Month: February 2011

CHANGES IN R VERSION 2.12.2: http://cran.r-project.org/src/base/NEWS

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Complex arithmetic (notably z^n for complex z and integer n) gave
      incorrect results since R 2.10.0 on platforms without C99 complex
      support.  This and some lesser issues in trignometric functions
      have been corrected.

      Such platforms were rare (we know of Cygwin and FreeBSD).
      However, because of new compiler optimizations in the way complex
      arguments are handled, the same code was selected on x86_64 Linux
      with gcc 4.5.x at the default -O2 optimization (but not at -O).

    • There is a workaround for crashes seen with several packages on
      systems using zlib 1.2.5: see the INSTALLATION section.

  NEW FEATURES:

    • PCRE has been updated to 8.12 (two bug-fix releases since 8.10).

    • rep(), seq(), seq.int() and seq_len() report more often when the
      first element is taken of an argument of incorrect length.

    • The Cocoa back-end for the quartz() graphics device on Mac OS X
      provides a way to disable event loop processing temporarily
      (useful, e.g., for forked instances of R).

    • kernel()'s default for m was not appropriate if coef was a set of
      coefficients.  (Reported by Pierre Chausse.)

    • bug.report() has been updated for the current R bug tracker,
      which does not accept emailed submissions.

    • R CMD check now checks for the correct use of $(LAPACK_LIBS) (as
      well as $(BLAS_LIBS)), since several CRAN recent submissions have
      ignored ‘Writing R Extensions’.

  INSTALLATION:

    • The zlib sources in the distribution are now built with all
      symbols remapped: this is intended to avoid problems seen with
      packages such as XML and rggobi which link to zlib.so.1 on
      systems using zlib 1.2.5.

    • The default for FFLAGS and FCFLAGS with gfortran on x86_64 Linux
      has been changed back to -g -O2: however, setting -g -O may still
      be needed for gfortran 4.3.x.

  PACKAGE INSTALLATION:

    • A LazyDataCompression field in the DESCRIPTION file will be used
      to set the value for the --data-compress option of R CMD INSTALL.

    • Files R/sysdata.rda of more than 1Mb are now stored in the
      lazyload daabase using xz compression: this for example halves
      the installed size of package Imap.

    • R CMD INSTALL now ensures that directories installed from inst
      have search permission for everyone.

      It no longer installs files inst/doc/Rplots.ps and
      inst/doc/Rplots.pdf.  These are almost certainly left-overs from
      Sweave runs, and are often large.

  DEPRECATED & DEFUNCT:

    • The ‘experimental’ alternative specification of a name space via
      .Export() etc is now deprecated.

    • zip.file.extract() is now deprecated.

    • Zip-ing data sets in packages (and hence R CMD INSTALL
      --use-zip-data and the ZipData: yes field in a DESCRIPTION file)
      is deprecated: using efficiently compressed .rda images and
      lazy-loading of data has superseded it.

  BUG FIXES:

    • identical() could in rare cases generate a warning about
      non-pairlist attributes on CHARSXPs.  As these are used for
      internal purposes, the attribute check should be skipped.
      (Reported by Niels Richard Hansen).

    • If the filename extension (usually .Rnw) was not included in a
      call to Sweave(), source references would not work properly and
      the keep.source option failed.  (PR#14459)

    • format.data.frame() now keeps zero character column names.

    • pretty(x) no longer raises an error when x contains solely
      non-finite values. (PR#14468)

    • The plot.TukeyHSD() function now uses a line width of 0.5 for its
      reference lines rather than lwd = 0 (which caused problems for
      some PDF and PostScript viewers).

    • The big.mark argument to prettyNum(), format(), etc. was inserted
      reversed if it was more than one character long.

    • R CMD check failed to check the filenames under man for Windows'
      reserved names.

    • The "Date" and "POSIXt" methods for seq() could overshoot when to
      was supplied and by was specified in months or years.

    • The internal method of untar() now restores hard links as file
      copies rather than symbolic links (which did not work for
      cross-directory links).

    • unzip() did not handle zip files which contained filepaths with
      two or more leading directories which were not in the zipfile and
      did not already exist.  (It is unclear if such zipfiles are valid
      and the third-party C code used did not support them, but
      PR#14462 created one.)

    • combn(n, m) now behaves more regularly for the border case m = 0.
      (PR#14473)

    • The rendering of numbers in plotmath expressions (e.g.
      expression(10^2)) used the current settings for conversion to
      strings rather than setting the defaults, and so could be
      affected by what has been done before.  (PR#14477)

    • The methods of napredict() and naresid() for na.action =
      na.exclude fits did not work correctly in the very rare event
      that every case had been omitted in the fit.  (Reported by Simon
      Wood.)

    • weighted.residuals(drop0=TRUE) returned a vector when the
      residuals were a matrix (e.g. those of class "mlm").  (Reported
      by Bill Dunlap.)

    • Package HTML index files /html/00Index.html were generated
      with a stylesheet reference that was not correct for static
      browsing in libraries.

    • ccf(na.action = na.pass) was not implemented.

    • The parser accepted some incorrect numeric constants, e.g. 20x2.
      (Reported by Olaf Mersmann.)

    • format(*, zero.print) did not always replace the full zero parts.

    • Fixes for subsetting or subassignment of "raster" objects when
      not both i and j are specified.

    • R CMD INSTALL was not always respecting the ZipData: yes field of
      a DESCRIPTION file (although this is frequently incorrectly
      specified for packages with no data or which specify lazy-loading
      of data).

      R CMD INSTALL --use-zip-data was incorrectly implemented as
      --use-zipdata since R 2.9.0.

    • source(file, echo=TRUE) could fail if the file contained #line
      directives.  It now recovers more gracefully, but may still
      display the wrong line if the directive gives incorrect
      information.

    • atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms
      without C99 complex support.

    • library() failed to cache S4 metadata (unlike loadNamespace())
      causing failures in S4-using packages without a namespace (e.g.
      those using reference classes).

    • The function qlogis(lp, log.p=TRUE) no longer prematurely
      overflows to Inf when exp(lp) is close to 1.

    • Updating S4 methods for a group generic function requires
      resetting the methods tables for the members of the group (patch
      contributed by Martin Morgan).

    • In some circumstances (including for package XML), R CMD INSTALL
      installed version-control directories from source packages.

    • Added PROTECT calls to some constructed expressions used in C
      level eval calls.

    • utils:::create.post() (used by bug.report() and help.request())
      failed to quote arguments to the mailer, and so often failed.

    • bug.report() was naive about how to extract maintainer email
      addresses from package descriptions, so would often try mailing
      to incorrect addresses.

    • debugger() could fail to read the environment of a call to a
      function with a ... argument.  (Reported by Charlie Roosen.)    • prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work
      correctly.

Related Articles

• R 2.12.2 scheduled for February 25 (revolutionanalytics.com)
• Sweave Tutorial 3: Console Input and Output – Multiple Choice Test Analysis (r-bloggers.com)