This blog is updated daily.
A general description is here.
Building badly-written vignettes which used the default device
(‘pdf(file = "Rplots.pdf")’ could leave the device open and hence the
file ‘Rplots.pdf’ could not be removed on Windows: all devices are now
closed.
In some circumstances the caret (cursor) could be positioned
incorrectly. (PR#14460)
When loading ‘Rconsole’ from disk, a spurious warning message was
sometimes shown.
In R 2.12.1, ‘system()’ sometimes passed an empty input stream to the
new process rather than allowing user input.
The internal method for ‘untar()’ does a better job of unravelling
symbolic links in the tarball (but still with many limitations).
Building badly-written vignettes which used the default device (‘pdf(file = "Rplots.pdf")’ could leave the device open and hence the file ‘Rplots.pdf’ could not be removed on Windows: all devices are now closed.
In some circumstances the caret (cursor) could be positioned incorrectly. (PR#14460)
When loading ‘Rconsole’ from disk, a spurious warning message was sometimes shown.
In R 2.12.1, ‘system()’ sometimes passed an empty input stream to the new process rather than allowing user input.
The internal method for ‘untar()’ does a better job of unravelling symbolic links in the tarball (but still with many limitations).
Bug fixes for drawing raster objects on ‘windows()’. The symptom was the occasional raster image not being drawn, especially when drawing multiple raster images in a single expression. Thanks to Michael Sumner for report and testing.
Complex arithmetic (notably ‘z^n’ for complex ‘z’ and integer ‘n’) gave
incorrect results since R 2.10.0 on platforms without complex 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.
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.)
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’.
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.
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.
‘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 ‘<pkg>/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 logit() function ‘qlogis(lp, log.p=TRUE)’ no longer prematurely
overflows to ‘Inf’ when p := 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.
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.
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.
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’.
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.
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.
‘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 ‘<pkg>/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 logit() function ‘qlogis(lp, log.p=TRUE)’ no longer prematurely overflows to ‘Inf’ when p := 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.