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-------------------------------------------------------------------
Tue Mar 7 08:25:48 UTC 2017 - detlef.steuer@gmx.de
- a change in OBS now requires a BuildRequire: shadow for
some openSUSE releases.
-------------------------------------------------------------------
Mon Mar 6 11:36:54 UTC 2017 - detlef.steuer@gmx.de
- upstream release 3.3.3
- Most important changes
CHANGES IN R 3.3.3:
NEW FEATURES:
* Changes when redirection of a http:// URL to a https:// URL is
encountered:
* The internal methods of download.file() and url() now report
that they cannot follow this (rather than failing silently).
* (Unix-alike) download.file(method = "auto") (the default)
re-tries with method = "libcurl".
* (Unix-alike) url(method = "default") with an explicit open
argument re-tries with method = "libcurl". This covers many
of the usages, e.g. readLines() with a URL argument.
INSTALLATION on a UNIX-ALIKE:
* The configure check for the zlib version is now robust to
versions longer than 5 characters, including 1.2.11.
UTILITIES:
* Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD
check reports failing tests (see SS8 of the 'R Internals' manual).
DEPRECATED AND DEFUNCT:
* (C-level Native routine registration.) The undocumented styles
field of the components of R_CMethodDef and R_FortranMethodDef is
deprecated.
BUG FIXES:
* vapply(x, *) now works with long vectors x. (PR#17174)
* isS3method("is.na.data.frame") and similar are correct now.
(PR#17171)
* grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a
patch by Mikko Korpela. (PR#17132)
* Package installation into a library where the package exists
_via_ symbolic link now should work wherever Sys.readlink()
works, resolving PR#16725.
* "Cincinnati" was missing an "n" in the precip dataset.
* Fix buffer overflow vulnerability in pdf() when loading an
encoding file. Reported by Talos (TALOS-2016-0227).
* getDLLRegisteredRoutines() now produces its warning correctly
when multiple DLLs match, thanks to Matt Dowle's PR#17184.
* Sys.timezone() now returns non-NA also on platforms such as
Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186.
* format(x) for an illegal "POSIXlt" object x no longer segfaults.
* methods(f) now also works for f "(" or "{".
* (Windows only) dir.create() did not check the length of the path
to create, and so could overflow a buffer and crash R.
(PR#17206)
* On some systems, very small hexadecimal numbers in hex notation
would underflow to zero. (PR#17199)
* pmin() and pmax() now work again for ordered factors and 0-length
S3 classed objects, thanks to Suharto Anggono's PR#17195 and
PR#17200.
* bug.report() did not do any validity checking on a package's
BugReports field. It now ignores an empty field, removes leading
whitespace and only attempts to open http:// and https:// URLs,
falling back to emailing the maintainer.
* Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers
or incorrectly reported an error (because of integer overflow)
for inputs longer than 46341. Similarly for bw.bcv() at length
5793.
Another possible integer overflow is checked and may result in an
error report (rather than an incorrect result) for much longer
inputs (millions for a smooth distribution).
* findMethod() failed if the active signature had expanded beyond
what a particular package used. (Example with packages XR and
XRJulia on CRAN.)
* qbeta() underflowed too early in some very asymmetric cases.
(PR#17178)
* R CMD Rd2pdf had problems with packages with non-ASCII titles in
.Rd files (usually the titles were omitted).
-------------------------------------------------------------------
Mon Oct 31 11:50:08 UTC 2016 - detlef.steuer@gmx.de
- upstream release 3.3.2
- Most important changes
CHANGES IN R 3.3.2:
NEW FEATURES:
* extSoftVersion() now reports the version (if any) of the readline
library in use.
* The version of LAPACK included in the sources has been updated to
3.6.1, a bug-fix release including a speedup for the
non-symmetric case of eigen().
* Use options(deparse.max.lines=) to limit the number of lines
recorded in .Traceback and other deparsing activities.
* format(<AsIs>) looks more regular, also for non-character atomic
matrices.
* abbreviate() gains an option named = TRUE.
* The online documentation for package methods is extensively
rewritten. The goals are to simplify documentation for basic
use, to note old features not recommended and to correct
out-of-date information.
* Calls to setMethod() no longer print a message when creating a
generic function in those cases where that is natural: S3
generics and primitives.
INSTALLATION and INCLUDED SOFTWARE:
* Versions of the readline library >= 6.3 had been changed so that
terminal window resizes were not signalled to readline: code has
been added using a explicit signal handler to work around that
(when R is compiled against readline >= 6.3). (PR#16604)
* configure works better with Oracle Developer Studio 12.5.
UTILITIES:
* R CMD check reports more dubious flags in files
src/Makevars[.in], including -w and -g.
* R CMD check has been set up to filter important warnings from
recent versions of gfortran with -Wall -pedantic: this now
reports non-portable GNU extensions such as out-of-order
declarations.
* R CMD config works better with paths containing spaces, even
those of home directories (as reported by Ken Beath).
DEPRECATED AND DEFUNCT:
* Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
are included by R headers from C++ as from R 3.3.0, so it should
no longer be needed).
BUG FIXES:
* The check for non-portable flags in R CMD check could be stymied
by src/Makevars files which contained targets.
* (Windows only) When using certain desktop themes in Windows 7 or
higher, Alt-Tab could cause Rterm to stop accepting input.
(PR#14406; patch submitted by Jan Gleixner.)
* pretty(d, ..) behaves better for date-time d (PR#16923).
* When an S4 class name matches multiple classes in the S4 cache,
perform a dynamic search in order to obey namespace imports.
This should eliminate annoying messages about multiple hits in
the class cache. Also, pass along the package from the
ClassExtends object when looking up superclasses in the cache.
* sample(NA_real_) now works.
* Packages using non-ASCII encodings in their code did not install
data properly on systems using different encodings.
* merge(df1, df2) now also works for data frames with column names
"na.last", "decreasing", or "method". (PR#17119)
* contour() caused a segfault if the labels argument had length
zero. (Reported by Bill Dunlap.)
* unique(warnings()) works more correctly, thanks to a new
duplicated.warnings() method.
* findInterval(x, vec = numeric(), all.inside = TRUE) now returns
0s as documented. (Reported by Bill Dunlap.)
* (Windows only) R CMD SHLIB failed when a symbol in the resulting
library had the same name as a keyword in the .def file.
(PR#17130)
* pmax() and pmin() now work with (more ?) classed objects, such
as "Matrix" from the Matrix package, as documented for a long
time.
* axis(side, x = D) and hence Axis() and plot() now work correctly
for "Date" and time objects D, even when "time goes backward",
e.g., with decreasing xlim. (Reported by William May.)
* str(I(matrix(..))) now looks as always intended.
* plot.ts(), the plot() method for time series, now respects cex,
lwd and lty. (Reported by Greg Werbin.)
* parallel::mccollect() now returns a named list (as documented)
when called with wait = FALSE. (Reported by Michel Lang.)
* If a package added a class to a class union in another package,
loading the first package gave erroneous warnings about
"undefined subclass".
* c()'s argument use.names is documented now, as belonging to the
(C internal) default method. In "parallel", argument recursive
is also moved from the generic to the default method, such that
the formal argument list of base generic c() is just (...).
* rbeta(4, NA) and similarly rgamma() and rnbinom() now return
NaN's with a warning, as other r<dist>(), and as documented.
(PR#17155)
* Using options(checkPackageLicense = TRUE) no longer requires
acceptance of the licence for non-default standard packages such
as compiler. (Reported by Mikko Korpela.)
* split(<very_long>, *) now works even when the split off parts are
long. (PR#17139)
* min() and max() now also work correctly when the argument list
starts with character(0). (PR#17160)
* Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
thanks to Michael Schubmehl's PR#17158.
* bartlett.test() used residual sums of squares instead of
variances, when the argument was a list of lm objects. (Reported
by Jens Ledet Jensen).
* plot(<lm>, which = *) now correctly labels the contour lines for
the standardized residuals for which = 6. It also takes the
correct p in case of singularities (also for which = 5).
(PR#17161)
* xtabs(~ exclude) no longer fails from wrong scope, thanks to
Suharto Anggono's PR#17147.
* Reference class calls to methods() did not re-analyse previously
defined methods, meaning that calls to methods defined later
would fail. (Reported by Charles Tilford).
* findInterval(x, vec, left.open = TRUE) misbehaved in some cases.
(Reported by Dmitriy Chernykh.)
-------------------------------------------------------------------
Fri Jul 1 16:17:11 UTC 2016 - toddrme2178@gmail.com
- Fix typo in Group tag.
-------------------------------------------------------------------
Tue Jun 21 09:26:17 UTC 2016 - detlef.steuer@gmx.de
- upstream release 3.3.1
- Most important changes
CHANGES IN R 3.3.1:
BUG FIXES:
* R CMD INSTALL and hence install.packages() gave an internal error
installing a package called description from a tarball on a
case-insensitive file system.
* match(x, t) (and hence x %in% t) failed when x was of length one,
and either character and x and t only differed in their Encoding
or when x and t where complex with NAs or NaNs. (PR#16885.)
* unloadNamespace(ns) also works again when ns is a 'namespace', as
from getNamespace().
* rgamma(1,Inf) or rgamma(1, 0,0) no longer give NaN but the
correct limit.
* length(baseenv()) is correct now.
* pretty(d, ..) for date-time d rarely failed when "halfmonth" time
steps were tried (PR#16923) and on 'inaccurate' platforms such as
32-bit windows or a configuration with --disable-long-double; see
comment #15 of PR#16761.
* In text.default(x, y, labels), the rarely(?) used default for
labels is now correct also for the case of a 2-column matrix x
and missing y.
* as.factor(c(a = 1L)) preserves names() again as in R < 3.1.0.
* strtrim(""[0], 0[0]) now works.
* Use of Ctrl-C to terminate a reverse incremental search started
by Ctrl-R in the readline-based Unix terminal interface is now
supported for readline >= 6.3 (Ctrl-G always worked). (PR#16603)
* diff(<difftime>) now keeps the "units" attribute, as subtraction
already did, PR#16940.
-------------------------------------------------------------------
Wed May 18 07:58:59 UTC 2016 - detlef.steuer@gmx.de
- further cleanup of spec file.
Removed unneeded explicit Requires for
libcairo2/libfreetype6/liblzma5/libreadline6
Removed removal of backup file that was meanwhile removed upstream.
-------------------------------------------------------------------
Wed May 11 14:36:53 UTC 2016 - detlef.steuer@gmx.de
- clean up of spec file after comments from Jan Engelhardt in
https://build.opensuse.org/request/show/393426
Some unneeded explicit BuildRequires removed.
-------------------------------------------------------------------
Tue May 3 13:31:13 UTC 2016 - detlef.steuer@gmx.de
- tre.patch was removed.
-------------------------------------------------------------------
Tue May 3 11:30:09 UTC 2016 - detlef.steuer@gmx.de
- and libbz2-devel needed, too.
-------------------------------------------------------------------
Tue May 3 11:00:15 UTC 2016 - detlef.steuer@gmx.de
- added BuildRequires: bzip2
for i586.
-------------------------------------------------------------------
Tue May 3 10:24:09 UTC 2016 - detlef.steuer@gmx.de
- upstream release 3.3.0
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:
* The print method for methods() gains a byclass argument.
* New functions validEnc() and validUTF8() to give access to the
validity checks for inputs used by grep() and friends.
* Experimental new functionality for S3 method checking, notably
isS3method().
Also, the names of the R 'language elements' are exported as
character vector tools::langElts.
* str(x) now displays "Time-Series" also for matrix (multivariate)
time-series, i.e. when is.ts(x) is true.
* (Windows only) The GUI menu item to install local packages now
accepts *.tar.gz files as well as *.zip files (but defaults to
the latter).
* New programmeR's utility function chkDots().
* D() now signals an error when given invalid input, rather than
silently returning NA. (Request of John Nash.)
* formula objects are slightly more "first class": e.g., formula()
or new("formula", y ~ x) are now valid. Similarly, for "table",
"ordered" and "summary.table". Packages defining S4 classes with
the above S3/S4 classes as slots should be reinstalled.
* New function strrep() for repeating the elements of a character
vector.
* rapply() preserves attributes on the list when how = "replace".
* New S3 generic function sigma() with methods for extracting the
estimated standard deviation aka "residual standard deviation"
from a fitted model.
* news() now displays R and package news files within the HTML help
system if it is available. If no news file is found, a visible
NULL is returned to the console.
