R 3.3.1 is released

R 3.3.1 (codename “Bug in Your Hair”) was released yesterday You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of bug fixes is provided below new features and (this release does not introduce new features).

Upgrading to R 3.3.1 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE) # only for R versions older than 3.3.0
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package. If you only see the option to upgrade to an older version of R, then change your mirror or try again in a few hours (it usually take around 24 hours for all CRAN mirrors to get the latest version of R).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.

Continue reading “R 3.3.1 is released”

R 3.3.0 is released!

R 3.3.0 (codename “Supposedly Educational”) was released today. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.3.0 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE)
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package. If you only see the option to upgrade to an older version of R, then change your mirror or try again in a few hours (it usually take around 24 hours for all CRAN mirrors to get the latest version of R).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.

CHANGES IN R 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

Continue reading “R 3.3.0 is released!”

R 3.2.4 is released

R 3.2.4 (codename “Very Secure Dishes”) was released today. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.2.4 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE)
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package.

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.

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 ‘build_vignettes.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

  • 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)

 

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R 3.2.3 is released (with improvements for Windows users, and general bug fixes)

R 3.2.3 (codename “Wooden Christmas Tree”) was released several days ago. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Major changes in R 3.2.3

As highlighted by David Smith, this release makes a few small improvements and bug fixes to R, including:

  • Improved support for users of the Windows OS in time zones, OS version identification, FTP connections, and printing (in the GUI).
  • Performance improvements and more support for long vectors in some functions including which.max
  • Improved accuracy for the Chi-Square distribution functions in some extreme cases

Upgrading to R 3.2.3 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE)
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package.

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.

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() andSys.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.)

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.

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’.

R 3.2.2 is released

R 3.2.2 (codename “Fire Safety”) was released last weekend. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

SOME OF THE CHANGES

I personally found two things particularly interesting in this release:

  1. setInternet2(TRUE) is now the default for windows (which will save people from getting “Error in file(con, “r”)” when using the installr package)
  2. The dendrogram method of labels() is much more efficient for large dendrograms since it now uses rapply(). This is expected to speedup various functions in the dendextend R package (a package for visualizing, adjusting, and comparing dendrograms, which heavily relies on labels.dendrogram).

Also, David Smith (from Revolution/Microsoft) highlighted in his post several of the updates in R 3.2.2 he found interesting – mentioning how the new default for accessing the web with R will rely on the HTTPS protocol, and of improving the accuracy in the extreme tails of the t and hypergeometric distributions.

Upgrading to R 3.2.2 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE)
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package.

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.

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 forlibcurl 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

Continue reading “R 3.2.2 is released”

R 3.2.1 is released

R 3.2.1 (codename “World-Famous Astronaut”) was released yesterday. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.2.1 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package.

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.

CHANGES IN R 3.2.1:

 

NEW FEATURES

  • utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not.
  • install.packages() now allows type = "both" with repos = NULL if it can infer the type of file.
  • nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability.
  • news() more flexibly extracts dates from package ‘NEWS.Rd’ files.
  • lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar.
  • The included version of PCRE has been updated to 8.37, a bug-fix release.
  • diag() no longer duplicates a matrix when extracting its diagonal.
  • as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted.

BUG FIXES

Continue reading “R 3.2.1 is released”

A step by step (screenshots) tutorial for upgrading R on Windows

tl;dr

If you are running R on Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) # install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). just press “next”, “OK”, and “Yes” on everything…

A GUI interface to updating R on Windows

Starting from installr version 0.15.0, the upgradingprocess can be done with a click-on-menus GUI interface. Here is how to use it.

Continue reading “A step by step (screenshots) tutorial for upgrading R on Windows”

R 3.2.0 is released (+ using the installr package to upgrade in Windows OS)

R 3.2.0 (codename “Full of Ingredients”) was released yesterday. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.2.0 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) #load / install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to leave a comment below.

CHANGES IN R 3.2.0:

As always, David smith mentioned in his post some of the main changes, writing how many of the changes in this release have happened behind the scenes to improve R’s engine for performance and reliability. These include:

  • A number of fixes proposed by Radford Neal, bringing some of the performance improvements of pqR to R while maintaining backwards compatibility.
  • more progress in handling big in-memory data objects (for example, you can now cbind/rbind matrices with more than 2 billion elements).
  • some significant updates to R’s byte compiler with 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.
  • the package-checking system now does a more thorough job of making sure contributed packages comply with CRAN policies.

And here is also the full list of new features, bug fixes, etc:

Continue reading “R 3.2.0 is released (+ using the installr package to upgrade in Windows OS)”

R 3.1.3 is released (+ easy upgrading for Windows users with the installr package)

R 3.1.3 (codename “Smooth Sidewalk”) was released today. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.1.3 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) #load / install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to leave a comment below.

CHANGES IN R 3.1.3:

As always, David smith mentioned in his post some of the main changes, writing:

As has become usual in March, this release is primarily for minor bugs and improvements in R, as the development switches focus to the next major release (R 3.2.0 is expected on April 16). Improvements include: ability to download files greater than 2GB on 32-bit builds; better handling of complex (imaginary) numbers for several functions; improved command completion in the Windows GUI; and improved performance when using S4 classes. (See the complete list here.)

And here is also the full list:

Continue reading “R 3.1.3 is released (+ easy upgrading for Windows users with the installr package)”

R 3.1.2 release (and upgrading for Windows users)

R 3.1.2 (codename “Pumpkin Helmet“) was released last week. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.1.2 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) #load / install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to leave a comment below.

If you use the global library system (as I do), you can run the following in the new version of R:

source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
New.R.RunMe()

CHANGES IN R 3.1.2:

David smith mentioned in his post some of the main changes, writing:

[…] improvements for the log-Normal distribution function, improved axis controls for histograms, a fix to the nlminb optimizer which was causing rare crashes on Windows (and traced to a bug in the gcc compiler), and some compatibility updates for the Yosemite release of OS X on Macs.

And here is also the full list:

Continue reading “R 3.1.2 release (and upgrading for Windows users)”