| Age | Commit message (Collapse) | Author | Files | Lines |
|---|
|
|
|
|
|
This reduces # of variables to define in an R extension package.
|
|
|
|
|
|
|
|
This package was already using libblas from the Accelerate framework
on Darwin through /usr/lib/libblas.dylib. This change makes it
explicit and removes unnecessary dependencies on math/blas and
math/lapack.
Bump PKGREVISION.
|
|
The actual fix as been done by "pkglint -F */*/buildlink3.mk", and was
reviewed manually.
There are some .include lines that still are indented with zero spaces
although the surrounding .if is indented. This is existing practice.
|
|
|
|
|
|
Upstream changes:
CHANGES IN R 3.4.3:
INSTALLATION on a UNIX-ALIKE:
* A workaround has been added for the changes in location of
time-zone files in macOS 10.13 'High Sierra' and again in
10.13.1, so the default time zone is deduced correctly from the
system setting when R is configured with --with-internal-tzcode
(the default on macOS).
* R CMD javareconf has been updated to recognize the use of a Java
9 SDK on macOS.
BUG FIXES:
* raw(0) & raw(0) and raw(0) | raw(0) again return raw(0) (rather
than logical(0)).
* intToUtf8() converts integers corresponding to surrogate code
points to NA rather than invalid UTF-8, as well as values larger
than the current Unicode maximum of 0x10FFFF. (This aligns with
the current RFC3629.)
* Fix calling of methods on S4 generics that dispatch on ... when
the call contains ....
* Following Unicode 'Corrigendum 9', the UTF-8 representations of
U+FFFE and U+FFFF are now regarded as valid by utf8ToInt().
* range(c(TRUE, NA), finite = TRUE) and similar no longer return
NA. (Reported by Lukas Stadler.)
* The self starting function attr(SSlogis, "initial") now also
works when the y values have exact minimum zero and is slightly
changed in general, behaving symmetrically in the y range.
* The printing of named raw vectors is now formatted nicely as for
other such atomic vectors, thanks to Lukas Stadler.
|
|
|
|
CHANGES IN R 3.4.2:
NEW FEATURES:
* Setting the LC_ALL category in Sys.setlocale() invalidates any
cached locale-specific day/month names and the AM/PM indicator
for strptime() (as setting LC_TIME has since R 3.1.0).
* The version of LAPACK included in the sources has been updated to
3.7.1, a bug-fix release.
* The default for tools::write_PACKAGES(rds_compress=) has been
changed to "xz" to match the compression used by CRAN.
* c() and unlist() are now more efficient in constructing the
names(.) of their return value, thanks to a proposal by Suharto
Anggono. (PR#17284)
CHANGES IN R 3.4.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* (Unix-alike) The default methods for download.file() and url()
now choose "libcurl" except for file:// URLs. There will be
small changes in the format and wording of messages, including in
rare cases if an issue is a warning or an error. For example,
when HTTP re-direction occurs, some messages refer to the final
URL rather than the specified one.
Those who use proxies should check that their settings are
compatible (see ?download.file: the most commonly used forms work
for both "internal" and "libcurl").
* table() has been amended to be more internally consistent and
become back compatible to R <= 2.7.2 again. Consequently,
table(1:2, exclude = NULL) no longer contains a zero count for
<NA>, but useNA = "always" continues to do so.
* summary.default() no longer rounds, but its print method does
resulting in less extraneous rounding, notably of numbers in the
ten thousands.
* factor(x, exclude = L) behaves more rationally when x or L are
character vectors. Further, exclude = <factor> now behaves as
documented for long.
* Arithmetic, logic (&, |) and comparison (aka 'relational', e.g.,
<, ==) operations with arrays now behave consistently, notably
for arrays of length zero.
Arithmetic between length-1 arrays and longer non-arrays had
silently dropped the array attributes and recycled. This now
gives a warning and will signal an error in the future, as it has
always for logic and comparison operations in these cases (e.g.,
compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3).