* as.raster(x) now also accepts raw arrays x assuming values in
0:255.
* Subscripting of matrix/array objects of type "expression" is now
supported.
* type.convert("i") now returns a factor instead of a complex value
with zero real part and missing imaginary part.
* Graphics devices cairo_pdf() and cairo_ps() now allow non-default
values of the cairographics 'fallback resolution' to be set.
This now defaults to 300 on all platforms: that is the default
documented by cairographics, but apparently was not used by all
system installations.
* file() gains an explicit method argument rather than implicitly
using getOption("url.method", "default").
* Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically
faster than x[which(x != 0)] (in the case where x has no NAs, the
two are equivalent).
* read.table() now always uses the names for a named colClasses
argument (previously names were only used when colClasses was too
short). (In part, wish of PR#16478.)
* (Windows only) download.file() with default method = "auto" and a
ftps:// URL chooses "libcurl" if that is available.
* The out-of-the box Bioconductor mirror has been changed to one
using https://: use chooseBioCmirror() to choose a http:// mirror
if required.
* The data frame and formula methods for aggregate() gain a drop
argument.
* available.packages() gains a repos argument.
* The undocumented switching of methods for url() on https: and
ftps: URLs is confined to method = "default" (and documented).
* smoothScatter() gains a ret.selection argument.
* qr() no longer has a ... argument to pass additional arguments to
methods.
* [ has a method for class "table".
* It is now possible (again) to replayPlot() a display list
snapshot that was created by recordPlot() in a different R
session.
It is still not a good idea to use snapshots as a persistent
storage format for R plots, but it is now not completely silly to
use a snapshot as a format for transferring an R plot between two
R sessions.
The underlying changes mean that packages providing graphics
devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will
need to be reinstalled.
Code for restoring snapshots was contributed by Jeroen Ooms and
JJ Allaire.
Some testing code is available at <URL:
https://github.com/pmur002/R-display-list>.
* tools::undoc(dir = D) and codoc(dir = D) now also work when D is
a directory whose normalizePath()ed version does not end in the
package name, e.g. from a symlink.
* abbreviate() has more support for multi-byte character sets - it
no longer removes bytes within characters and knows about Latin
vowels with accents. It is still only really suitable for (most)
European languages, and still warns on non-ASCII input.
abbreviate(use.classes = FALSE) is now implemented, and that is
more suitable for non-European languages.
* match(x, table) is faster (sometimes by an order of magnitude)
when x is of length one and incomparables is unchanged, thanks to
Peter Haverty (PR#16491).
* More consistent, partly not back-compatible behavior of NA and
NaN coercion to complex numbers, operations less often resulting
in complex NA (NA_complex_).
* lengths() considers methods for length and [[ on x, so it should
work automatically on any objects for which appropriate methods
on those generics are defined.
* The logic for selecting the default screen device on OS X has
been simplified: it is now quartz() if that is available even if
environment variable DISPLAY has been set by the user.
The choice can easily be overridden _via_ environment variable
R_INTERACTIVE_DEVICE.
* On Unix-like platforms which support the getline C library
function, system(*,intern = TRUE) no longer truncates (output)
lines longer than 8192 characters, thanks to Karl Millar.
(PR#16544)
* rank() gains a ties.method = "last" option, for convenience (and
symmetry).
* regmatches(invert = NA) can now be used to extract both
non-matched and matched substrings.
* data.frame() gains argument fix.empty.names; as.data.frame.list()
gets new cut.names, col.names and fix.empty.names.
* plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *).
* recordPlot() has new arguments load and attach to allow package
names to be stored as part of a recorded plot. replayPlot() has
new argument reloadPkgs to load/attach any package names that
were stored as part of a recorded plot.
* S4 dispatch works within calls to .Internal(). This means
explicit S4 generics are no longer needed for unlist() and
as.vector().
* Only font family names starting with "Hershey" (and not "Her" as
before) are given special treatment by the graphics engine.
* S4 values are automatically coerced to vector (via as.vector)
when subassigned into atomic vectors.
* findInterval() gets a left.open option.
* The version of LAPACK included in the sources has been updated to
3.6.0, including those 'deprecated' routines which were
previously included. _Ca_ 40 double-complex routines have been
added at the request of a package maintainer.
As before, the details of what is included are in
src/modules/lapack/README and this now gives information on
earlier additions.
* tapply() has been made considerably more efficient without
changing functionality, thanks to proposals from Peter Haverty
and Suharto Anggono. (PR#16640)
* match.arg(arg) (the one-argument case) is faster; so is
sort.int(). (PR#16640)
* The format method for object_size objects now also accepts
"binary" units such as "KiB" and e.g., "Tb". (Partly from
PR#16649.)
* Profiling now records calls of the form foo::bar and some similar
cases directly rather than as calls to <Anonymous>. Contributed
by Winston Chang.
* New string utilities startsWith(x, prefix) and endsWith(x,
suffix). Also provide speedups for some grepl("^...",*) uses
(related to proposals in PR#16490).
* Reference class finalizers run at exit, as well as on garbage
collection.
* Avoid parallel dependency on stats for port choice and random
number seeds. (PR#16668)
* The radix sort algorithm and implementation from data.table
(forder) replaces the previous radix (counting) sort and adds a
new method for order(). Contributed by Matt Dowle and Arun
Srinivasan, the new algorithm supports logical, integer (even
with large values), real, and character vectors. It outperforms
all other methods, but there are some caveats (see ?sort).
* The order() function gains a method argument for choosing between
"shell" and "radix".
* New function grouping() returns a permutation that stably
rearranges data so that identical values are adjacent. The
return value includes extra partitioning information on the
groups. The implementation came included with the new radix
sort.
* rhyper(nn, m, n, k) no longer returns NA when one of the three
parameters exceeds the maximal integer.
* switch() now warns when no alternatives are provided.
* parallel::detectCores() now has default logical = TRUE on all
platforms - as this was the default on Windows, this change only
affects Sparc Solaris.
Option logical = FALSE is now supported on Linux and recent
versions of OS X (for the latter, thanks to a suggestion of Kyaw
Sint).
* hist() for "Date" or "POSIXt" objects would sometimes give
misleading labels on the breaks, as they were set to the day
before the start of the period being displayed. The display
format has been changed, and the shift of the start day has been
made conditional on right = TRUE (the default). (PR#16679)
* R now uses a new version of the logo (donated to the R Foundation
by RStudio). It is defined in .svg format, so will resize
without unnecessary degradation when displayed on HTML
pages-there is also a vector PDF version. Thanks to Dirk
Eddelbuettel for producing the corresponding X11 icon.
* New function .traceback() returns the stack trace which
traceback() prints.
* lengths() dispatches internally.
* dotchart() gains a pt.cex argument to control the size of points
separately from the size of plot labels. Thanks to Michael
Friendly and Milan Bouchet-Valat for ideas and patches.
* as.roman(ch) now correctly deals with more diverse character
vectors ch; also arithmetic with the resulting roman numbers
works in more cases. (PR#16779)
* prcomp() gains a new option rank. allowing to directly aim for
less than min(n,p) PC's. The summary() and its print() method
have been amended, notably for this case.
* gzcon() gains a new option text, which marks the connection as
text-oriented (so e.g. pushBack() works). It is still always
opened in binary mode.
* The import() namespace directive now accepts an argument except
which names symbols to exclude from the imports. The except
expression should evaluate to a character vector (after
substituting symbols for strings). See Writing R Extensions.
* New convenience function Rcmd() in package tools for invoking R
CMD tools from within R.
* New functions makevars_user() and makevars_site() in package
tools to determine the location of the user and site specific
Makevars files for customizing package compilation.
-------------------------------------------------------------------
Fri Apr 15 08:40:10 UTC 2016 - detlef.steuer@gmx.de
- CHANGES IN R 3.2.5:
BUG FIXES:
• format.POSIXlt() behaved incorrectly in R 3.2.4. E.g. the output
of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"),
usetz = TRUE) ended in two "CEST" time formats.
• A typo in the Makefile for src/extra/xz prevented builds of
liblzma.a. (Notice that this will become unbundled in 3.3.0.)
-------------------------------------------------------------------
Thu Mar 17 09:32:01 UTC 2016 - detlef.steuer@gmx.de
- upstrem releases minorst bug fix release
NEWS: The 3.2.4 release had two annoyances which we would rather
not have in an "ultra-stable" release, designed to hang around
for the duration of the 3.3 series. One was a relatively minor
Makefile issue affecting system using R's bundled lzma library.
The other, rather more serious, affected printing and formatting
of POSIXlt objects, which would unpredictably get the Daylight
Savings Time wrong.
-------------------------------------------------------------------
Fri Mar 11 15:53:46 UTC 2016 - detlef.steuer@gmx.de
- Some version numbers of recommended packages corrected
-------------------------------------------------------------------
Fri Mar 11 15:38:35 UTC 2016 - detlef.steuer@gmx.de
- Release numbers for sub-packages improved
-------------------------------------------------------------------
Fri Mar 11 09:58:13 UTC 2016 - detlef.steuer@gmx.de
- added MakefileTypo.patch to enable building for 12.2
was a one charcter show stopper
-------------------------------------------------------------------
Thu Mar 10 12:52:04 UTC 2016 - detlef.steuer@gmx.de
- upstream release 3.2.4, only minor improvements
CHANGES IN R 3.2.4:
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.
-------------------------------------------------------------------
Mon Mar 7 12:54:57 UTC 2016 - detlef.steuer@gmx.de
- The big split up. What was a monolithic R-base*rpm now is
divided over 30 something packages, with the following layout.
R-base-3.2.3: dummy packages, contains all of R
Use R-base, if you don´t have a good understandig what it means
to install only parts of it!
R-base-devel-3.2.3: dummy, contains R-core-devel
R-core-3.2.3: R core, no packages at all
R-core-devel-3.2.3: devel files
R-core-libs-3.2.3: contains Rlib
R-core-doc-3.2.3: all the documentation of R-core
R-core-packages-3.2.3: dummy package to load all core packages, that are
R-compiler-3.2.3,
R-datasets-3.2.3,
R-grDevices-3.2.3,
R-graphics-3.2.3,
R-grid-3.2.3,
R-methods-3.2.3,
R-parallel-3.2.3,
R-splines-3.2.3,
R-stats-3.2.3,
R-stats4-3.2.3,
R-tcltk-3.2.3,
R-tools-3.2.3,
R-utils-3.2.3.
Each of these packages may be installed alone.
R-recommended-packages-3.2.3: dummy package to load all recommeded
packages, that are
R-boot-1.3.17,
R-class-7.3.14,
R-cluster-2.0.3,
R-codetools-0.2.14,
R-foreign-0.8.66,
R-KernSmooth-2.23.15,
R-lattice-0.20.33,
R-MASS-7.3.45,
R-Matrix-1.2.3, R-Matrix-devel-1.2.3,
R-mgcv-1.8.9,
R-nlme-3.1.122,
R-nnet-7.3.11,
R-rpart-4.1.10,
R-spatial-7.3.11,
R-survival-2.38.3.
Each of these packages may be installed alone.
-------------------------------------------------------------------
Fri Dec 11 08:46:52 UTC 2015 - detlef.steuer@gmx.de
- Upstream release R-3.2.3
CHANGES IN R 3.2.3:
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() and Sys.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.)
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.
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 Herv'e Pag`es 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 M"uller.)
* 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.
-------------------------------------------------------------------
Thu Dec 10 15:48:39 UTC 2015 - detlef.steuer@gmx.de
- Reverse the whole split. Back to the big package.
Had user reports of broken installations.
R-base, R-base-devel and R-base-libs are provided for now.
The big split will come for 3.3.0
-------------------------------------------------------------------
Wed Dec 9 10:11:26 UTC 2015 - detlef.steuer@gmx.de
- R-base was changed from a giant monolith to thirty-some packages.
There were requests to use the libs without the interpreter.
Furthermore it is now possible to use a frugal installation of R.
The following binaries are built now:
R-base-3.2.2-5.1.x86_64.rpm : A Meta-package. Use this, and it looks
just like it looked the last 10 years.
Requires base and recommended packages.
R-base-devel-3.2.2-5.1.x86_64.rpm: Just for backward compatibility.
R-core-3.2.2-5.1.x86_64.rpm
R-core-libs-3.2.2-5.1.x86_64.rpm
R-core-devel-3.2.2-5.1.x86_64.rpm : The R-core packages install
a bare-bones R. No packages inculded.
