely silly to use a snapshot as a format for transferring an R plot between two R sessions.

    The underlying changes mean that packages providing graphics devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will need to be reinstalled.

    Code for restoring snapshots was contributed by Jeroen Ooms and JJ Allaire.

    Some testing code is available at https://github.com/pmur002/R-display-list.

  • tools::undoc(dir = D) and codoc(dir = D) now also work when D is a directory whose normalizePath()ed version does not end in the package name, e.g. from a symlink.

  • abbreviate() has more support for multi-byte character sets – it no longer removes bytes within characters and knows about Latin vowels with accents. It is still only really suitable for (most) European languages, and still warns on non-ASCII input.

    abbreviate(use.classes = FALSE) is now implemented, and that is more suitable for non-European languages.

  • match(x, table) is faster (sometimes by an order of magnitude) when x is of length one and incomparables is unchanged, thanks to Peter Haverty (PR#16491).

  • More consistent, partly not back-compatible behavior of NA and NaN coercion to complex numbers, operations less often resulting in complex NA (NA_complex_).

  • lengths() considers methods for length and [[ on x, so it should work automatically on any objects for which appropriate methods on those generics are defined.

  • The logic for selecting the default screen device on OS X has been simplified: it is now quartz() if that is available even if environment variable DISPLAY has been set by the user.

    The choice can easily be overridden via environment variable R_INTERACTIVE_DEVICE.

  • On Unix-like platforms which support the getline C library function, system(*,intern = TRUE) no longer truncates (output) lines longer than 8192 characters, thanks to Karl Millar. (PR#16544)

  • rank() gains a ties.method = "last" option, for convenience (and symmetry).

  • regmatches(invert = NA) can now be used to extract both non-matched and matched substrings.

  • data.frame() gains argument fix.empty.names; as.data.frame.list() gets new cut.names, col.names and fix.empty.names.

  • plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *).

  • recordPlot() has new arguments load and attach to allow package names to be stored as part of a recorded plot. replayPlot() has new argument reloadPkgs to load/attach any package names that were stored as part of a recorded plot.

  • S4 dispatch works within calls to .Internal(). This means explicit S4 generics are no longer needed for unlist() and as.vector().

  • Only font family names starting with "Hershey" (and not "Her" as before) are given special treatment by the graphics engine.

  • S4 values are automatically coerced to vector (via as.vector) when subassigned into atomic vectors.

  • findInterval() gets a left.open option.

  • The version of LAPACK included in the sources has been updated to 3.6.0, including those ‘deprecated’ routines which were previously included. Ca 40 double-complex routines have been added at the request of a package maintainer.

    As before, the details of what is included are in ‘src/modules/lapack/README’ and this now gives information on earlier additions.

  • tapply() has been made considerably more efficient without changing functionality, thanks to proposals from Peter Haverty and Suharto Anggono. (PR#16640)

  • match.arg(arg) (the one-argument case) is faster; so is sort.int(). (PR#16640)

  • The format method for object_size objects now also accepts “binary” units such as "KiB" and e.g., "Tb". (Partly from PR#16649.)

  • Profiling now records calls of the form foo::bar and some similar cases directly rather than as calls to <Anonymous>. Contributed by Winston Chang.

  • New string utilities startsWith(x, prefix) and endsWith(x, suffix). Also provide speedups for some grepl("^...",*) uses (related to proposals in PR#16490).

  • Reference class finalizers run at exit, as well as on garbage collection.

  • Avoid parallel dependency on stats for port choice and random number seeds. (PR#16668)

  • The radix sort algorithm and implementation from data.table (forder) replaces the previous radix (counting) sort and adds a new method for order(). Contributed by Matt Dowle and Arun Srinivasan, the new algorithm supports logical, integer (even with large values), real, and character vectors. It outperforms all other methods, but there are some caveats (see ?sort).

  • The order() function gains a method argument for choosing between "shell" and "radix".

  • New function grouping() returns a permutation that stably rearranges data so that identical values are adjacent. The return value includes extra partitioning information on the groups. The implementation came included with the new radix sort.

  • rhyper(nn, m, n, k) no longer returns NA when one of the three parameters exceeds the maximal integer.