* The JIT ('Just In Time') byte-code compiler is now enabled by
default at its level 3. This means functions will be compiled on
first or second use and top-level loops will be compiled and then
run. (Thanks to Tomas Kalibera for extensive work to make this
possible.)
For now, the compiler will not compile code containing explicit
calls to browser(): this is to support single stepping from the
browser() call.
JIT compilation can be disabled for the rest of the session using
compiler::enableJIT(0) or by setting environment variable
R_ENABLE_JIT to 0.
* xtabs() works more consistently with NAs, also in its result no
longer setting them to 0. Further, a new logical option addNA
allows to count NAs where appropriate. Additionally, for the
case sparse = TRUE, the result's dimnames are identical to the
default case's.
* Matrix products now consistently bypass BLAS when the inputs have
NaN/Inf values. Performance of the check of inputs has been
improved. Performance when BLAS is used is improved for
matrix/vector and vector/matrix multiplication (DGEMV is now used
instead of DGEMM).
One can now choose from alternative matrix product
implementations _via_ options(matprod = ). The "internal"
implementation is not optimized for speed but consistent in
precision with other summations in R (using long double
accumulators where available). "blas" calls BLAS directly for
best speed, but usually with undefined behavior for inputs with
NaN/Inf.
NEW FEATURES:
* User errors such as integrate(f, 0:1, 2) are now caught.
* Add signature argument to debug(), debugonce(), undebug() and
isdebugged() for more conveniently debugging S3 and S4 methods.
(Based on a patch by Gabe Becker.)
* Add utils::debugcall() and utils::undebugcall() for debugging the
function that would be called by evaluating the given expression.
When the call is to an S4 generic or standard S3 generic,
debugcall() debugs the method that would be dispatched. A number
of internal utilities were added to support this, most notably
utils::isS3stdGeneric(). (Based on a patch by Gabe Becker.)
And many more - see the NEWS file for details.
|
|
PkgSrc changes:
* On Darwin, use Aqua interface instead of X11
* Cairo support also requires Pango
* Allow Cairo with other backends, not only X11 (e.g. to make it work on Darwin)
|
|
Also move fixes from configure to configure.ac
m4/R.m4 fix by @joerg
Oked @joerg
|
|
cpow and clog are not implemented on FreeBSD and the configure checks only
emit warnings instead of errors.
Ok@ markd
|
|
|
|
|
|
|
|
|
|
Upstream 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 §8 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).
|
|
|
|
Upstream 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.)
|
|
|
|
NetBSD 7.0 and earlier.
|
|
|
|
Upstream 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.
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.
UTILITIES:
* R CMD check has a new option --ignore-vignettes for use with
non-Sweave vignettes whose VignetteBuilder package is not
available.
* R CMD check now by default checks code usage (_via_ codetools)
with only the base package attached. Functions from default
packages other than base which are used in the package code but
not imported are reported as undefined globals, with a suggested
addition to the NAMESPACE file.
* R CMD check --as-cran now also checks DOIs in package CITATION
and Rd files.
* R CMD Rdconv and R CMD Rd2pdf each have a new option
--RdMacros=pkglist which allows Rd macros to be specified before
processing.
DEPRECATED AND DEFUNCT:
* The previously included versions of zlib, bzip2, xz and PCRE have
been removed, so suitable external (usually system) versions are
required (see the 'R Installation and Administration' manual).
* The unexported and undocumented Windows-only devices cairo_bmp(),
cairo_png() and cairo_tiff() have been removed. (These devices
should be used as e.g. bmp(type = "cairo").)
* (Windows only) Function setInternet2() has no effect and will be
removed in due course. The choice between methods "internal" and
"wininet" is now made by the method arguments of url() and
download.file() and their defaults can be set _via_ options. The
out-of-the-box default remains "wininet" (as it has been since R
3.2.2).