R-grid-3.2.2-5.1.x86_64.rpm
R-graphics-3.2.2-5.1.x86_64.rpm
R-grDevices-3.2.2-5.1.x86_64.rpm
R-datasets-3.2.2-5.1.x86_64.rpm
R-stats4-3.2.2-5.1.x86_64.rpm
R-methods-3.2.2-5.1.x86_64.rpm
R-tcltk-3.2.2-5.1.x86_64.rpm
R-compiler-3.2.2-5.1.x86_64.rpm
R-parallel-3.2.2-5.1.x86_64.rpm
R-splines-3.2.2-5.1.x86_64.rpm
R-stats-3.2.2-5.1.x86_64.rpm
R-utils-3.2.2-5.1.x86_64.rpm
R-tools-3.2.2-5.1.x86_64.rpm : All the base packages.
R-recommended-3.2.2-5.1.x86_64.rpm : A meta-package including all
recommended packages.
R-cluster-2.0.3-5.1.x86_64.rpm
R-nlme-3.1.121-5.1.x86_64.rpm
R-lattice-0.20.33-5.1.x86_64.rpm
R-class-7.3.13-5.1.x86_64.rpm
R-Matrix-devel-1.2.2-5.1.x86_64.rpm
R-codetools-0.2.14-5.1.x86_64.rpm
R-survival-2.38.3-5.1.x86_64.rpm
R-rpart-4.1.10-5.1.x86_64.rpm
R-MASS-7.3.43-5.1.x86_64.rpm
R-mgcv-1.8.7-5.1.x86_64.rpm
R-foreign-0.8.65-5.1.x86_64.rpm
R-nnet-7.3.10-5.1.x86_64.rpm
R-Matrix-1.2.2-5.1.x86_64.rpm
R-boot-1.3.17-5.1.x86_64.rpm
R-KernSmooth-2.23.15-5.1.x86_64.rpm
R-spatial-7.3.10-5.1.x86_64.rpm : All recommended packaged.
Note: They now have their own version
numbers, so it should be much easier to
use newer Versions of the recommended
packages.
And the source RPM for all the above.
R-base-3.2.2-5.1.src.rpm
-------------------------------------------------------------------
Wed Aug 19 08:47:27 UTC 2015 - badshah400@gmail.com
- Disable building man files for openSUSE:42.
-------------------------------------------------------------------
Mon Aug 17 14:41:24 UTC 2015 - detlef.steuer@gmx.de
- Upstream release 3.2.2
- Most important
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 for libcurl 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:
* cmdscale() gets new option list. for increased flexibility when a
list should be returned.
* configure now supports texinfo version 6.0, which (unlike the
change from 4.x to 5.0) is a minor update. (Wish of PR#16456.)
* (Non-Windows only) download.file() with default method = "auto"
now chooses "libcurl" if that is available and a https:// or
ftps:// URL is used.
* (Windows only) setInternet2(TRUE) is now the default. The
command-line option --internet2 and environment variable
R_WIN_INTERNET2 are now ignored.
Thus by default the "internal" method for download.file() and
url() uses the "wininet" method: to revert to the previous
default use setInternet2(FALSE).
This means that https:// can be read by default by
download.file() (they have been readable by file() and url()
since R 3.2.0).
There are implications for how proxies need to be set (see
?download.file): also, cacheOK = FALSE is not supported.
* chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
in preference to HTTP mirrors. This changes the interpretation
of their ind arguments: see their help pages.
* capture.output() gets optional arguments type and split to pass
to sink(), and hence can be used to capture messages.
C-LEVEL FACILITIES:
* Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
the alloca.h header (it is needed to define alloca on Solaris and
AIX, at least: see 'Writing R Extensions' for how to use it).
INSTALLATION and INCLUDED SOFTWARE:
* The libtool script generated by configure has been modified to
support FreeBSD >= 10 (PR#16410).
BUG FIXES:
* The HTML help page links to demo code failed due to a change in R
3.2.0. (PR#16432)
* If the na.action argument was used in model.frame(), the original
data could be modified. (PR#16436)
* getGraphicsEvent() could cause a crash if a graphics window was
closed while it was in use. (PR#16438)
* matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
"expression".
* strptime() could overflow the allocated storage on the C stack
when the timezone had a non-standard format much longer than the
standard formats. (Part of PR#16328.)
* options(OutDec = s) now signals a warning (which will become an
error in the future) when s is not a string with exactly one
character, as that has been a documented requirement.
* prettyNum() gains a new option input.d.mark which together with
other changes, e.g., the default for decimal.mark, fixes some
format()ting variants with non-default getOption("OutDec") such
as in PR#16411.
* download.packages() failed for type equal to either "both" or
"binary". (Reported by Dan Tenenbaum.)
* The dendrogram method of labels() is much more efficient for
large dendrograms, now using rapply(). (Comment #15 of PR#15215)
* The "port" algorithm of nls() could give spurious errors.
(Reported by Radford Neal.)
* Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited class.
Fixing this requires adding the ability for methods to be
"external", with the object supplied explicitly as the first
argument, named .self. See "Inter-Package Superclasses" in the
documentation.
* readBin() could fail on the SPARC architecture due to alignment
issues. (Reported by Radford Neal.)
* qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
of returning NaN. (PR#16475)
* Auto-printing of S3 and S4 values now searches for print() in the
base namespace and show() in the methods namespace instead of
searching the global environment.
* polym() gains a coefs = NULL argument and returns class "poly"
just like poly() which gets a new simple=FALSE option. They now
lead to correct predict()ions, e.g., on subsets of the original
data.
* rhyper(nn, <large>) now works correctly. (PR#16489)
* ttkimage() did not (and could not) work so was removed. Ditto for
tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
missing subcommands for Tk's image command: ttkscale(),
ttkspinbox(), tkimage.delete(), tkimage.height(),
tkimage.inuse(), tkimage.type(), tkimage.types(),
tkimage.width(). (PR#15372, PR#16450)
* getClass("foo") now also returns a class definition when it is
found in the cache more than once.
-------------------------------------------------------------------
Thu Jun 18 11:59:24 UTC 2015 - detlef.steuer@gmx.de
- Upstream release 3.2.1
- Improvement of build: include libcurl and texlive-dvips/
texlive-hevetic
- Most important
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:
* acf() and ccf() now guarantee values strictly in [-1,1] (instead
of sometimes very slightly outside). PR#15832.
* as.integer("111111111111") now gives NA (with a warning) as it
does for the corresponding numeric or negative number coercions.
Further, as.integer(M + 0.1) now gives M (instead of NA) when M
is the maximal representable integer.
* On some platforms nchar(x, "c") and nchar(x, "w") would return
values (possibly NA) for inputs which were declared to be UTF-8
but were not, or for invalid strings without a marked encoding in
a multi-byte locale, rather than give an error. Additional
checks have been added to mitigate this.
* apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
containing "X" and "Y" (as in R < 3.2.0).
* (Windows only) In some cases, the --clean option to R CMD INSTALL
could fail. (PR#16178)
* (Windows only) choose.files() would occasionally include
characters from the result of an earlier call in the result of a
later one. (PR#16270)
* A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
URLs. (PR#16329)
* Rscript and command line R silently ignored incomplete statements
at the end of a script; now they are reported as parse errors.
(PR#16350)
* Parse data for very long strings was not stored. (PR#16354)
* plotNode(), the workhorse of the plot method for "dendrogram"s is
no longer recursive, thanks to Suharto Anggono, and hence also
works for deeply nested dendrograms. (PR#15215)
* The parser could overflow internally when given numbers in
scientific format with extremely large exponents. (PR#16358)
* If the CRAN mirror was not set, install.packages(type = "both")
and related functions could repeatedly query the user for it.
(Part of PR#16362)
* The low-level functions .rowSums() etc. did not check the length
of their argument, so could segfault. (PR#16367)
* The quietly argument of library() is now correctly propagated
from .getRequiredPackages2().
* Under some circumstances using the internal PCRE when building R
fron source would cause external libs such as -llzma to be
omitted from the main link.
* The .Primitive default methods of the logic operators, i.e., !, &
and |, now give correct error messages when appropriate, e.g.,
for `&`(TRUE) or `!`(). (PR#16385)
* cummax(x) now correctly propagates NAs also when x is of type
integer and begins with an NA.
* summaryRprof() could fail when the profile contained only two
records. (PR#16395)
* HTML vignettes opened using vignette() did not support links into
the rest of the HTML help system. (Links worked properly when
the vignette was opened using browseVignettes() or from within
the help system.)
* arima(*, xreg = .) (for d >= 1) computes estimated variances
based on a the number of effective observations as in R version
3.0.1 and earlier. (PR#16278)
* slotNames(.) is now correct for "signature" objects (mostly used
internally in methods).
* On some systems, the first string comparison after a locale
change would result in NA.
-------------------------------------------------------------------
Thu Apr 16 14:52:43 UTC 2015 - detlef.steuer@gmx.de
- Upstream release 3.2.0
- Most important
CHANGES IN 3.2.0:
NEW FEATURES:
* anyNA() gains a recursive argument.
* When x is missing and names is not false (including the default
value), Sys.getenv(x, names) returns an object of class "Dlist"
and hence prints tidily.
* (Windows.) shell() no longer consults the environment variable
SHELL: too many systems have been encountered where it was set
incorrectly (usually to a path where software was compiled, not
where it was installed). R_SHELL, the preferred way to select a
non-default shell, can be used instead.
* Some unusual arguments to embedFonts() can now be specified as
character vectors, and the defaults have been changed
accordingly.
* Functions in the Summary group duplicate less. (PR#15798)
* (Unix-alikes.) system(cmd, input = ) now uses
'shell-execution-environment' redirection, which will be more
natural if cmd is not a single command (but requires a
POSIX-compliant shell). (Wish of PR#15508)
* read.fwf() and read.DIF() gain a fileEncoding argument, for
convenience.
* Graphics devices can add attributes to their description in
.Device and .Devices. Several of those included with R use a
"filepath" attribute.
* pmatch() uses hashing in more cases and so is faster at the
expense of using more memory. (PR#15697)
* pairs() gains new arguments to select sets of variables to be
plotted against each other.
* file.info(, extra_cols = FALSE) allows a minimal set of columns
to be computed on Unix-alikes: on some systems without
properly-configured caching this can be significantly faster with
large file lists.
* New function dir.exists() in package base to test efficiently
whether one or more paths exist and are directories.
* dput() and friends gain new controls hexNumeric and digits17
which output double and complex quantities as, respectively,
binary fractions (exactly, see sprintf("%a")) and as decimals
with up to 17 significant digits.
* save(), saveRDS() and serialize() now support ascii = NA which
writes ASCII files using sprintf("%a") for double/complex
quantities. This is read-compatible with ascii = TRUE but avoids
binary->decimal->binary conversions with potential loss of
precision. Unfortunately the Windows C runtime's lack of C99
compliance means that the format cannot be read correctly there
in R before 3.1.2.
* The default for formatC(decimal.mark =) has been changed to be
getOption("OutDec"); this makes it more consistent with format()
and suitable for use in print methods, e.g. those for classes
"density", "ecdf", "stepfun" and "summary.lm".
getOption("OutDec") is now consulted by the print method for
class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
when constructing labels and for the report from legend(trace =
TRUE).
(In part, wish of PR#15819.)
* printNum() and hence format() and formatC() give a warning if
big.mark and decimal.mark are set to the same value (period and
comma are not uncommonly used for each, and this is a check that
conventions have not got mixed).
* merge() can create a result which uses long vectors on 64-bit
platforms.
* dget() gains a new argument keep.source which defaults to FALSE
for speed (dput() and dget() are most often used for data objects
where this can make dget() many times faster).
* Packages may now use a file of common macro definitions in their
help files, and may import definitions from other packages.
* A number of macros have been added in the new share/Rd directory
for use in package overview help pages, and promptPackage() now
makes use of them.
* tools::parse_Rd() gains a new permissive argument which converts
unrecognized macros into text. This is used by
utils:::format.bibentry to allow LaTeX markup to be ignored.
* options(OutDec =) can now specify a multi-byte character, e.g.,
options(OutDec = "\u00b7") in a UTF-8 locale.
* is.recursive(x) is no longer true when x is an external pointer,
a weak reference or byte code; the first enables all.equal(x, x)
when x <- getClass(.).
* ls() (aka objects()) and as.list.environment() gain a new
argument sorted.
* The "source" attribute (which has not been added to functions by
R since before R version 2.14.0) is no longer treated as special.