  • switch() now warns when no alternatives are provided.

  • parallel::detectCores() now has default logical = TRUE on all platforms – as this was the default on Windows, this change only affects Sparc Solaris.

    Option logical = FALSE is now supported on Linux and recent versions of OS X (for the latter, thanks to a suggestion of Kyaw Sint).

  • hist() for "Date" or "POSIXt" objects would sometimes give misleading labels on the breaks, as they were set to the day before the start of the period being displayed. The display format has been changed, and the shift of the start day has been made conditional on right = TRUE (the default). (PR#16679)

  • R now uses a new version of the logo (donated to the R Foundation by RStudio). It is defined in ‘.svg’ format, so will resize without unnecessary degradation when displayed on HTML pages—there is also a vector PDF version. Thanks to Dirk Eddelbuettel for producing the corresponding X11 icon.

  • New function .traceback() returns the stack trace which traceback() prints.

  • lengths() dispatches internally.

  • dotchart() gains a pt.cex argument to control the size of points separately from the size of plot labels. Thanks to Michael Friendly and Milan Bouchet-Valat for ideas and patches.

  • as.roman(ch) now correctly deals with more diverse character vectors ch; also arithmetic with the resulting roman numbers works in more cases. (PR#16779)

  • prcomp() gains a new option rank. allowing to directly aim for less than min(n,p) PC's. The summary() and its print() method have been amended, notably for this case.

  • gzcon() gains a new option text, which marks the connection as text-oriented (so e.g. pushBack() works). It is still always opened in binary mode.

  • The import() namespace directive now accepts an argument except which names symbols to exclude from the imports. The except expression should evaluate to a character vector (after substituting symbols for strings). See Writing R Extensions.

  • New convenience function Rcmd() in package tools for invoking R CMD tools from within R.

  • New functions makevars_user() and makevars_site() in package tools to determine the location of the user and site specific ‘Makevars’ files for customizing package compilation.

UTILITIES

  • R CMD check has a new option --ignore-vignettes for use with non-Sweave vignettes whose VignetteBuilder package is not available.

  • R CMD check now by default checks code usage (via codetools) with only the base package attached. Functions from default packages other than base which are used in the package code but not imported are reported as undefined globals, with a suggested addition to the NAMESPACE file.

  • R CMD check --as-cran now also checks DOIs in package ‘CITATION’ and Rd files.

  • R CMD Rdconv and R CMD Rd2pdf each have a new option --RdMacros=pkglist which allows Rd macros to be specified before processing.

DEPRECATED AND DEFUNCT

  • The previously included versions of zlib, bzip2, xz and PCRE have been removed, so suitable external (usually system) versions are required (see the ‘R Installation and Administration’ manual).

  • The unexported and undocumented Windows-only devices cairo_bmp(), cairo_png() and cairo_tiff() have been removed. (These devices should be used as e.g. bmp(type = "cairo").)

  • (Windows only) Function setInternet2() has no effect and will be removed in due course. The choice between methods "internal" and "wininet" is now made by the method arguments of url() and download.file() and their defaults can be set via options. The out-of-the-box default remains "wininet" (as it has been since R 3.2.2).

  • [<- with an S4 value into a list currently embeds the S4 object into its own list such that the end result is roughly equivalent to using [[<-. That behavior is deprecated. In the future, the S4 value will be coerced to a list with as.list().

  • Package tools' functions package.dependencies(), pkgDepends(), etc are deprecated now, mostly in favor of package_dependencies() which is both more flexible and efficient.

INSTALLATION and INCLUDED SOFTWARE

  • Support for very old versions of valgrind (e.g., 3.3.0) has been removed.

  • The included libtool script (generated by configure) has been updated to version 2.4.6 (from 2.2.6a).

  • libcurl version 7.28.0 or later with support for the https protocol is required for installation (except on Windows).

  • BSD networking is now required (except on Windows) and so capabilities("http/ftp") is always true.

  • configure uses pkg-config for PNG, TIFF and JPEG where this is available. This should work better with multiple installs and with those using static libraries.

