R 2.15.1 is released

From: Peter Dalgaard <pd.mes_at_cbs.dk>
Date: Fri, 22 Jun 2012 11:33:55 +0200


The build system has rolled up R-2.15.1.tar.gz (codename "Roasted Marshmallows") at 9:00 this morning. This is a maintenance release; see the list below for details.

You can get it from

http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.

For the R Core Team

Peter Dalgaard

These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted:

MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = fa1101eba3c4c01ffa154053a5dcd2d6
MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e
MD5 (NEWS) = 8d6a52daa2d18630a8aa7a8e7a58ddf6
MD5 (NEWS.html) = 4a8f2f5824ba44427719e2badc5128d1
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = fcdf247e707fdade82b78bcf911a54f1
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = a7a02d98a407c3cb8674d067608f14fc
MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc
MD5 (R-2/R-2.15.1.tar.gz) = fcdf247e707fdade82b78bcf911a54f1


This is the relevant part of the NEWS file:

CHANGES IN R VERSION 2.15.1:   NEW FEATURES:     o source() now uses withVisible() rather than

      .Internal(eval.with.vis).  This sometimes alters tracebacks
      slightly.

    o install.packages("pkg_version.tgz") on Mac OS X now has sanity
      checks that this is actually a binary package (as people have
      tried it with incorrectly named source packages).

    o splineDesign() and spline.des() in package splines have a new
      option sparse which can be used for efficient construction of a
      sparse B-spline design matrix (_via_ Matrix).

    o norm() now allows type = "2" (the 'spectral' or 2-norm) as well,
      mainly for didactical completeness.

    o pmin() and pmax()) now also work when one of the inputs is of
      length zero and others are not, returning a zero-length vector,
      analogously to, say, +.

    o colorRamp() (and hence colorRampPalette()) now also works for the
      boundary case of just one color when the ramp is flat.

    o qqline() has new optional arguments distribution, probs and
      qtype, following the example of lattice's panel.qqmathline().

    o .C() gains some protection against the misuse of character vector
      arguments.  (An all too common error is to pass character(N),
      which initializes the elements to "", and then attempt to edit
      the strings in-place, sometimes forgetting to terminate them.)

    o Calls to the new function globalVariables() in package utils
      declare that functions and other objects in a package should be
      treated as globally defined, so that CMD check will not note
      them.

    o print(packageDescription(*)) trims the Collate field by default.

    o The included copy of zlib has been updated to version 1.2.7.

    o A new option "show.error.locations" has been added. When set to

      TRUE, error messages will contain the location of the most recent
      call containing source reference information. (Other values are
      supported as well; see ?options.)

    o The NA warning messages from e.g. pchisq() now report the call to
      the closure and not that of the .Internal.

    o Added Polish translations by <c5><81>ukasz Daniel.

  PERFORMANCE IMPROVEMENTS:     o In package parallel, makeForkCluster() and the multicore-based

      functions use native byte-order for serialization (deferred from
      2.15.0).

    o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of
      objects, mainly by using .Call() rather than .Fortran().

    o .C() and .Fortran() do less copying: arguments which are raw,
      logical, integer, real or complex vectors and are unnamed are not
      copied before the call, and (named or not) are not copied after
      the call.  Lists are no longer copied (they are supposed to be
      used read-only in the C code).

    o tabulate() makes use of .C(DUP = FALSE) and hence does not copy
      bin.  (Suggested by Tim Hesterberg.)  It also avoids making a
      copy of a factor argument bin.

    o Other functions (often or always) doing less copying include
      cut(), dist(), the complex case of eigen(), hclust(), image(),
      kmeans(), loess(), stl() and svd(LINPACK = TRUE).

    o There is less copying when using primitive replacement functions
      such as names(), attr() and attributes().

  DEPRECATED AND DEFUNCT:     o The converters for use with .C() (see ?getCConverterDescriptions)

      are deprecated: use the .Call() interface instead.  There are no
      known examples (they were never fully documented).

  UTILITIES:     o For R CMD check, a few people have reported problems with

      junctions on Windows (although they were tested on Windows 7, XP
      and Server 2008 machines and it is unknown under what
      circumstances the problems occur).  Setting the environment
      variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
      ~/.R/check.Renviron) will force copies to be used instead.

  INSTALLATION:     o R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value
(as done by R CMD check --as-cran) now restricts the packages

      available when lazy-loading as well as when test-loading (since
      packages such as ETLUtils and agsemisc had top-level calls to
      library() for undeclared packages).

      This check is now also available on Windows.

  C-LEVEL FACILITIES:     o C entry points mkChar and mkCharCE now check that the length of

      the string they are passed does not exceed 2^31-1 bytes: they
      used to overflow with unpredictable consequences.

    o C entry points R_GetCurrentSrcref and R_GetSrcFilename have been
      added to the API to allow debuggers access to the source
      references on the stack.

  WINDOWS-SPECIFIC CHANGES:     o Windows-specific changes will now be announced in this file
(NEWS). Changes up and including R 2.15.0 remain in the CHANGES
      file.

    o There are two new environment variables which control the       defaults for command-line options.