* Function returnValue() has been added to give on.exit() code
access to a function's return value for debugging purposes.
* crossprod(x, y) allows more matrix coercions when x or y are
vectors, now equalling t(x) %*% y in these cases (also reported
by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in
more cases with vector arguments.
* Utility function dynGet() useful for detecting cycles, aka
infinite recursions.
* The byte-code compiler and interpreter include 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.
* apply(m, 2, identity) is now the same as the matrix m when it has
_named_ row names.
* A new function debuggingState() has been added, allowing to
temporarily turn off debugging.
* example() gets a new optional argument run.donttest and
tools::Rd2ex() a corresponding commentDonttest, with a default
such that example(..) in help examples will run \donttest code
only if used interactively (a change in behaviour).
* rbind.data.frame() gains an optional argument make.row.names, for
potential speedup.
* New function extSoftVersion() to report on the versions of
third-party software in use in this session. Currently reports
versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
the iconv implementation.
A similar function grSoftVersion() in package grDevices reports
on third-party graphics software.
Function tcltk::tclVersion() reports the Tcl/Tk version.
* Calling callGeneric() without arguments now works with primitive
generics to some extent.
* vapply(x, FUN, FUN.VALUE) is more efficient notably for large
length(FUN.VALUE); as extension of PR#16061.
* as.table() now allows tables with one or more dimensions of
length 0 (such as as.table(integer())).
* names(x) <- NULL now clears the names of call and ... objects.
* library() will report a warning when an insufficient dependency
version is masking a sufficient one later on the library search
path.
* A new plot() method for class "raster" has been added.
* New check_packages_in_dir_changes() function in package tools for
conveniently analyzing how changing sources impacts the check
results of their reverse dependencies.
* Speed-up from Peter Haverty for ls() and
methods:::.requirePackage() speeding up package loading.
(PR#16133)
* New get0() function, combining exists() and get() in one call,
for efficiency.
* match.call() gains an envir argument for specifying the
environment from which to retrieve the ... in the call, if any;
this environment was wrong (or at least undesirable) when the
definition argument was a function.
* topenv() has been made .Internal() for speedup, based on Peter
Haverty's proposal in PR#16140.
* getOption() no longer calls options() in the main case.
* Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
for Internet access:
* capabilities("libcurl") reports if this is available.
* libcurlVersion() reports the version in use, and other
details of the "libcurl" build including which URL schemes it
supports.
* curlGetHeaders() retrieves the headers for http://, https://,
ftp:// and ftps:// URLs: analysis of these headers can
provide insights into the `existence' of a URL (it might for
example be permanently redirected) and is so used in R CMD
check --as-cran.
* download.file() has a new optional method "libcurl" which
will handle more URL schemes, follow redirections, and allows
simultaneous downloads of multiple URLs.
* url() has a new method "libcurl" which handles more URL
schemes and follows redirections. The default method is
controlled by a new option url.method, which applies also to
the opening of URLs _via_ file() (which happens implicitly in
functions such as read.table.)
* When file() or url() is invoked with a https:// or ftps://
URL which the current method cannot handle, it switches to a
suitable method if one is available.
* (Windows.) The DLLs internet.dll and internet2.dll have been
merged. In this version it is safe to switch (repeatedly)
between the internal and Windows internet functions within an R
session.
The Windows internet functions are still selected by flag
--internet2 or setInternet2(). This can be overridden for an
url() connection _via_ its new method argument.
download.file() has new method "wininet", selected as the default
by --internet2 or setInternet2().
* parent.env<- can no longer modify the parent of a locked
namespace or namespace imports environment. Contributed by Karl
Millar.
* New function isLoadedNamespace() for readability and speed.
* names(env) now returns all the object names of an environment
env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
and also to the names of the corresponding list,
names(as.list(env, all.names = TRUE)). Note that although
names() returns a character vector, the names have no particular
ordering.
* The memory manager now grows the heap more aggressively. This
reduces the number of garbage collections, in particular while
data or code are loaded, at the expense of slightly increasing
the memory footprint.
* New function trimws() for removing leading/trailing whitespace.
* cbind() and rbind() now consider S4 inheritance during S3
dispatch and also obey deparse.level.
* cbind() and rbind() will delegate recursively to methods::cbind2
(methods::rbind2) when at least one argument is an S4 object and
S3 dispatch fails (due to ambiguity).
* (Windows.) download.file(quiet = FALSE) now uses text rather
than Windows progress bars in non-interactive use.
* New function hsearch_db() in package utils for building and
retrieving the help search database used by help.search(), along
with functions for inspecting the concepts and keywords in the
help search database.
* New function .getNamespaceInfo(), a no-check version of
getNamespaceInfo() mostly for internal speedups.
* The help search system now takes \keyword entries in Rd files
which are not standard keywords (as given in KEYWORDS in the R
documentation directory) as concepts. For standard keyword
entries the corresponding descriptions are additionally taken as
concepts.
* New lengths() function for getting the lengths of all elements in
a list.
* New function toTitleCase() in package tools, tailored to package
titles.
* The matrix methods of cbind() and rbind() allow matrices as
inputs which have 2^31 or more elements. (For cbind(), wish of
PR#16198.)
* The default method of image() has an explicit check for a numeric
or logical matrix (which was always required).
* URLencode() will not by default encode further URLs which appear
to be already encoded.
* BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
fitted models, as nobs(mod) now gives the number of "used"
observations for such models. This fixes PR#16198, quite
differently than proposed there.
* The print() methods for "htest", "pairwise.htest" and
"power.htest" objects now have a digits argument defaulting to (a
function of) getOption("digits"), and influencing all printed
numbers coherently. Unavoidably, this changes the display of
such test results in some cases.
* Code completion for namespaces now recognizes all loaded
namespaces, rather than only the ones that are also attached.
* The code completion mechanism can now be replaced by a
user-specified completer function, for (temporary) situations
where the usual code completion is inappropriate.
* unzip() will now warn if it is able to detect truncation when
unpacking a file of 4GB or more (related to PR#16243).
* methods() reports S4 in addition to S3 methods; output is
simplified when the class argument is used. .S3methods() and
methods::.S4methods() report S3 and S4 methods separately.
* Higher order functions such as the apply functions and Reduce()
now force arguments to the functions they apply in order to
eliminate undesirable interactions between lazy evaluation and
variable capture in closures. This resolves PR#16093.
INSTALLATION and INCLUDED SOFTWARE:
* The \donttest sections of R's help files can be tested by
make check TEST_DONTTEST=TRUE .
* It is possible to request the use of system valgrind headers
_via_ configure option --with-system-valgrind-headers: note the
possible future incompatibility of such headers discussed in the
'R Installation and Administration' manual. (Wish of PR#16068.)
* The included version of liblzma has been updated to xz-utils
5.0.7 (minor bug fixes from 5.0.5).
* configure options --with-system-zlib, --with-system-bzlib and
--with-system-pcre are now the default. For the time being there
is fallback to the versions included in the R sources if no
system versions are found or (unlikely) if they are too old.
Linux users should check that the -devel or -dev versions of
packages zlib, bzip2/libbz2 and pcre as well as
xz-devel/liblzma-dev (or similar names) are installed.
* configure by default looks for the texi2any script from texinfo
5.1 or later, rather than the makeinfo program. (makeinfo is a
link to the Perl script texi2any in texinfo 5.x.)
* R CMD INSTALL gains an option --built-timestamp=STAMP allowing
100% reproducible package building, thanks to Dirk Eddelbuettel.
UTILITIES:
* There is support for testing the \dontrun and \donttest parts of
examples in packages.
tools::testInstalledPackage() accepts new arguments
commentDontrun = FALSE and commentDonttest = FALSE.
R CMD check gains options --run-dontrun and --run-donttest.
* The HTML generated by tools::Rd2HTML() and tools::toHTML()
methods is now 'XHTML 1.0 Strict'.
* The compiler package's utility function setCompilerOptions() now
returns the old values invisibly. The initial optimization level
can also be set with the environment variable
R_COMPILER_OPTIMIZE.
* R CMD build adds a NeedsCompilation field if one is not already
present in the DESCRIPTION file.
* R CMD check gains option --test-dir to specify an alternative set
of tests to run.
* R CMD check will now by default continue with testing after many
types of errors, and will output a summary count of errors at the
end if any have occurred.
* R CMD check now checks that the Title and Description fields are
correctly terminated.
* R CMD check --as-cran now:
* checks a README.md file can be processed: this needs pandoc
installed.
* checks the existence and accessibility of URLs in the
DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the
help files (provided the build has libcurl support).
* reports non-ASCII characters in R source files when there is
no package encoding declared in the DESCRIPTION file.
* reports (apparent) S3 methods exported but not registered.
* reports overwriting registered S3 methods from
base/recommended packages. (Such methods are replaced in the
affected package for the rest of the session, even if the
replacing namespace is unloaded.)
* reports if the Title field does not appear to be in title
case (see 'Writing R Extensions': there may be false
positives, but note that technical words should be
single-quoted and will then be accepted).
Most of these checks can also be selected by environment
variables: see the 'R Internals' manual.
C-LEVEL FACILITIES:
* New C API utility logspace_sum(logx[], n).
* Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
default) to Rf_rbinom_mu etc. This requires packages using them
to be re-installed.
* .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
arguments are duplicated if DUP = TRUE would do so. As their
help has long said, .Call() is much preferred.
* New entry point R_allocLD, like R_alloc but guaranteed to have
sufficient alignment for long double pointers.
* isPairList() now returns TRUE for DOTSXP.
WINDOWS BUILD CHANGES:
A number of changes to the Windows build system are in development.
The following are currently in place.
* Installation using external binary distributions of zlib, bzip2,
liblzma, pcre, libpng, jpeglib and libtiff is now required, and
the build instructions have been revised.
* A new make target rsync-extsoft has been added to obtain copies
of the external libraries from CRAN.
* Building the manuals now requires texi2any from texinfo 5.1 or
later. CRAN binary builds include the manuals, but by default
builds from source will not, and they will be accessed from CRAN.
See the comments in src/gnuwin32/MkRules.dist for how to specify
the location of texi2any.
* (Windows) Changes have been made to support an experimental
Windows toolchain based on GCC 4.9.2. The default toolchain
continues to be based on GCC 4.6.3, as the new toolchain is not
yet stable enough. A change to a new toolchain is expected
during the R 3.2.x lifetime.
PACKAGE INSTALLATION:
* (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
(which has not been documented for a long time) now requires an
external libz.a to be available (it is part of the 'goodies' used
to compile Windows binary packages). It would be simpler to use
-lz instead.
* The default for option pkgType on platforms using binary packages
is now "both", so source packages will be tried if binary
versions are not available or not up to date.
There are options for what install.packages(type = "both")
(possibly called _via_ update.packages()) will do if compilation
of a source package is desirable: see ?options (under utils).
If you intend not to accept updates as source packages, you
should use update.packages(type = "binary").
DEPRECATED AND DEFUNCT:
* download.file(method = "lynx") is defunct.
* Building R using the included versions of zlib, bzip2, xz and
PCRE is deprecated: these are frozen (bar essential bug-fixes)
and will be removed for R 3.3.0.
* The configure option --with-valgrind-instrumentation=3 has been
withdrawn, as it did not work with recent valgrind headers: it is
now treated as level 2.
* The MethodsList class in package methods had been deprecated in R
2.11.0 and is defunct now. Functions using it are defunct if
they had been deprecated in R 2.11.0, and are deprecated now,
otherwise.
BUG FIXES:
* Fixed two obscure bugs in pairlist subassignment, reported by
Radford Neal as part of pqR issue 16.
* Fixes for bugs in handling empty arguments and argument matching
by name in log().
* all.equal() gains methods for environments and refClasses.
* [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
class information by the S3 methods.
* callNextMethod() should now work within a .local call when ... is
absent from formals(.local).
* dput(pairlist(x)) generates a call to the pairlist constructor
instead of the list constructor.
* Fix missing() when arguments are propagated through ... .
(PR#15707)
* eigen(m) now defaults to symmetric = TRUE even when the dimnames
are asymmetric if the matrix is otherwise symmetric. (PR#16151)
* Fix issues with forwarding ... through callGeneric() and
callNextMethod(). (PR#16141)
* callGeneric() now works after a callNextMethod().
* Subclass information is kept consistent when replacing an
ordinary S4 class with an "old class" _via_ the S4Class argument
to setOldClass(). Thus, for example, a data.frame is valid for a
list argument in the signature, and a factor is valid for vector
arguments.