  • The minimum supported version of OS X is 10.6 (‘Snow Leopard’): even that has been unsupported by Apple since 2012.

  • The configure default on OS X is --disable-R-framework: enable this if you intend to install under ‘/Library/Frameworks’ and use with R.app.

  • The minimum preferred version of PCRE has since R 3.0.0 been 8.32 (released in Nov 2012). Versions 8.10 to 8.31 are now deprecated (with warnings from configure), but will still be accepted until R 3.4.0.

  • configure looks for C functions cospi, sinpi and __tanpi and uses these if cospi etc are not found. (OS X is the main instance.)

  • (Windows) R is now built using gcc 4.9.3. This build will require recompilation of at least those packages that include C++ code, and possibly others. A build of R-devel using the older toolchain will be temporarily available for comparison purposes.

    During the transition, the environment variable R_COMPILED_BY has been defined to indicate which toolchain was used to compile R (and hence, which should be used to compile code in packages). The COMPILED_BY variable described below will be a permanent replacement for this.

  • (Windows) A make and R CMD config variable named COMPILED_BY has been added. This indicates which toolchain was used to compile R (and hence, which should be used to compile code in packages).

PACKAGE INSTALLATION

  • The make macro AWK which used to be made available to files such as ‘src/Makefile’ is no longer set.

C-LEVEL FACILITIES

  • The API call logspace_sum introduced in R 3.2.0 is now remapped as an entry point to Rf_logspace_sum, and its first argument has gained a const qualifier. (PR#16470)

    Code using it will need to be reinstalled.

    Similarly, entry point log1pexp also defined in ‘Rmath.h’ is remapped there to Rf_log1pexp

  • R_GE_version has been increased to 11.

  • New API call R_orderVector1, a faster one-argument version of R_orderVector.

  • When R headers such as ‘R.h’ and ‘Rmath.h’ are called from C++ code in packages they include the C++ versions of system headers such as ‘<cmath>’ rather than the legacy headers such as ‘<math.h>’. (Headers ‘Rinternals.h’ and ‘Rinterface.h’ already did, and inclusion of system headers can still be circumvented by defining NO_C_HEADERS, including as from this version for those two headers.)

    The manual has long said that R headers should not be included within an extern "C" block, and almost all the packages affected by this change were doing so.

  • Including header ‘S.h’ from C++ code would fail on some platforms, and so gives a compilation error on all.

  • The deprecated header ‘Rdefines.h’ is now compatible with defining R_NO_REMAP.

  • The connections API now includes a function R_GetConnection() which allows packages implementing connections to convert R connection objects to Rconnection handles used in the API. Code which previously used the low-level R-internal getConnection() entry point should switch to the official API.

BUG FIXES

  • C-level asChar(x) is fixed for when x is not a vector, and it returns "TRUE"/"FALSE" instead of "T"/"F" for logical vectors.

  • The first arguments of .colSums() etc (with an initial dot) are now named x rather than X (matching colSums()): thus error messages are corrected.

  • A coef() method for class "maov" has been added to allow vcov() to work with multivariate results. (PR#16380)

  • method = "libcurl" connections signal errors rather than retrieving HTTP error pages (where the ISP reports the error).

  • xpdrows.data.frame() was not checking for unique row names; in particular, this affected assignment to non-existing rows via numerical indexing. (PR#16570)

  • tail.matrix() did not work for zero rows matrices, and could produce row “labels” such as "[1e+05,]".

  • Data frames with a column named "stringsAsFactors" now format and print correctly. (PR#16580)

  • cor() is now guaranteed to return a value with absolute value less than or equal to 1. (PR#16638)

  • Array subsetting now keeps names(dim(.)).

  • Blocking socket connection selection recovers more gracefully on signal interrupts.

  • The data.frame method of rbind() construction row.names works better in borderline integer cases, but may change the names assigned. (PR#16666)

  • (X11 only) getGraphicsEvent() miscoded buttons and missed mouse motion events. (PR#16700)

  • methods(round) now also lists round.POSIXt.