      If R_WIN_INTERNET2 is set to a non-empty value, it is as if
      --internet2 was used.

      If R_MAX_MEM_SIZE is set, it gives the default memory limit if
      --max-mem-size is not specified: invalid values being ignored.

  BUG FIXES:     o lsfit() lost the names from the residuals.

    o More cases in which merge() could create a data frame with

      duplicate column names now give warnings.  Cases where names
      specified in by match multiple columns are errors.

    o Nonsense uses such as seq(1:50, by = 5) (from package plotrix)
      and seq.int(1:50, by = 5) are now errors.

    o The residuals in the 5-number summary printed by summary() on an
      "lm" object are now explicitly labelled as weighted residuals
      when non-constant weights are present.  (Wish of PR#14840.)

    o tracemem() reported that all objects were copied by .C() or
      .Fortran() whereas only some object types were ever copied.

      It also reported and marked as copies _some_ transformations such
      as rexp(n, x): it no longer does so.

    o The plot() method for class "stepfun" only used the optional xval
      argument to compute xlim and not the points at which to plot (as
      documented).  (PR#14864)

    o Names containing characters which need to be escaped were not
      deparsed properly.  (PR#14846)

    o Trying to update (recommended) packages in R_HOME/library without
      write access is now dealt with more gracefully.  Further, such
      package updates may be skipped (with a warning), when a newer
      installed version is already going to be used from .libPaths().

(PR#14866)
o hclust() is now fast again (as up to end of 2003), with a different fix for the "median"/"centroid" problem. (PR#4195). o get_all_vars() failed when the data came entirely from vectors in the global environment. (PR#14847) o R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as done by the --as-cran option) could issue false errors if there was an indirect dependency on a recommended package. o formatC() uses the C entry point str_signif which could write beyond the length allocated for the output string. o Missing default argument added to implicit S4 generic for backsolve(). (PR#14883) o Some bugs have been fixed in handling load actions that could fail to export assigned items or generate spurious warnings in CMD check on loading. o For tiff(type = "windows"), the numbering of per-page files except the last was off by one. o On Windows, loading package stats (which is done for a default session) would switch line endings on stdout and stderr from CRLF to LF. This affected Rterm and R CMD BATCH. o On Windows, the compatibility function x11() had not kept up with changes to windows(), and issued warnings about bad parameters.
(PR#14880)
o On Windows, the Sys.glob() function did not handle UNC paths as it was designed to try to do. (PR#14884) o In package parallel, clusterApply() and similar failed to handle a (pretty pointless) length-1 argument. (PR#14898) o Quartz Cocoa display reacted asynchronously to dev.flush() which means that the redraw could be performed after the plot has been already modified by subsequent code. The redraw is now done synchronously in dev.flush() to allow animations without sleep cycles. o Source locations reported in traceback() were incorrect when byte-compiled code was on the stack. o plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early for large x (e.g. 800). o ?Arithmetic's "1 ^ y and y ^ 0 are 1, _always_" now also applies for integer vectors y. o X11-based pixmap devices like png(type = "Xlib") were trying to set the cursor style, which triggered some warnings and hangs. o Code executed by the built-in HTTP server no longer allows other HTTP clients to re-enter R until the current worker evaluation finishes, to prevent cascades. o The plot() and Axis() methods for class "table" now respect graphical parameters such as cex.axis. (Reported by Martin Becker.) o Under some circumstances package.skeleton() would give out progress reports that could not be translated and so were displayed by question marks. Now they are always in English.
(This was seen for CJK locales on Windows, but may have occurred
elsewhere.) o The evaluator now keeps track of source references outside of functions, e.g. when source() executes a script. o The replacement method for window() now works correctly for multiple time series of class "mts". (PR#14925) o is.unsorted() gave incorrect results on non-atomic objects such as data frames. (Reported by Matthew Dowle.) o The value returned by tools::psnice() for invalid pid values was not always NA as documented. o Closing an X11() window while locator() was active could abort the R process. o getMethod(f, sig) produced an incorrect error message in some cases when f was not a string). o Using a string as a "call" in an error condition with options(showErrorCalls=TRUE) could cause a segfault. (PR#14931) o The string "infinity" allowed by C99 was not accepted as a numerical string value by e.g. scan() and as.character().
(PR#14933)
o In legend(), setting some entries of lwd to NA was inconsistent
(depending on the graphics device) in whether it would suppress
those lines; now it consistently does so. (PR#14926) o by() failed for a zero-row data frame. (Reported by Weiqiang Qian) o Yates correction in chisq.test() could be bigger than the terms it corrected, previously leading to an infinite test statistic in some corner cases which are now reported as NaN. o xgettext() and related functions sometimes returned items that were not strings for translation. (PR#14935) o plot(<lm>, which=5) now correctly labels the factor level combinations for the special case where all h[i,i] are the same.
(PR#14837)
-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes_at_cbs.dk  Priv: PDalgd_at_gmail.com

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