* In qbeta() the inversion of pbeta() is much more sophisticated.
This works better in corner cases some of which failed completely
previously (PR#15755), or were using too many iterations.
* Auto-printing no longer duplicates objects when printing is
dispatched to a method.
* kmeans(x, k) would fail when nrow(x) >= 42949673. (Comment 6 of
PR#15364)
* 'Abbreviated' locale-specific day and month names could have been
truncated in those rare locales where there are the same as the
full names.
* An irrelevant warning message from updating subclass information
was silenced (the namespace would not be writable in this case).
-------------------------------------------------------------------
Mon Mar 9 10:26:51 UTC 2015 - detlef.steuer@gmx.de
- Upstream release 3.1.3
- Most important
CHANGES IN R 3.1.3:
NEW FEATURES:
* The internal method of download.file() can now handle files
larger than 2GB on 32-bit builds which support such files (tested
on 32-bit R running on 64-bit Windows).
* kruskal.test() warns on more types of suspicious input.
* The as.dendrogram() method for "hclust" objects gains a check
argument protecting against memory explosion for invalid inputs.
* capabilities() has a new item long.double which indicates if the
build uses a long double type which is longer than double.
* nlm() no longer modifies the callback argument in place (a new
vector is allocated for each invocation, which mimics the
implicit duplication that occurred in R < 3.1.0); note that this
is a change from the previously documented behavior. (PR#15958)
* icuSetCollate() now accepts locale = "ASCII" which uses the basic
C function strcmp and so collates strings byte-by-byte in
numerical order.
* sessionInfo() tries to report the OS version in use (not just
that compiled under, and including details of Linux
distributions).
* model.frame() (used by lm() and many other modelling functions)
now warns when it drops contrasts from factors. (Wish of
PR#16119)
* install.packages() and friends now accept the value type =
"binary" as a synonym for the native binary type on the platform
(if it has one).
* Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type and
repos = NULL will be inferred.
* New function pcre_config() to report on some of the configuration
options of the version of PCRE in use. In particular, this
reports if regular expressions using \p{xx} are supported.
* (Windows.) download.file(cacheOK = FALSE) is now supported when
internet2.dll is used.
* browseURL() has been updated to work with Firefox 36.0 which has
dropped support for the -remote interface.
INSTALLATION and INCLUDED SOFTWARE:
* The included version of PCRE has been updated to 8.36.
* configure accepts MAKEINFO=texi2any as another way to ensure
texinfo 5.x is used when both 5.x and 4.x are installed.
UTILITIES:
* R CMD check now checks the packages used in \donttest sections of
the examples are specified in the DESCRIPTION file. (These are
needed to run the examples interactively.)
* R CMD check checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
R CMD build will correct line endings in all Makefiles, not just
those in the src directory.
* R CMD check notes uses of library() and require() in package
code: see the section 'Suggested packages' of 'Writing R
Extensions' for good practice.
DEPRECATED AND DEFUNCT:
* The configure option --with-valgrind-instrumentation=3 is
deprecated and will be removed in R 3.2.0.
BUG FIXES:
* (Windows.) Rscript.exe was missing a manifest specifying the
modern style for common controls (e.g., the download progress
bar).
* If a package had extra documentation files but no vignette, the
HTML help system produced an empty index page.
* The parser now gives an error if a null character is included in
a string using Unicode escapes. (PR#16046)
* qr.Q() failed on complex arguments due to pre-3.0(!) typo.
(PR#16054)
* abs() failed with named arguments when the argument was complex.
(PR#16047)
* "noquote" objects may now be used as columns in dataframes.
(PR#15997)
* Some values with extremely long names were printed incorrectly.
(PR#15999)
* Extremely large exponents on zero expressed in scientific
notation (e.g. 0.0e50000) could give NaN. (PR#15976)
* download.file() reported downloaded sizes as 0KB if less than
1MB, only for R 3.1.2 and only on big-endian platforms.
* prompt() did not escape percent signs in the automatically
generated usage section of help files.
* drop.terms() dropped some of the attributes of the object it was
working with. (PR#16029)
* (Windows.) The command completion in Rgui.exe messed up the
console. (PR#15791)
* (Windows.) The choose.files() command returned a blank string
when the user asked for a single file but cancelled the request.
(PR#16074)
* Math2 S4 group generics failed to correctly dispatch "structure"-
and "nonStructure"-derived classes.
* loadNamespace() imposed undocumented restrictions on the
versionCheck parameter. (Reported by Geoff Lee.)
* Rare over-runs detected by AddressSanitizer in substr() and its
replacement version have been avoided.
_Inter alia_ that fix gives the documented behaviour for
substr(x, 1, 2) <- "" (subsequently reported as PR#16214).
* Loading packages incorrectly defining an S4 generic followed by a
function of the same name caused an erroneous cyclic namespace
dependency error.
* Declared vignette encodings are now always passed to the vignette
engine.
* Port Tomas Kalibera's fix from R-devel that restores the
loadMethod() fast path, effectively doubling the speed of S4
dispatch.
* power.t.test() and power.prop.test() now make use of the
extendInt option of uniroot() and hence work in more extreme
cases. (PR#15792)
* If a package was updated and attached when its namespace was
already loaded, it could end up with parts from one version and
parts from the other. (PR#16120)
* tools:::.Rdconv() didn't accept --encoding= due to a typo.
(PR#16121)
* Unix-alike builds without a suitable makeinfo were documented to
link the missing HTML manuals to CRAN, but did not.
* save(*, ascii=TRUE) and load() now correctly deal with NaN's.
(PR#16137)
* split.Date() retains fractional representations while avoiding
incomplete class propagation.
* R_ext/Lapack.h had not been updated for changes made by LAPACK to
the argument lists of its (largely internal) functions dlaed2 and
dlaed3. (PR#16157)
* RShowDoc("NEWS", "txt") had not been updated for the layout
changes of R 3.1.0.
* The xtfrm() method for class "Surv" has been corrected and its
description expanded.
* mode(x) <- y would incorrectly evaluate x before changing its
mode. (PR#16215)
* besselJ(1, 2^64) and besselY(..) now signal a warning, returning
NaN instead of typically segfaulting. (Issue 3 of PR#15554)
* HTML conversion of \href markup in .Rd files did not remove the
backslash from \% and so gave an invalid URL. In a related
change, the \ escape is now required in such URLs.
-------------------------------------------------------------------
Fri Dec 12 13:16:25 UTC 2014 - sbahling@suse.com
- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
older SLE releases).
-------------------------------------------------------------------
Fri Oct 31 11:59:25 UTC 2014 - detlef.steuer@gmx.de
- Upstream release 3.1.2
- Most important
CHANGES IN R 3.1.2:
NEW FEATURES:
* embedFonts() now defaults to format = "ps2write" for .ps and .eps
files. This is available in Ghostscript 9.x (since 2010) whereas
the previous default, format = "pswrite", was removed in
Ghostscript 9.10.
* For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
point mass at exp(mulog) rather than return NaN (for an error).
* capabilities() now reports if ICU is compiled in for use for
collation (it is only actually used if a suitable locale is set
for collation, and never for a C locale).
* (OS X only.) Package tcltk checks when loaded if it is linked
against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
component and the X11 libraries are installed. This allows more
informative error messages to be given advising the installation
of the missing component or of XQuartz.
The X11() device and X11-based versions of the data editor and
viewer (invoked by edit() and View() for data frames and matrices
from command-line R) check that the X11 libraries are installed
and if not advises installing XQuartz.
* icuSetCollate() allows locale = "default", and locale = "none" to
use OS services rather than ICU for collation.
Environment variable R_ICU_LOCALE can be used to set the default
ICU locale, in case the one derived from the OS locale is
inappropriate (this is currently necessary on Windows).
* New function icuGetCollate() to report on the ICU collation
locale in use (if any).
* utils::URLencode() was updated to use unreserved and reserved
characters from RFC 3986, <URL:
http://tools.ietf.org/html/rfc3986>, instead of RFC 1738.
* unique(warnings()) and c(warnings()) are now supported.
* The Bioconductor 'version' used by setRepositories() now defaults
to 3.0. (It can be set at runtime _via_ environment variable
R_BIOC_VERSION.)
INSTALLATION and INCLUDED SOFTWARE:
* The configure script reports on the more important
capabilities/options which will not be compiled in.
More types of external BLAS are recognized by name in that
report.
* When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
flag is placed earlier in the link commands used during
installation and when packages are installed: this helps ensure
that the current build has priority if an R shared library has
already been installed by e.g. install-libR in a library
mentioned in LDFLAGS (and not in 'your system's library
directory' as documented). (Wish of PR#15790.)
* LaTeX package upquote is no longer required for R's use of
inconsolata.
* (Windows only) If both 32 and 64 bit versions of R are installed,
the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
(To run 32 bit R, overwrite these files with copies of
bin/i386/Rfe.exe.)
UTILITIES:
* Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
the VignetteBuilder packages available even if they are listed in
Suggests, since they are needed to recognise and process
non-Sweave vignettes.
* R CMD check now reports empty importFrom declarations in a
NAMESPACE file, as these are common errors (writing
importFrom(Pkg) where import(Pkg) was intended).
* R CMD check now by default checks code usage directly on the
package namespace without loading and attaching the package and
its suggests and enhances. For good practice with packages in
the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'. For
use of lazy-data objects in the package's own code, see ?data.
BUG FIXES:
* dmultinom() did not handle non-finite probabilities correctly.
* prettyNum(x, zero.print=*) now also works when x contains NAs.
* A longstanding bug exhibited by nlminb() on Windows was traced to
a compiler bug in gcc 4.6.3; a workaround has been put in place.
(PR#15244 and PR#15914).
* Rendering of \command in HTML versions of help pages has been
improved: this is particularly evident on the help page for
INSTALL.
* as.hexmode(x) and as.octmode(x) now behave correctly for some
numeric x, e.g., c(NA, 1) or c(1, pi).
* drop1() failed if the scope argument had no variables to drop.
(PR#15935)
* edit() (and hence fix()) failed if an object had a non-character
attribute named "source" (an attribute that had been used in R
prior to version 2.14.0).
* callGeneric() could fail if the generic had ... as a formal
argument. (PR#15937).
* Forking in package parallel called C entry point exit in the
child. This was unsafe (_exit should have been called), and
could flush stdin of the main R process (seen most often on
Solaris).
As good practice, stdout is now flushed before forking a child.
* R objects such as list(`a\b` = 1) now print correctly.
* getAnywhere("C_pbinom") now returns correctly a single object
(rather than unlisting it).
* The confint() method for nls() fits failed it these has specified
parameter limits despite using an algorithm other than "port".
(PR#15960)
* Subclassing an S4 class failed if the class required arguments to
the generator, through its initialize() method.
* removeSource() did not properly handle expressions containing
arguments that were supplied as missing, e.g. x[i,]. (PR#15957)
* as.environment(list()) now works, and as.list() of such an
environment is now the same as list().
* Several tcltk functions failed when run in unusual environments.
(PR#15970)
* options(list()) now works (trivially). (PR#15979)
* merge(<dendrogram>, ..) now works correctly for two `independent'
dendrograms (PR#15648), and still compatibly via adjust = "auto"
e.g. for two branches of an existing dendrogram.
* The plot method for "hclust" objects gets an optional argument
check; When that is true (the default) it checks more carefully
for valid input.
* (Windows only) If a user chose to install 64 bit R but not 32 bit
R, the bin/R and bin/Rscript executables failed to run.
(PR#15981)
* Various possible buffer overruns have been prevented, and missed
memory protection added. (PR#15990)
* Rscript no longer passes --args to R when there are no extra
("user") arguments.
* objects like getClass("refClass")@prototype now print() and str()
without error.
* identical() now also looks at the S4 bit.
* hist(x, breaks) is more robust in adding a small fuzz to few
breaks when some are very large. (PR#15988)
* sub() and gsub() did not handle regular expressions like "\s{2,}"
properly if the text contained NA or non-ascii elements in a
UTF-8 locale. Part of this was due to a bug in the TRE library.
(PR#16009)
* RShowDoc("NEWS") now displays the PDF version.
* Matrices and arrays with last dimension zero did not print at all
or incompletely. (PR#16012)
* plot.histogram() and hence hist() now respect the xaxs, yaxs and
lab graphics parameters. (PR#16021)
* bw.SJ(x) and other bw.*() no longer segfault when x contains
non-finite values. (PR#16024)
* R CMD Rd2pdf unintentionally ignored its --os option.