  • tar() now works with the default files = NULL. (PR#16716)

  • Jumps to outer contexts, for example in error recovery, now make intermediate jumps to contexts where on.exit() actions are established instead of trying to run all on.exit() actions before jumping to the final target. This unwinds the stack gradually, releases resources held on the stack, and significantly reduces the chance of a segfault when running out of C stack space. Error handlers established using withCallingHandlers() and options("error") specifications are ignored when handling a C stack overflow error as attempting one of these would trigger a cascade of C stack overflow errors. (These changes resolve PR#16753.)

  • The spacing could be wrong when printing a complex array. (Report and patch by Lukas Stadler.)

  • pretty(d, n, min.n, *) for date-time objects d works again in border cases with large min.n, returns a labels attribute also for small-range dates and in such cases its returned length is closer to the desired n. (PR#16761) Additionally, it finally does cover the range of d, as it always claimed.

  • tsp(x) <- NULL did not handle correctly objects inheriting from both "ts" and "mts". (PR#16769)

  • install.packages() could give false errors when options("pkgType") was "binary". (Reported by Jose Claudio Faria.)

  • A bug fix in R 3.0.2 fixed problems with locator() in X11, but introduced problems in Windows. Now both should be fixed. (PR#15700)

  • download.file() with method = "wininet" incorrectly warned of download file length difference when reported length was unknown. (PR#16805)

  • diag(NULL, 1) crashed because of missed type checking. (PR#16853)

logo.jpgR 3.2.5 (AND R-3.2.4-revised)

NEW FEATURES

  • install.packages() and related functions now give a more informative warning when an attempt is made to install a base package.

  • summary(x) now prints with less rounding when x contains infinite values. (Request of PR#16620.)

  • provideDimnames() gets an optional unique argument.

  • shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows. (Response to PR#16636.)

  • The data.frame method of rbind() gains an optional argument stringsAsFactors (instead of only depending on getOption("stringsAsFactors")).

  • smooth(x, *) now also works for long vectors.

  • tools::texi2dvi() has a workaround for problems with the texi2dvi script supplied by texinfo 6.1.

    It extracts more error messages from the LaTeX logs when in emulation mode.

UTILITIES

  • R CMD check will leave a log file ‘buildvignettes.log’ from the re-building of vignettes in the ‘.Rcheck’ directory if there is a problem, and always if environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT is set to a true value.

DEPRECATED AND DEFUNCT

  • Use of SUPPORT_OPENMP from header ‘Rconfig.h’ is deprecated in favour of the standard OpenMP define _OPENMP.

    (This has been the recommendation in the manual for a while now.)

  • The make macro AWK which is long unused by R itself but recorded in file ‘etc/Makeconf’ is deprecated and will be removed in R 3.3.0.

  • The C header file ‘S.h’ is no longer documented: its use should be replaced by ‘R.h’.

BUG FIXES

     In R-3.2.5:

  • format.POSIXlt() behaved incorrectly in R 3.2.4. E.g. the output of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"), usetz = TRUE) ended in two "CEST" time formats.

  • A typo in the Makefile for ‘src/extra/xz’ prevented builds of ‘liblzma.a’. (Notice that this will become unbundled in 3.3.0.)

     In R-3.2.4:

  • kmeans(x, centers = <1-row>) now works. (PR#16623)

  • Vectorize() now checks for clashes in argument names. (PR#16577)

  • file.copy(overwrite = FALSE) would signal a successful copy when none had taken place. (PR#16576)

  • ngettext() now uses the same default domain as gettext(). (PR#14605)

  • array(.., dimnames = ) now warns about non-list dimnames and, from R 3.3.0, will signal the same error for invalid dimnames as matrix() has always done.

  • addmargins() now adds dimnames for the extended margins in all cases, as always documented.

  • heatmap() evaluated its add.expr argument in the wrong environment. (PR#16583)

  • require() etc now give the correct entry of lib.loc in the warning about an old version of a package masking a newer required one.

  • The internal deparser did not add parentheses when necessary, e.g. before [] or [[]]. (Reported by Lukas Stadler; additional fixes included as well).

  • as.data.frame.vector(, row.names=) no longer produces ‘corrupted’ data frames from row names of incorrect length, but rather warns about them. This will become an error.

