Changes in R

The ‘Changes in R’ article from the 2015-2 issue.

CHANGES IN R 3.2.3

NEW FEATURES

• Some recently-added Windows time zone names have been added to the conversion table used to convert these to Olson names. (Including those relating to changes for Russia in Oct 2014, as in PR#16503.)

• (Windows) Compatibility information has been added to the manifests for Rgui.exe, Rterm.exe and Rscript.exe. This should allow win.version() and Sys.info() to report the actual Windows version up to Windows 10.

• Windows "wininet" FTP first tries EPSV / PASV mode rather than only using active mode (reported by Dan Tenenbaum).

• which.min(x) and which.max(x) may be much faster for logical and integer x and now also work for long vectors.

• The ‘emulation’ part of tools::texi2dvi() has been somewhat enhanced, including supporting quiet = TRUE. It can be selected by texi2dvi = "emulation".

  (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015: tools::texi2dvi() tries texify.exe if it is not found.

• (Windows only) Shortcuts for printing and saving have been added to menus in Rgui.exe. (Request of PR#16572.)

• loess(..., iterTrace=TRUE) now provides diagnostics for robustness iterations, and the print() method for summary(<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.

CHANGES IN R 3.2.2

SIGNIFICANT USER-VISIBLE CHANGES

• It is now easier to use secure downloads from https:// URLs on builds which support them: no longer do non-default options need to be selected to do so. In particular, packages can be installed from repositories which offer https:// URLs, and those listed by setRepositories() now do so (for some of their mirrors).

  Support for https:// URLs is available on Windows, and on other platforms if support for libcurl was compiled in and if that supports the https protocol (system installations can be expected to do). So https:// support can be expected except on rather old OSes (an example being OS X ‘Snow Leopard’, where a non-system version of libcurl can be used).

  (Windows only) The default method for accessing URLs via download.file() and url() has been changed to be "wininet" using Windows API calls. This changes the way proxies need to be set and security settings made: there have been some reports of ftp: 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:// URLs 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).

• 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.