* The internal method of download.file() was not reporting file
sizes and progress correctly on files larger than 2GB (inherited
from libxml2). This is corrected for 64-bit builds (32-bit
platforms may not support such files, but where possible will be
supported in future versions of R).
* Work around a bug in OS X Yosemite where key environment
variables may be duplicated causing issues in subprocesses. The
duplicates are now removed on R startup (via Rprofile).
(PR#16042)
* Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
latest XQuartz.
-------------------------------------------------------------------
Thu Jul 10 12:35:42 UTC 2014 - detlef.steuer@gmx.de
- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
CHANGES IN R 3.1.1:
CHANGES IN R 3.1.1:
NEW FEATURES:
* When attach() reports conflicts, it does so compatibly with
library() by using message().
* R CMD Sweave no longer cleans any files by default, compatibly
with versions of R prior to 3.1.0. There are new options
--clean, --clean=default and --clean=keepOuts.
* tools::buildVignette() and tools::buildVignettes() with clean =
FALSE no longer remove any created files. buildvignette() gains
a keep argument for more cleaning customization.
* The Bioconductor 'version' used by setRepositories() can now be
set by environment variable R_BIOC_VERSION at runtime, not just
when R is installed. (It has been stated that Bioconductor will
switch from 'version' 2.14 to 'version' 3.0 during the lifetime
of the R 3.1 series.)
* Error messages from bugs in embedded Sexpr code in Sweave
documents now report the source location.
* type.convert(), read.table() and similar read.*() functions get a
new numerals argument, specifying how numeric input is converted
when its conversion to double precision loses accuracy. The
default value, "allow.loss" allows accuracy loss, as in R
versions before 3.1.0.
* For some compilers, integer addition could overflow without a
warning. R's internal code for both integer addition and
subtraction is more robust now. (PR#15774)
* The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().
* dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
for a = 0, b = 0, or infinite a and b (where they typically
returned NaN before).
* Many package authors report that the RStudio graphics device does
not work correctly with their package's use of dev.new(). The
new option dev.new(noRStudioGD = TRUE) replaces the RStudio
override by the default device as selected by R itself, still
respecting environment variables R_INTERACTIVE_DEVICE and
R_DEFAULT_DEVICE.
* readRDS() now returns visibly.
* Modifying internal logical scalar constants now results in an
error instead of a warning.
* install.packages(repos = NULL) now accepts http:// or ftp:// URLs
of package archives as well as file paths, and will download as
required. In most cases repos = NULL can be deduced from the
extension of the URL.
* The warning when using partial matching with the $ operator on
data frames is now only given when
options("warnPartialMatchDollar") is TRUE.
* Package help requests like package?foo now try the package foo
whether loaded or not.
* General help requests now default to trying all loaded packages,
not just those on the search path.
* Added a new function promptImport(), to generate a help page for
a function that was imported from another package (and presumably
re-exported, or help would not be needed).
INSTALLATION and INCLUDED SOFTWARE:
* configure option --with-internal-tzcode can now be used with
variable rsharedir.
* The included version of PCRE has been updated to 8.35.
* There is a new target make uninstall-libR to remove an installed
shared/static libR.
make install-libR now works if a sub-architecture is used,
although the user will need to specify libdir differently for
different sub-architectures.
* There is more extensive advice on which LaTeX packages are
required to install R or to make package manuals (as done by R
CMD check) in the 'Writing R Extensions' manual.
* Compilers/linkers were handling the visibility controls in
src/extra/xz inconsistently (and apparently in some cases
incorrectly), so it has been simplified. (PR#15327)
* (Windows) There is updated support for the use of ICU for
collation: see the 'R Installation and Administration Manual'.
BUG FIXES:
* dbinom(x, n), pbinom(), dpois(), etc, are slightly less
restrictive in checking if n is integer-valued. (Wish of
PR#15734.)
* pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
100, ncp = 1, log = TRUE). (Based on PR#15635 and a suggestion
by Roby Joehanes.)
* The s ("step into") command in the debugger would cause R to step
into expressions evaluated there, not just into functions being
debugged. (PR#15770)
* The C code used by strptime() rejected time-zone offsets of more
than +1200 (+1245, +1300 and +1400 can occur). (PR#15768)
* (Windows only.) png(type = "cairo", antialias = "gray") was not
accepted. (PR#15760)
* Use of save(..., envir=) with named objects could fail.
(PR#15758)
* Sweave() mis-parsed Sexpr expressions that contained backslashes.
(PR#15779)
* The return value from options(foo = NULL) was not the previous
value of the option. (PR#15781)
* enc2utf8() and enc2native() did not always mark the encoding of
the return values when it was known.
* dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
to -Inf for large mu, thanks to a suggestion from Alessandro
Mammana (MPI MolGen, Berlin).
* pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
a small x-region) because of denormalized numbers. Also,
pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
time".
* The "CRAN" filter (see available.packages()) no longer removes
duplicates other than of packages on CRAN, and does not fail if
there is no CRAN repository in getOption("repos").
* The device listing from dev2bitmap() and bitmap() was truncated
to 1000 characters: modern versions of GhostScript on most
platforms have many more devices.
* (Windows.) Commands such as Sys.which() and pipe() which needed
to find the full path to a command could segfault if the 'long'
path name was much longer than the 'short' path name (which
Sys.which() returns), as the behaviour of the Windows API call
had changed.
* R CMD build will fail with an error if one of the packages
specified in the VignetteBuilder field is not installed.
(Without loading those packages it cannot be ascertained which
files are intended to be vignettes. This means that the
VignetteBuilder packages have to be installed for package
checking too.) (Wish of PR#15775.)
* Misguided attempts to use chull() with non-finite points now give
an error (related to PR#15777).
* For a formula with exactly 32 variables the 32nd variable was
aliased to the intercept in some C-level computations of terms,
so that for example attempting to remove it would remove the
intercept instead (and leave a corrupt internal structure).
(PR#15735)
* anyDuplicated() silently returned wrong values when the first
duplicate was at an index which was too large to be stored in an
integer vector (although a lot of RAM and patience would have
been needed to encounter this).
* tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
one line.
* Hexadecimal constants such as 0x110p-5L which were incorrectly
qualified by L were parsed incorrectly since R 3.0.0, with a
slightly garbled warning. (PR#15753)
* system() returned success on some platforms even if the system
was unable to launch a process. (PR#15796)
* (Windows Rgui console.) Unbuffered output was sometimes not
output immediately if the prompt was not on the last line of the
console.
* The built-in help server did not declare the encoding for the
DESCRIPTION or other text files to be the package encoding, so
non-ASCII characters could be displayed incorrectly.
* R is now trying harder to not cleanup child processes that were
not spawned by mcparallel() on platforms that provide information
about the source process of the SIGCHLD signal. This allows 3rd
party libraries to manage the exit status of children that they
spawn without R interfering.
* mcmapply() was only parallelizing if the number of jobs was
bigger than the number of cores. It now parallelizes if the
number of jobs is more than one.
* Auto-printing would re-evaluate its argument when trying to
dispatch to a print method. This is now avoided when possible.
* Unserializing (including load() and readRDS()) could silently
return incorrect numeric values from ASCII saves if there was a
read error.
* getParseData() could return incorrect values for the parents of
some elements. (Reported by Andrew Redd.)
* Attempting to use data frames of 2^31 or more rows with merge()
or to create a merged data frame of that size now gives a clearer
error message.
* parse() did not check its file argument was a connection if it
was not a character string, so e.g. parse(FALSE) attempted to
read from stdin.
Nor did dump() and dput().
* The "help.try.all.packages" option was ignored when the shortcut
syntax for help was used, e.g. ?foo.
* A potential segfault in string allocation has been fixed. (Found
by Radford Neal.)
* Potential memory protection errors in sort() and D() have been
fixed. (Found by Radford Neal.)
* Fixed a lack of error checking in graphics event functions.
(Found by Radford Neal; a different patch used here than the one
in pqR.)
* numericDeriv() sometimes miscalculated the gradient. (PR#15849,
reported originally by Radford Neal)
-------------------------------------------------------------------
Fri Jun 20 18:26:23 UTC 2014 - darin@darins.net
- added parallel provides
-------------------------------------------------------------------
Fri May 9 18:18:25 UTC 2014 - detlef.steuer@gmx.de
- Removed / commented out symlink to %{_bindir}/r
new package 'littler' should be used instead for packages
that need /usr/bin/r
-------------------------------------------------------------------
Thu May 1 15:29:30 UTC 2014 - darin@darins.net
- Add make dependency for Rcmd
-------------------------------------------------------------------
Tue Apr 29 15:31:15 UTC 2014 - darin@darins.net
- Created symlink to %{_bindir}/r
Many CRAN packages ship with scripts which call %{_bindir}/r,
which creates a dependency on it, this fixes that.
-------------------------------------------------------------------
Thu Apr 10 10:58:30 UTC 2014 - detlef.steuer@gmx.de
- Upstream release 3.1.0
- Most impotant
CHANGES IN R 3.1.0:
NEW FEATURES:
* type.convert() (and hence by default read.table()) returns a
character vector or factor when representing a numeric input as a
double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of
decimal places that are intended to be read as numeric, specify
colClasses in read.table() to be "numeric".
* tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
of diff -b (as distinct from the description in the man pages of
most systems).
* New function anyNA(), a version of any(is.na(.)) which is fast
for atomic vectors, based on a proposal by Tim Hesterberg. (Wish
of PR#15239.)
* arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
TRUE) now make use of names(.dimnames) when available.
* is.unsorted() now also works for raw vectors.
* The "table" method for as.data.frame() (also useful as
as.data.frame.table()) now passes sep and base arguments to
provideDimnames().
* uniroot() gets new optional arguments, notably extendInt,
allowing to auto-extend the search interval when needed. The
return value has an extra component, init.it.
* switch(f, ...) now warns when f is a factor, as this typically
happens accidentally where the useR meant to pass a character
string, but f is treated as integer (as always documented).
* The parser has been modified to use less memory.
* The way the unary operators (+ - !) handle attributes is now more
consistent. If there is no coercion, all attributes (including
class) are copied from the input to the result: otherwise only
names, dims and dimnames are.
* colorRamp() and colorRampPalette() now allow non-opaque colours
and a ramp in opacity via the new argument alpha = TRUE.
(Suggested by Alberto Krone-Martins, but optionally as there are
existing uses which expect only RGB values.)
* grid.show.layout() and grid.show.viewport() get an optional vp.ex
argument.
* There is a new function find_gs_cmd() in the tools package to
locate a GhostScript executable. (This is an enhanced version of
a previously internal function there.)
* object.size() gains a format() method.
* There is a new family, "ArialMT", for the pdf() and postscript()
devices. This will only be rendered correctly on viewers which
have access to Monotype TrueType fonts (which are sometimes
requested by journals).
* The text and PDF news files, including NEWS and NEWS.2, have been
moved to the doc directory.
* combn(x, simplify = TRUE) now gives a factor result for factor
input x (previously user error). (Related to PR#15442.)
* Added utils::fileSnapshot() and utils::changedFiles() functions
to allow snapshots and comparison of directories of files.
* make.names(names, unique=TRUE) now tries to preserve existing
names. (Suggestion of PR#15452.)
* New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
computation of cos(pi*x), etc, both in R and the C API. Using
these gains accuracy in some cases, e.g., inside lgamma() or
besselI(). (Suggested by Morten Welinder in PR#15529.)
* print.table(x, zero.print = ".") now also has an effect when x is
not integer-valued.
* There is more support to explore the system's idea of time-zone
names. Sys.timezone() tries to give the current system setting
by name (and succeeds at least on Linux, OS X, Solaris and
Windows), and OlsonNames() lists the names in the system's Olson
database. Sys.timezone(location = FALSE) gives the previous
behaviour.
* Platforms with a 64-bit time_t type are allowed to handle
conversions between the "POSIXct" and "POSIXlt" classes for
date-times outside the 32-bit range (before 1902 or after 2037):
the existing workarounds are used on other platforms. (Note that
time-zone information for post-2037 is speculative at best, and
the OS services are tested for known errors and so not used on OS
X.)
Currently time_t is usually long and hence 64-bit on Unix-alike
64-bit platforms: however it several cases the time-zone database
is 32-bit. On R for Windows it is 64-bit (for both architectures
as from this version).