  • url connections with method = "libcurl" are destroyed properly. (PR#16681)

  • withCallingHandler() now (again) handles warnings even during S4 generic's argument evaluation. (PR#16111)

  • deparse(..., control = "quoteExpressions") incorrectly quoted empty expressions. (PR#16686)

  • format()ting datetime objects ("POSIX[cl]?t") could segfault or recycle wrongly. (PR#16685)

  • plot.ts(<matrix>, las = 1) now does use las.

  • saveRDS(, compress = "gzip") now works as documented. (PR#16653)

  • (Windows only) The Rgui front end did not always initialize the console properly, and could cause R to crash. (PR#16998)

  • dummy.coef.lm() now works in more cases, thanks to a proposal by Werner Stahel (PR#16665). In addition, it now works for multivariate linear models ("mlm", manova) thanks to a proposal by Daniel Wollschlaeger.

  • The as.hclust() method for "dendrogram"s failed often when there were ties in the heights.

  • reorder() and midcache.dendrogram() now are non-recursive and hence applicable to somewhat deeply nested dendrograms, thanks to a proposal by Suharto Anggono in PR#16424.

  • cor.test() now calculates very small p values more accurately (affecting the result only in extreme not statistically relevant cases). (PR#16704)

  • smooth(, do.ends=TRUE) did not always work correctly in R versions between 3.0.0 and 3.2.3.

  • pretty(D) for date-time objects D now also works well if range(D) is (much) smaller than a second. In the case of only one unique value in D, the pretty range now is more symmetric around that value than previously.
    Similarly, pretty(dt) no longer returns a length 5 vector with duplicated entries for Date objects dt which span only a few days.

  • The figures in help pages such as ?points were accidentally damaged, and did not appear in R 3.2.3. (PR#16708)

  • available.packages() sometimes deleted the wrong file when cleaning up temporary files. (PR#16712)

  • The X11() device sometimes froze on Red Hat Enterprise Linux 6. It now waits for MapNotify events instead of Expose events, thanks to Siteshwar Vashisht. (PR#16497)

  • [dpqr]nbinom(, size=Inf, mu=.) now works as limit case, for ‘dpq’ as the Poisson. (PR#16727)
    pnbinom() no longer loops infinitely in border cases.

  • approxfun(*, method="constant") and hence ecdf() which calls the former now correctly “predict” NaN values as NaN.

  • summary.data.frame() now displays NAs in Date columns in all cases. (PR#16709)

logo.jpgR-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(<loess>) 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 Hervé Pagès 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 Müller.)

  • 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.

logo.jpgR-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, <large>) 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.

logo.jpgR-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 &amp;(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.

logo.jpgR-3.2.0

R-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 isNamespaceLoaded() 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.

R 3.2.0 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.

R 3.2.0 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.

R 3.2.0 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.

R 3.2.0 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.

R 3.2.0 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").

R 3.2.0 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.

R 3.2.0 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).

logo.jpgR 3.1.3

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.

R 3.1.3 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.

R 3.1.3 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.

R 3.1.3 DEPRECATED AND DEFUNCT

  • The configure option --with-valgrind-instrumentation=3 is deprecated and will be removed in R 3.2.0.

R 3.1.3 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.

logo.jpgR 3.1.2

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, http://tools.ietf.org/html/rfc3986, 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.)

R 3.1.2 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’.)

R 3.1.2 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 §1.1.3.1 of ‘Writing R Extensions’. For use of lazy-data objects in the package's own code, see ?data.

R 3.1.2 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(<dendrogram>, ..) 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.

logo.jpgR 3.1.1

R 3.1.1 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).

R 3.1.1 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 control 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’.

R 3.1.1 BUG FIXES

  • dbinom(x, n), pbinom(), dpois(), etc, are slightly less restrictive in checking if n is integer-valued. (Wish of PR#15734.)

  • pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df = 100, ncp = 1, log = TRUE). (Based on PR#15635 and a suggestion by Roby Joehanes.)