* [<- with an S4 value into a list currently embeds the S4 object
into its own list such that the end result is roughly equivalent
to using [[<-. That behavior is deprecated. In the future, the
S4 value will be coerced to a list with as.list().
* Package tools' functions package.dependencies(), pkgDepends(),
etc are deprecated now, mostly in favor of package_dependencies()
which is both more flexible and efficient.
INSTALLATION and INCLUDED SOFTWARE:
* Support for very old versions of valgrind (e.g., 3.3.0) has been
removed.
* The included libtool script (generated by configure) has been
updated to version 2.4.6 (from 2.2.6a).
* libcurl version 7.28.0 or later with support for the https
protocol is required for installation (except on Windows).
* BSD networking is now required (except on Windows) and so
capabilities("http/ftp") is always true.
* configure uses pkg-config for PNG, TIFF and JPEG where this is
available. This should work better with multiple installs and
with those using static libraries.
* The minimum supported version of OS X is 10.6 ('Snow Leopard'):
even that has been unsupported by Apple since 2012.
* The configure default on OS X is --disable-R-framework: enable
this if you intend to install under /Library/Frameworks and use
with R.app.
* The minimum preferred version of PCRE has since R 3.0.0 been 8.32
(released in Nov 2012). Versions 8.10 to 8.31 are now deprecated
(with warnings from configure), but will still be accepted until
R 3.4.0.
* configure looks for C functions __cospi, __sinpi and __tanpi and
uses these if cospi _etc_ are not found. (OS X is the main
instance.)
* (Windows) R is now built using gcc 4.9.3. This build will
require recompilation of at least those packages that include C++
code, and possibly others. A build of R-devel using the older
toolchain will be temporarily available for comparison purposes.
During the transition, the environment variable R_COMPILED_BY has
been defined to indicate which toolchain was used to compile R
(and hence, which should be used to compile code in packages).
The COMPILED_BY variable described below will be a permanent
replacement for this.
* (Windows) A make and R CMD config variable named COMPILED_BY has
been added. This indicates which toolchain was used to compile R
(and hence, which should be used to compile code in packages).
PACKAGE INSTALLATION:
* The make macro AWK which used to be made available to files such
as src/Makefile is no longer set.
C-LEVEL FACILITIES:
* The API call logspace_sum introduced in R 3.2.0 is now remapped
as an entry point to Rf_logspace_sum, and its first argument has
gained a const qualifier. (PR#16470)
Code using it will need to be reinstalled.
Similarly, entry point log1pexp also defined in Rmath.h is
remapped there to Rf_log1pexp
* R_GE_version has been increased to 11.
* New API call R_orderVector1, a faster one-argument version of
R_orderVector.
* When R headers such as R.h and Rmath.h are called from C++ code
in packages they include the C++ versions of system headers such
as <cmath> rather than the legacy headers such as <math.h>.
(Headers Rinternals.h and Rinterface.h already did, and inclusion
of system headers can still be circumvented by defining
NO_C_HEADERS, including as from this version for those two
headers.)
The manual has long said that R headers should *not* be included
within an extern "C" block, and almost all the packages affected
by this change were doing so.
* Including header S.h from C++ code would fail on some platforms,
and so gives a compilation error on all.
* The deprecated header Rdefines.h is now compatible with defining
R_NO_REMAP.
* The connections API now includes a function R_GetConnection()
which allows packages implementing connections to convert R
connection objects to Rconnection handles used in the API. Code
which previously used the low-level R-internal getConnection()
entry point should switch to the official API.
BUG FIXES:
* C-level asChar(x) is fixed for when x is not a vector, and it
returns "TRUE"/"FALSE" instead of "T"/"F" for logical vectors.
* The first arguments of .colSums() etc (with an initial dot) are
now named x rather than X (matching colSums()): thus error
messages are corrected.
* A coef() method for class "maov" has been added to allow vcov()
to work with multivariate results. (PR#16380)
* method = "libcurl" connections signal errors rather than
retrieving HTTP error pages (where the ISP reports the error).
