CHANGES IN R VERSION 2.12.2: http://cran.r-project.org/src/base/NEWS
SIGNIFICANT USER-VISIBLE CHANGES:
â€¢ 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).
â€¢ There is a workaround for crashes seen with several packages on
systems using zlib 1.2.5: see the INSTALLATION section.
â€¢ PCRE has been updated to 8.12 (two bug-fix releases since 8.10).
â€¢ rep(), seq(), seq.int() and seq_len() report more often when the
first element is taken of an argument of incorrect length.
â€¢ 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).
â€¢ kernel()'s default for m was not appropriate if coef was a set of
coefficients. (Reported by Pierre Chausse.)
â€¢ bug.report() has been updated for the current R bug tracker,
which does not accept emailed submissions.
â€¢ R CMD check now checks for the correct use of $(LAPACK_LIBS) (as
well as $(BLAS_LIBS)), since several CRAN recent submissions have
ignored â€˜Writing R Extensionsâ€™.
â€¢ 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.
â€¢ 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.
â€¢ A LazyDataCompression field in the DESCRIPTION file will be used
to set the value for the --data-compress option of R CMD INSTALL.
â€¢ 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.
â€¢ 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:
â€¢ The â€˜experimentalâ€™ alternative specification of a name space via
.Export() etc is now deprecated.
â€¢ zip.file.extract() is now deprecated.
â€¢ 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.
â€¢ 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).
â€¢ 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)
â€¢ format.data.frame() now keeps zero character column names.
â€¢ pretty(x) no longer raises an error when x contains solely
non-finite values. (PR#14468)
â€¢ 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).
â€¢ The big.mark argument to prettyNum(), format(), etc. was inserted
reversed if it was more than one character long.
â€¢ R CMD check failed to check the filenames under man for Windows'
â€¢ The "Date" and "POSIXt" methods for seq() could overshoot when to
was supplied and by was specified in months or years.
â€¢ The internal method of untar() now restores hard links as file
copies rather than symbolic links (which did not work for
â€¢ 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.)
â€¢ combn(n, m) now behaves more regularly for the border case m = 0.
â€¢ 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)
â€¢ 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
â€¢ weighted.residuals(drop0=TRUE) returned a vector when the
residuals were a matrix (e.g. those of class "mlm"). (Reported
by Bill Dunlap.)
â€¢ Package HTML index files /html/00Index.html were generated
with a stylesheet reference that was not correct for static
browsing in libraries.
â€¢ ccf(na.action = na.pass) was not implemented.
â€¢ The parser accepted some incorrect numeric constants, e.g. 20x2.
(Reported by Olaf Mersmann.)
â€¢ format(*, zero.print) did not always replace the full zero parts.
â€¢ Fixes for subsetting or subassignment of "raster" objects when
not both i and j are specified.
â€¢ 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
R CMD INSTALL --use-zip-data was incorrectly implemented as
--use-zipdata since R 2.9.0.
â€¢ 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
â€¢ atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms
without C99 complex support.
â€¢ library() failed to cache S4 metadata (unlike loadNamespace())
causing failures in S4-using packages without a namespace (e.g.
those using reference classes).
â€¢ The function qlogis(lp, log.p=TRUE) no longer prematurely
overflows to Inf when exp(lp) is close to 1.
â€¢ Updating S4 methods for a group generic function requires
resetting the methods tables for the members of the group (patch
contributed by Martin Morgan).
â€¢ In some circumstances (including for package XML), R CMD INSTALL
installed version-control directories from source packages.
â€¢ Added PROTECT calls to some constructed expressions used in C
level eval calls.
â€¢ utils:::create.post() (used by bug.report() and help.request())
failed to quote arguments to the mailer, and so often failed.
â€¢ bug.report() was naive about how to extract maintainer email
addresses from package descriptions, so would often try mailing
to incorrect addresses.
â€¢ debugger() could fail to read the environment of a call to a
function with a ... argument. (Reported by Charlie Roosen.) â€¢ prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work
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