  • The s (“step into”) command in the debugger would cause R to step into expressions evaluated there, not just into functions being debugged. (PR#15770)

  • The C code used by strptime() rejected time-zone offsets of more than +1200 (+1245, +1300 and +1400 can occur). (PR#15768)

  • (Windows only.) png(type = "cairo", antialias = "gray") was not accepted. (PR#15760)

  • Use of save(..., envir=) with named objects could fail. (PR#15758)

  • Sweave() mis-parsed Sexpr expressions that contained backslashes. (PR#15779)

  • The return value from options(foo = NULL) was not the previous value of the option. (PR#15781)

  • enc2utf8() and enc2native() did not always mark the encoding of the return values when it was known.

  • dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows to -Inf for large mu, thanks to a suggestion from Alessandro Mammana (MPI MolGen, Berlin).

  • pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in a small x-region) because of denormalized numbers. Also, pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates “in real time”.

  • The "CRAN" filter (see available.packages()) no longer removes duplicates other than of packages on CRAN, and does not fail if there is no CRAN repository in getOption("repos").

  • The device listing from dev2bitmap() and bitmap() was truncated to 1000 characters: modern versions of GhostScript on most platforms have many more devices.

  • (Windows.) Commands such as Sys.which() and pipe() which needed to find the full path to a command could segfault if the ‘long’ path name was much longer than the ‘short’ path name (which Sys.which() returns), as the behaviour of the Windows API call had changed.

  • R CMD build will fail with an error if one of the packages specified in the VignetteBuilder field is not installed. (Without loading those packages it cannot be ascertained which files are intended to be vignettes. This means that the VignetteBuilder packages have to be installed for package checking too.) (Wish of PR#15775.)

  • Misguided attempts to use chull() with non-finite points now give an error (related to PR#15777).

  • For a formula with exactly 32 variables the 32nd variable was aliased to the intercept in some C-level computations of terms, so that for example attempting to remove it would remove the intercept instead (and leave a corrupt internal structure). (PR#15735)

  • anyDuplicated() silently returned wrong values when the first duplicate was at an index which was too large to be stored in an integer vector (although a lot of RAM and patience would have been needed to encounter this).

  • tools::Rd2ex(commentDontrun = FALSE) failed if the block had only one line.

  • Hexadecimal constants such as 0x110p-5L which were incorrectly qualified by L were parsed incorrectly since R 3.0.0, with a slightly garbled warning. (PR#15753)

  • system() returned success on some platforms even if the system was unable to launch a process. (PR#15796)

  • (Windows Rgui console.) Unbuffered output was sometimes not output immediately if the prompt was not on the last line of the console.

  • The built-in help server did not declare the encoding for the ‘DESCRIPTION’ or other text files to be the package encoding, so non-ASCII characters could be displayed incorrectly.

  • R is now trying harder to not cleanup child processes that were not spawned by mcparallel() on platforms that provide information about the source process of the SIGCHLD signal. This allows 3rd party libraries to manage the exit status of children that they spawn without R interfering.

  • mcmapply() was only parallelizing if the number of jobs was bigger than the number of cores. It now parallelizes if the number of jobs is more than one.

  • Auto-printing would re-evaluate its argument when trying to dispatch to a print method. This is now avoided when possible.

  • Unserializing (including load() and readRDS()) could silently return incorrect numeric values from ASCII saves if there was a read error.

  • getParseData() could return incorrect values for the parents of some elements. (Reported by Andrew Redd.)

  • Attempting to use data frames of 2^31 or more rows with merge() or to create a merged data frame of that size now gives a clearer error message.

  • parse() did not check its file argument was a connection if it was not a character string, so e.g. parse(FALSE) attempted to read from stdin.

    Nor did dump() and dput().

  • The "help.try.all.packages" option was ignored when the shortcut syntax for help was used, e.g. ?foo.

  • A potential segfault in string allocation has been fixed. (Found by Radford Neal.)

  • Potential memory protection errors in sort() and D() have been fixed. (Found by Radford Neal.)

  • Fixed a lack of error checking in graphics event functions. (Found by Radford Neal; a different patch used here than the one in pqR.)

  • numericDeriv() sometimes miscalculated the gradient. (PR#15849, reported originally by Radford Neal)

R NEWS sourced from the R distribution and distributed under the terms of the GPL-2 license.