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Upstream changes:
0.58 2016-05-21
[API Changes]
- prev_prime($n) where $n <= 2 now returns undef instead of 0. This
may enable catching range errors, and is technically more correct.
- nth_prime(0) now returns undef instead of 0. This should help catch
cases where the base wasn't understood. The change is similar for
all the nth_* functions (e.g. nth_twin_prime).
- sumdigits(n,base) will interpret n as a number in the given base,
rather than the Pari/GP method of converting decimal n to that base
then summing. This allows sumdigits to easily sum hex strings.
The old behavior is easily done with vecsum(todigits(n, base)).
- binary() was not intended to be released (todigits and todigitstring
are supersets), but the documentation got left in. Remove docs.
[ADDED]
- addmod(a, b, n) a + b mod n
- mulmod(a, b, n) a * b mod n
- divmod(a, b, n) a / b mod n
- powmod(a, b, n) a ^ b mod n
- sqrtmod(a, n) modular square root
- is_euler_pseudoprime(n,a[...]) Euler test to given bases
- is_primitive_root(r, n) is r a primitive root mod n
- is_quasi_carmichael(n) is n a Quasi-Carmichael number
- hclassno(n) Hurwitz class number H(n) * 12
- sieve_range(n, width, depth) sieve to given depth, return offsets
[FUNCTIONALITY AND PERFORMANCE]
- Fixed incorrect table entries for 2^16th Ramanujan prime count and
nth_ramanujan_prime(23744).
- foroddcomposites with certain arguments would start with 10 instead of 9.
- lucasu and lucasv should return bigint types.
- vecsum will handle 128-bit sums internally (performance increase).
- Speedup is_carmichael.
- Speedup znprimroot, 10% for small inputs, 10x for large composites.
- Speedup znlog ~2x. It is now Rho racing an interleaved BSGS.
- Change AKS to Bernstein 2003 theorem 4.1.
5-20x faster than Bornemann, 20000+x faster than V6.
- sum_primes now uses tables for native sizes (performance increase).
- ramanujan_tau uses Cohen's hclassno method instead of the sigma
calculation. This is 3-4x faster than the GMP code for inputs > 300k,
and much faster than the older PP code.
- fromdigits much faster for large base-10 arrays. Timing is better than
split plus join when output is a bigint.
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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)
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