* The "save.defaults" option can include a value for
compression_level. (Wish of PR#15579.)
* colSums() and friends now have support for arrays and data-frame
columns with 2^31 or more elements.
* as.factor() is faster when f is an unclassed integer vector (for
example, when called from tapply()).
* fft() now works with longer inputs, from the 12 million
previously supported up to 2 billion. (PR#15593)
* Complex svd() now uses LAPACK subroutine ZGESDD, the complex
analogue of the routine used for the real case.
* Sweave now outputs .tex files in UTF-8 if the input encoding is
declared to be UTF-8, regardless of the local encoding. The
UTF-8 encoding may now be declared using a LaTeX comment
containing the string %\SweaveUTF8 on a line by itself.
* file.copy() gains a copy.date argument.
* Printing of date-times will make use of the time-zone
abbreviation in use at the time, if known. For example, for
Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable
this, the "POSIXlt" class has an optional component "zone"
recording the abbreviation for each element.
For platforms which support it, there is also a component
"gmtoff" recording the offset from GMT where known.
* (On Windows, by default on OS X and optionally elsewhere.) The
system C function strftime has been replaced by a more
comprehensive version with closer conformance to the POSIX 2008
standard.
* dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
|x| > 5; as suggested in PR#15620.
* Some versions of the tiff() device have further compression
options.
* read.table(), readLines() and scan() have a new argument to
influence the treatment of embedded nuls.
* Avoid duplicating the right hand side values in complex
assignments when possible. This reduces copying of replacement
values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
package code has relied on there being copies.
Also, a number of other changes to reduce copying of objects; all
contributed by or based on suggestions by Michael Lawrence.
* The fast argument of KalmanLike(), KalmanRun() and
KalmanForecast() has been replaced by update, which instead of
updating mod in place, optionally returns the updated model in an
attribute "mod" of the return value.
* arima() and makeARIMA() get a new optional argument SSinit,
allowing the choice of a different *s*tate *s*pace initialization
which has been observed to be more reliable close to
non-stationarity: see PR#14682.
* warning() has a new argument noBreaks., to simplify
post-processing of output with options(warn = 1).
* pushBack() gains an argument encoding, to support reading of
UTF-8 characters using scan(), read.table() and related functions
in a non-UTF-8 locale.
* all.equal.list() gets a new argument use.names which by default
labels differing components by names (if they match) rather than
by integer index. Saved R output in packages may need to be
updated.
* The methods for all.equal() and attr.all.equal() now have
argument check.attributes after ... so it cannot be partially nor
positionally matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of
passing empty arguments (no object between commas) to all.equal()
are detected and reported.
There are explicit checks that check.attributes is logical,
tolerance is numeric and scale is NULL or numeric. This catches
some unintended positional matching.
The message for all.equal.numeric() reports a "scaled difference"
only for scale != 1.
* all.equal() now has a "POSIXt" method replacing the "POSIXct"
method.
* The "Date" and "POSIXt" methods of seq() allows by = "quarter"
for completeness (by = "3 months" always worked).
* file.path() removes any trailing separator on Windows, where they
are invalid (although sometimes accepted). This is intended to
enhance the portability of code written by those using POSIX file
systems (where a trailing / can be used to confine path matching
to directories).
* New function agrepl() which like grepl() returns a logical
vector.
* fifo() is now supported on Windows. (PR#15600)
* sort.list(method = "radix") now allows negative integers (wish of
PR#15644).
* Some functionality of print.ts() is now available in
.preformat.ts() for more modularity.
* mcparallel() gains an option detach = TRUE which allows execution
of code independently of the current session. It is based on a
new estranged = TRUE argument to mcfork() which forks child
processes such that they become independent of the parent
process.
* The pdf() device omits circles and text at extremely small sizes,
since some viewers were failing on such files.
* The rightmost break for the "months", "quarters" and "years"
cases of hist.POSIXlt() has been increased by a day. (Inter
alia, fixes PR#15717.)
* The handling of DF[i,] <- a where i is of length 0 is improved.
(Inter alia, fixes PR#15718.)
* hclust() gains a new method "ward.D2" which implements Ward's
method correctly. The previous "ward" method is "ward.D" now,
with the old name still working. Thanks to research and
proposals by Pierre Legendre.
* The sunspot.month dataset has been amended and updated from the
official source, whereas the sunspots and sunspot.year datasets
will remain immutable. The documentation and source links have
been updated correspondingly.
* The summary() method for "lm" fits warns if the fit is
essentially perfect, as most of the summary may be computed
inaccurately (and with platform-dependent values).
Programmers who use summary() in order to extract just a
component which will be reliable (e.g. $cov.unscaled) should wrap
their calls in suppressWarnings().
INSTALLATION and INCLUDED SOFTWARE:
* The included version of LAPACK has been updated to 3.5.0.
* There is some support for parallel testing of an installation, by
setting TEST_MC_CORES to an integer greater than one to indicate
the maximum number of cores to be used in parallel. (It is worth
specifying at least 8 cores if available.) Most of these require
a make program (such as GNU make and dmake) which supports the
$MAKE -j nproc syntax.
Except on Windows: the tests of standard package examples in make
check are done in parallel. This also applies to running
tools::testInstalledPackages().
The more time-consuming regression tests are done in parallel.
The package checks in make check-devel and make check-recommended
are done in parallel.
* More of make check will work if recommended packages are not
installed: but recommended packages remain needed for thorough
checking of an R build.
* The version of tzcode included in src/extra/tzone has been
updated. (Formerly used only on Windows.)
* The included (64-bit) time-zone conversion code and Olson
time-zone database can be used instead of the system version: use
configure option --with-internal-tzcode. This is the default on
Windows and OS X. (Note that this does not currently work if a
non-default rsharedir configure variable is used.)
(It might be necessary to set environment variable TZ on OSes
where this is not already set, although the system timezone is
deduced correctly on at least Linux, OS X and Windows.)
This option also switches to the version of strftime included in
directory src/extra/tzone.
* configure now tests for a C++11-compliant compiler by testing
some basic features. This by default tries flags for the
compiler specified by CXX, but an alternative compiler, options
and standard can be specified by variables CXX1X, CXX1XFLAGS and
CXX1XSTD (e.g. -std=gnu++11).
* R can now optionally be compiled to use reference counting
instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in
Rinternals.h. This may become the default in the future.
* There is a new option --use-system-tre to use a suitable system
tre library: at present this means a version from their git
repository, after corrections. (Wish of PR#15660.)
-------------------------------------------------------------------
Thu Mar 6 10:08:59 UTC 2014 - detlef.steuer@gmx.de
- Upstream release 3.0.3
- Most important
CHANGES IN R 3.0.3:
NEW FEATURES:
* On Windows there is support for making .texi manuals using
texinfo 5.0 or later: the setting is in file
src/gnuwin32/MkRules.dist.
A packaging of the Perl script and modules for texinfo 5.2 has
been made available at <URL:
http://www.stats.ox.ac.uk/pub/Rtools/>.
* write.table() now handles matrices of 2^31 or more elements, for
those with large amounts of patience and disc space.
* There is a new function, La_version(), to report the version of
LAPACK in use.
* The HTML version of 'An Introduction to R' now has links to PNG
versions of the figures.
* There is some support to produce manuals in ebook formats. (See
doc/manual/Makefile. Suggested by Mauro Cavalcanti.)
* On a Unix-alike Sys.timezone() returns NA if the environment
variable TZ is unset, to distinguish it from an empty string
which on some OSes means the UTC time zone.
* The backtick may now be escaped in strings, to allow names
containing them to be constructed, e.g. `\``. (PR#15621)
* read.table(), readLines() and scan() now warn when an embedded
nul is found in the input. (Related to PR#15625 which was
puzzled by the behaviour in this unsupported case.)
* (Windows only.) file.symlink() works around the undocumented
restriction of the Windows system call to backslashes. (Wish of
PR#15631.)
* KalmanForecast(fast = FALSE) is now the default, and the help
contains an example of how fast = TRUE can be used in this
version. (The usage will change in 3.1.0.)
* strptime() now checks the locale only when locale-specific
formats are used and caches the locale in use: this can halve the
time taken on OSes with slow system functions (e.g. OS X).
* strptime() and the format() methods for classes "POSIXct",
"POSIXlt" and "Date" recognize strings with marked encodings:
this allows, for example, UTF-8 French month names to be read on
(French) Windows.
* iconv(to = "utf8") is now accepted on all platforms (some
implementations did already, but GNU libiconv did not: however
converted strings were not marked as being in UTF-8). The
official name, "UTF-8" is still preferred.
* available.packages() is better protected against corrupt metadata
files. (A recurring problem with Debian package shogun-r:
PR#14713.)
* Finalizers are marked to be run at garbage collection, but run
only at a somewhat safer later time (when interrupts are
checked). This circumvents some problems with finalizers running
arbitrary code during garbage collection (the known instances
being running options() and (C-level) path.expand()
re-entrantly).
-------------------------------------------------------------------
Fri Sep 27 13:20:39 UTC 2013 - detlef.steuer@gmx.de
- Removed outdated source file
-------------------------------------------------------------------
Wed Sep 25 14:01:26 UTC 2013 - detlef.steuer@gmx.de
- Upstream release 3.0.2
- Most important
CHANGES IN R 3.0.2:
NEW FEATURES:
* The NEWS files have been re-organized.
This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The
latter files are now installed when R is installed. An HTML
version of news from 2.10.0 to 2.15.3 is available as
doc/html/NEWS.2.html.
* sum() for integer arguments now uses an integer accumulator of at
least 64 bits and so will be more accurate in the very rare case
that a cumulative sum exceeds 2^53 (necessarily summing more than
4 million elements).
* The example() and tools::Rd2ex() functions now have parameters to
allow them to ignore \dontrun markup in examples. (Suggested by
Peter Solymos.)
* str(x) is considerably faster for very large lists, or factors
with 100,000 levels, the latter as in PR#15337.
* col2rgb() now converts factors to character strings not integer
codes (suggested by Bryan Hanson).
* tail(warnings()) now works, via the new `[` method.
* There is now support for the LaTeX style file zi4.sty which has
in some distributions replaced inconsolata.sty.
* unlist(x) now typically returns all non-list xs unchanged, not
just the "vector" ones. Consequently, format(lst) now also works
when the list lst has non-vector elements.
* The tools::getVignetteInfo() function has been added to give
information about installed vignettes.
* New assertCondition(), etc. utilities in tools, useful for
testing.
* Profiling now records non-inlined calls from byte-compiled code
to BUILTIN functions.
* Various functions in stats and elsewhere that use non-standard
evaluation are now more careful to follow the namespace scoping
rules. E.g. stats::lm() can now find stats::model.frame() even
if stats is not on the search path or if some package defines a
function of that name.
* If an invalid/corrupt .Random.seed object is encountered in the
workspace it is ignored with a warning rather than giving an
error. (This allows R itself to rely on a working RNG, e.g. to
choose a random port.)
* seq() and seq.int() give more explicit error messages if called
with invalid (e.g. NaN) inputs.
* When parse() finds a syntax error, it now makes partial parse
information available up to the location of the error. (Request
of Reijo Sund.)
* Methods invoked by NextMethod() had a different dynamic parent to
the generic. This was causing trouble where S3 methods invoked
via lazy evaluation could lose track of their generic.
(PR#15267)
* Code for the negative binomial distribution now treats the case
size == 0 as a one-point distribution at zero.
* abbreviate() handles without warning non-ASCII input strings
which require no abbreviation.
* read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
PR#15250.)
* formatC(x) no longer copies the class of x to the result, to
avoid misuse creating invalid objects as in PR#15303. A warning
is given if a class is discarded.
* Dataset npk has been copied from MASS to allow more tests to be
run without recommended packages being installed.
* The initialization of the regression coefficients for
non-degenerate differenced models in arima() has been changed and
in some examples avoids a local maximum. (PR#15396)
* termplot() now has an argument transform.x to control the display
of individual terms in the plot. (PR#15329)
* format() now supports digits = 0, to display nsmall decimal
places.
* There is a new read-only par() parameter called "page", which
returns a logical value indicating whether the next plot.new()
call will start a new page.
* Processing Sweave and Rd documents to PDF now renders backticks
and single quotes better in several instances, including in \code
and \samp expressions.
* utils::modifyList() gets a new argument keep.null allowing NULL
components in the replacement to be retained, instead of causing
corresponding components to be deleted.