* xpdrows.data.frame() was not checking for unique row names; in
particular, this affected assignment to non-existing rows via
numerical indexing. (PR#16570)
* tail.matrix() did not work for zero rows matrices, and could
produce row "labels" such as "[1e+05,]".
* Data frames with a column named "stringsAsFactors" now format and
print correctly. (PR#16580)
* cor() is now guaranteed to return a value with absolute value
less than or equal to 1. (PR#16638)
* Array subsetting now keeps names(dim(.)).
* Blocking socket connection selection recovers more gracefully on
signal interrupts.
* The data.frame method of rbind() construction row.names works
better in borderline integer cases, but may change the names
assigned. (PR#16666)
* (X11 only) getGraphicsEvent() miscoded buttons and missed mouse
motion events. (PR#16700)
* methods(round) now also lists round.POSIXt.
* tar() now works with the default files = NULL. (PR#16716)
* Jumps to outer contexts, for example in error recovery, now make
intermediate jumps to contexts where on.exit() actions are
established instead of trying to run all on.exit() actions before
jumping to the final target. This unwinds the stack gradually,
releases resources held on the stack, and significantly reduces
the chance of a segfault when running out of C stack space. Error
handlers established using withCallingHandlers() and
options("error") specifications are ignored when handling a C
stack overflow error as attempting one of these would trigger a
cascade of C stack overflow errors. (These changes resolve
PR#16753.)
* The spacing could be wrong when printing a complex array.
(Report and patch by Lukas Stadler.)
* pretty(d, n, min.n, *) for date-time objects d works again in
border cases with large min.n, returns a labels attribute also
for small-range dates and in such cases its returned length is
closer to the desired n. (PR#16761) Additionally, it finally
does cover the range of d, as it always claimed.
* tsp(x) <- NULL did not handle correctly objects inheriting from
both "ts" and "mts". (PR#16769)
* install.packages() could give false errors when
options("pkgType") was "binary". (Reported by Jose Claudio
Faria.)
* A bug fix in R 3.0.2 fixed problems with locator() in X11, but
introduced problems in Windows. Now both should be fixed.
(PR#15700)
* download.file() with method = "wininet" incorrectly warned of
download file length difference when reported length was unknown.
(PR#16805)
* diag(NULL, 1) crashed because of missed type checking.
(PR#16853)
|
|
|
|
|
|
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.
provideDimnames() gets an optional unique argument.
shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
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.
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’.
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.
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.
|
|
|
|
|
|
|
|
|
|
Problems found locating distfiles:
Package dfftpack: missing distfile dfftpack-20001209.tar.gz
Package eispack: missing distfile eispack-20001130.tar.gz
Package fftpack: missing distfile fftpack-20001130.tar.gz
Package linpack: missing distfile linpack-20010510.tar.gz
Package minpack: missing distfile minpack-20001130.tar.gz
Package odepack: missing distfile odepack-20001130.tar.gz
Package py-networkx: missing distfile networkx-1.10.tar.gz
Package py-sympy: missing distfile sympy-0.7.6.1.tar.gz
Package quadpack: missing distfile quadpack-20001130.tar.gz
Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden). All existing
SHA1 digests retained for now as an audit trail.
|
|
|
|
|
|
Upstream changes:
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.
|
|
|
|
Upstream changes:
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.
|
|
|
|
libtool changes. Fixes CHECK_WRKREF builds.
|
|
having a PKGNAME of p5-*, or depending such a package,
for perl-5.22.0.
|
|
* Fix build under NetBSD 6.1.5.
Newer texinfo is required. From wen@.
|
|
|
|
|
|
Changelog:
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).
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.
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.)
* Omegahat is no longer listed as providing Windows binary
packages, e.g. by setRepositories(). It has no binary packages
available for R 3.1.x and those for earlier versions were 32-bit
only.
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.
|
|
|
|
--with-internal-tzcode=yes
|
|
|