* tools::pkgVignettes() gains argument check; if set to TRUE, it
will warn when it appears a vignette requests a non-existent
vignette engine.
-------------------------------------------------------------------
Mon Aug 26 14:19:31 UTC 2013 - schwab@suse.de
- tre.patch: Fix tre library for aarch64 where wchar_t is unsigned int
-------------------------------------------------------------------
Thu May 16 13:17:09 UTC 2013 - detlef.steuer@gmx.de
- Improved spec file: R-base-devel requires R-base
-------------------------------------------------------------------
Thu May 16 11:21:09 UTC 2013 - detlef.steuer@gmx.de
- Upstream release 3.0.1
- Most important
CHANGES IN R 3.0.1:
NEW FEATURES:
o chooseCRANmirror() and chooseBioCmirror() gain an ind argument
(like setRepositories()).
o mcparallel has a new argument mc.interactive which can modify the
interactive flag in the child process. The new default is FALSE
which makes child processes non-interactive by default (this
prevents lock-ups due to children waiting for interactive input).
o scan() now warns when end-of-file occurs within a quoted string.
o count.fields() is now consistent with scan() in its handling of
newlines in quoted strings. Instead of triggering an error, this
results in the current line receiving NA as the field count, with
the next line getting the total count of the two lines.
o The default method of image() will plot axes of the class of xlim
and ylim (and hence of x and y if there is a suitable range()
method). Based on a suggestion of Michael Sumner.
o load() now has a verbose argument for debugging support, to print
the names of objects just before loading them.
o When loading a serialized object encounters a reference to a
namespace which cannot be loaded, this is replaced by a reference
to the global environment, with a warning.
o pairs() gains a line.main option for title placement.
o The remaining instances in which serialization to a raw vector
was limited to 2GB have been unlimited on a 64-bit platform, and
in most cases serialization to a vector of more than 1GB will be
substantially faster.
- Improved spec file. Lots of commented out lines finally removed
-------------------------------------------------------------------
Wed Apr 10 07:26:36 UTC 2013 - detlef.steuer@gmx.de
- R-base.spec improved: now uses R-%{version}.tar.bz2 explicitly.
Mistake when version bumping to 3.0.0 corrected
-------------------------------------------------------------------
Wed Apr 3 18:39:35 UTC 2013 - detlef.steuer@gmx.de
- Upstream release 3.0.0
- News for package: some new translation files
- News upstream: /usr/lib/R/doc/NEWS.html
- Most important
CHANGES IN R 3.0.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o Packages need to be (re-)installed under this version (3.0.0) of
R.
o There is a subtle change in behaviour for numeric index values
2^31 and larger. These never used to be legitimate and so were
treated as NA, sometimes with a warning. They are now legal for
long vectors so there is no longer a warning, and x[2^31] <- y
will now extend the vector on a 64-bit platform and give an error
on a 32-bit one.
o It is now possible for 64-bit builds to allocate amounts of
memory limited only by the OS. It may be wise to use OS
facilities (e.g. ulimit in a bash shell, limit in csh), to set
limits on overall memory consumption of an R process,
particularly in a multi-user environment. A number of packages
need a limit of at least 4GB of virtual memory to load.
64-bit Windows builds of R are by default limited in memory usage
to the amount of RAM installed: this limit can be changed by
command-line option --max-mem-size or setting environment
variable R_MAX_MEM_SIZE.
o Negative numbers for colours are consistently an error:
previously they were sometimes taken as transparent, sometimes
mapped into the current palette and sometimes an error.
-------------------------------------------------------------------
Mon Mar 18 14:38:57 UTC 2013 - schwab@suse.de
- Override LIBnn from %{_lib}
-------------------------------------------------------------------
Fri Mar 1 12:15:30 UTC 2013 - detlef.steuer@gmx.de
- There were a few new files in foreign and rpart.
Fixed now. Builds fine.
-------------------------------------------------------------------
Fri Mar 1 10:25:32 UTC 2013 - detlef.steuer@gmx.de
- Upstream release 2.15.3
- see, as usual, /usr/lib/R/doc/NEWS.html
- This is mostly a bugfix release and the final release for the
R-2.x.y series.
- Most important additions:
NEW FEATURES:
o lgamma(x) for very small x (in the denormalized range) is no
longer Inf with a warning.
o image() now sorts an unsorted breaks vector, with a warning.
o The internal methods for tar() and untar() do a slightly more
general job for 'ustar'-style handling of paths of more than 100
bytes.
o Packages compiler and parallel have been added to the reference
index (refman.pdf).
o untar(tar = "internal") has some support for pax headers as
produced by e.g. gnutar --posix (which seems prevalent on
OpenSUSE 12.2) or bsdtar --format pax, including long path and
link names.
o sQuote() and dQuote() now handle 0-length inputs. (Suggestion of
Ben Bolker.)
o summaryRprof() returns zero-row data frames rather than throw an
error if no events are recorded, for consistency.
o The included version of PCRE has been updated to 8.32.
o The tcltk namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child from package
parallel (as in e.g. mclapply()).
o parallel::makeCluster() recognizes the value random for the
environment variable R_PARALLEL_PORT: this chooses a random value
for the port and reduces the chance of conflicts when multiple
users start a cluster at the same time.
-------------------------------------------------------------------
Fri Oct 26 12:35:44 UTC 2012 - detlef.steuer@gmx.de
- Upstream release 2.15.2
- see, as usual, /usr/lib/R/doc/NEWS.html
- most relevant change for rpm are some added translation files
-------------------------------------------------------------------
Tue Jul 10 08:37:58 UTC 2012 - werner@suse.de
- Make it build with latest TeXLive 2012 with new package layout
-------------------------------------------------------------------
Fri Jun 22 14:22:25 UTC 2012 - detlef.steuer@gmx.de
- Fixed: R-base-2.15.1-48.1.x86_64.rpm: directories not owned by a package:
- /usr/lib64/R/share/locale/pl
- /usr/lib64/R/share/locale/pl/LC_MESSAGES
-------------------------------------------------------------------
Fri Jun 22 13:43:05 UTC 2012 - detlef.steuer@gmx.de
- one more forgotten file in polish translation ...
-------------------------------------------------------------------
Fri Jun 22 12:38:18 UTC 2012 - detlef.steuer@gmx.de
- spec file update to incorporate new polish translation
-------------------------------------------------------------------
Fri Jun 22 11:53:39 UTC 2012 - detlef.steuer@gmx.de
- Upstream bugfix only release 2.15.1
- see, as usual, /usr/lib/R/doc/NEWS.html
-------------------------------------------------------------------
Tue Apr 10 21:51:18 UTC 2012 - gregkh@opensuse.org
- make R-base-devel require R-base as some packages think this
dependancy is already there (i.e. some KDE packages).
-------------------------------------------------------------------
Fri Mar 30 09:26:11 UTC 2012 - detlef.steuer@gmx.de
- Upstream updated to 2.15.0
- see, as usual, /usr/lib/R/doc/NEWS.html
-------------------------------------------------------------------
Wed Feb 29 18:00:59 UTC 2012 - detlef.steuer@gmx.de
- upstream minor version increase to 2.14.2
- see, as usual, /usr/lib/R/doc/NEWS.html for details.
-------------------------------------------------------------------
Fri Feb 17 20:53:49 UTC 2012 - detlef.steuer@gmx.de
- Minor cleanup for easier automativ building of R-patched.spec
-------------------------------------------------------------------
Wed Feb 15 19:41:43 UTC 2012 - detlef.steuer@gmx.de
- changed licence string to "GPL-2.0 or GPL-3.0"
-------------------------------------------------------------------
Mon Feb 13 22:39:51 UTC 2012 - detlef.steuer@gmx.de
- uninstall rule for R.conf more than useless ... reverted.
-------------------------------------------------------------------
Mon Feb 13 21:59:13 UTC 2012 - detlef.steuer@gmx.de
- Applications like KDE's Cantor search for the R standard library
- using the library search path. However, in openSUSE's package,
- libraries are installed to %{_libdir}/R/lib, hence attempts to
- load them from these applications will fail.
- This revision adds a R.conf file to ld.so.conf.d to enable
- searching for libraries where R is installed. Once this change
- is in, applications are able to use libR.so.
- Thx to einar@heavensinferno.net for spotting this.
- Thought had done this for release of 2.14.0.
-------------------------------------------------------------------
Thu Dec 22 12:19:10 UTC 2011 - steuer@unibw-hamburg.de
- Upstream updated to 2.14.1
- see, as usual, /usr/lib/R/doc/NEWS.html for details.
- Only minor bug fixes + workaround for missing inconsolata.sty
- on older systems.
-------------------------------------------------------------------
Mon Oct 31 12:40:03 UTC 2011 - detlef.steuer@gmx.de
- merged change infor Oct 5th into working copy
-------------------------------------------------------------------
Mon Oct 31 12:34:30 UTC 2011 - detlef.steuer@gmx.de
- corrected subpackge version number in R-base-devel
-------------------------------------------------------------------
Mon Oct 31 11:12:24 UTC 2011 - detlef.steuer@gmx.de
- Upstream updated to 2.14.0
- see, as usual, /usr/lib/R/doc/NEWS.html for details.
- On system side most important, that /etc/ld.so.conf.d/R-base.conf
- was added to help third party programs, i.e. rpy2, tp link against
- R-base
-------------------------------------------------------------------
Wed Oct 5 07:13:03 UTC 2011 - detlef.steuer@gmx.de
- corrected version string for Matrix subpackage
-------------------------------------------------------------------
Tue Oct 4 14:00:04 UTC 2011 - detlef.steuer@gmx.de
- removed 4 warnings about unescaped macros in comments
-------------------------------------------------------------------
Tue Oct 4 12:13:18 UTC 2011 - detlef.steuer@gmx.de
- explicitly added some locale directories. Worked before implicitly.
-------------------------------------------------------------------
Tue Oct 4 11:10:56 UTC 2011 - detlef.steuer@gmx.de
- update to upstream version 2.13.2
- see, as usual, /usr/lib/R/doc/NEWS.html for details.
-------------------------------------------------------------------
Sat Sep 17 10:18:38 UTC 2011 - jengelh@medozas.de
- Remove redundant tags/sections from specfile
- Use %_smp_mflags for parallel build
-------------------------------------------------------------------
Fri Jul 8 19:32:45 UTC 2011 - detlef.steuer@gmx.de
- resolved some conflicts for R-base.spec after osc up -e && osc pull
-------------------------------------------------------------------
Fri Jul 8 12:51:05 UTC 2011 - detlef.steuer@gmx.de
- corrected version string in R-base.spec
-------------------------------------------------------------------
Fri Jul 8 11:51:35 UTC 2011 - detlef.steuer@gmx.de
- Upstream updated to 2.13.1. Licence change from GPLv2 to GPLv2 || GPLv3.
Packages rpart and survival now GPLed, too.
Various minor bugfixes.
See /usr/lib/R/doc/NEWS.html for details.
-------------------------------------------------------------------
Thu May 12 13:45:43 UTC 2011 - detlef.steuer@gmx.de
- Removed possible dangerous links of libraries. R`s internal
libraries now are only available in $lib/R/lib .
-------------------------------------------------------------------
Fri May 6 07:33:40 UTC 2011 - detlef.steuer@gmx.de
- Changed Licence string to GPLv2, taken from opensuse`s list aof allowed
licences, as requested from coolo
-------------------------------------------------------------------
Wed Apr 13 11:13:38 UTC 2011 - detlef.steuer@gmx.de
- Upstream update to 2.13.0; new package 'compiler'; some new language files
-------------------------------------------------------------------
Fri Mar 4 12:36:54 UTC 2011 - detlef.steuer@gmx.de
- update to 2.12.2
minor bugfixes
see /usr/lib/R/doc/html/NEWS.html for details
-------------------------------------------------------------------
Mon Jan 10 16:56:55 CET 2011 - detlef.steuer@gmx.de
- removed -n parameter from %build/%install
- removed %doc from man/info pages in files section
-------------------------------------------------------------------
Fri Dec 17 14:05:39 UTC 2010 - detlef.steuer@gmx.de
reverting mandir/infodir directiven, didn't build in some releases-
-------------------------------------------------------------------
Fri Dec 17 12:40:12 UTC 2010 - detlef.steuer@gmx.de
sorted out list of problems shown bei mrueckert-
-------------------------------------------------------------------
Mon Nov 29 20:08:31 UTC 2010 - detlef.steuer@gmx.de
Version, to be submitted to factory-
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