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From paradis at isem.univ-montp2.fr Thu May 18 10:51:48 2000
From: paradis at isem.univ-montp2.fr (Emmanuel Paradis)
Date: Thu, 18 May 2000 10:51:48 +0200 (MET DST)
Subject: tutorial =?iso-8859-1?Q?=22R_pour_les_d=E9butants=22_?= is
available on CRAN
Message-ID: <[email protected]>
Dear R-users,
Thanks to Friedrich Leisch, my document "R pour les d?butants" is available
on CRAN in the contributed documentation section:
http://cran.r-project.org/doc/contrib/Rdebuts.pdf.
It is written in French. "R pour les d?butants" ("R for beginners") gives a
starting point for people with no experience with R (or S). I tried to
explain the basics in the simplest way, as well as giving useful details
(mostly with tables). Any feed-back would be greatly appreciated. If some
people think that an English translation would be useful, I would be ready
to consider it.
Chers utilisateurs de R,
Gr?ce ? Friedrich Leisch, mon document "R pour les d?butants" est
disponible sur CRAN dans la section "contributed documentation":
http://cran.r-project.org/doc/contrib/Rdebuts.pdf.
Le but de "R pour les d?butants" est de fournir un point de d?part pour les
utilisateurs qui n'ont aucune exp?rience avec R (ou S). J'ai essay? de
simplifier les explications, tout en donnant des d?tails utiles (le plus
souvent sous forme de tableaux). Tout commentaire ou suggestion serait
grandement appr?ci?. Si certaines personnes pensent qu'une tranduction en
anglais serait utile, je serais pr?t ? examiner cette possibilit?.
Emmanuel Paradis
Laboratoire de Pal?ontologie
Institut des Sciences de l'Evolution
Universit? Montpellier II
F-34095 Montpellier c?dex 05
France
phone: +33 4 67 14 39 64
fax: +33 4 67 14 36 10
mailto:paradis at isem.univ-montp2.fr
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|
tutorial =?iso-8859-1?Q?=22R_pour_les_d=E9butants=22_?= is available on CRAN
|
Emmanuel Paradis
| 317 |
|
From pd.mes at cbs.dk Thu Dec 22 12:02:34 2011
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 22 Dec 2011 12:02:34 +0100
Subject: R 2.14.1 is released
Message-ID: <[email protected]>
The byte pixies have rolled up R-2.14.1.tar.gz (codename "December Snowflakes") at 9:00 this morning. This is a maintenance release; see the list below for details.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.14.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 3a8fc6d4f7ae7c6f7e42b028240a46b0
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 99d2842cf6a964716e960fadead402c4
MD5 (NEWS.html) = 592a459fecefd8bb4573ba45ea9d3f36
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = ba5b6fb15b660670ea29b885348f322a
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc
MD5 (R-2/R-2.14.1.tar.gz) = ba5b6fb15b660670ea29b885348f322a
This is the relevant part of the NEWS file (yes, I _have_ spotted the minor mishap....):
CHANGES IN R VERSION 2.14.0 patched:
NEW FEATURES:
o parallel::detectCores() is now able to find the number of
physical cores (rather than CPUs) on Sparc Solaris.
It can also do so on most versions of Windows; however the
default remains detectCores(logical = TRUE) on that platform.
o Reference classes now keep a record of which fields are locked.
$lock() with no arguments returns the names of the locked fields.
o HoltWinters() reports a warning rather than an error for some
optimization failures (where the answer might be a reasonable
one).
o tools::dependsOnPkg() now accepts the shorthand dependencies =
"all".
o parallel::clusterExport() now allows specification of an
environment from which to export.
o The quartz() device now does tilde expansion on its file
argument.
o tempfile() on a Unix-alike now takes the process ID into account.
This is needed with multicore (and as part of parallel) because
the parent and all the children share a session temporary
directory, and they can share the C random number stream used to
produce the uniaue part. Further, two children can call
tempfile() simultaneously.
o Option print in Sweave's RweaveLatex() driver now emulates
auto-printing rather than printing (which can differ for an S4
object by calling show() rather than print()).
o filled.contour() now accepts infinite values: previously it might
have generated invalid graphics files (e.g. containing NaN
values).
INSTALLATION:
o On 64-bit Linux systems, configure now only sets LIBnn to lib64
if /usr/lib64 exists. This may obviate setting LIBnn explicitly
on Debian-derived systems.
It is still necessary to set LIBnn = lib (or lib32) for 32-bit
builds of R on a 64-bit OS on those Linux distributions capable
for supporting that concept.
o configure looks for inconsolata.sty, and if not found adjusts the
default R_RD4PDF to not use it (with a warning, since it is
needed for high-quality rendering of manuals).
PACKAGE INSTALLATION:
o R CMD INSTALL will now do a test load for all sub-architectures
for which code was compiled (rather than just the primary
sub-architecture).
UTILITIES:
o When checking examples under more than one sub-architecture, R
CMD check now uses a separate directory examples_arch for each
sub-architecture, and leaves the output in file
pkgname-Ex_arch.Rout. Some packages expect their examples to be
run in a clean directory ....
BUG FIXES:
o stack() now gives an error if no vector column is selected,
rather than returning a 1-column data frame (contrary to its
documentation).
o summary.mlm() did not handle objects where the formula had been
specified by an expression. (Reported by Helios de Rosario
Martinez).
o tools::deparseLatex(dropBraces=TRUE) could drop text as well as
braces.
o colormodel = "grey" (new in R 2.14.0)) did not always work in
postscript() and pdf().
o file.append() could return TRUE for failures. (PR#14727)
o gzcon() connections are no longer subject to garbage collection:
it was possible for this to happen when unintended (e.g. when
calling load()).
o nobs() does not count zero-weight observations for glm() fits,
for consistency with lm(). This affects the BIC() values
reported for such glm() fits. (Spotted by Bill Dunlap.)
o options(warn = 0) failed to end a (C-level) context with more
than 50 accumulated warnings. (Spotted by Jeffery Horner.)
o The internal plot.default() code did not do sanity checks on a
cex argument, so invalid input could cause problems. (Reported
by Ben Bolker.)
o anyDuplicated(<array>, MARGIN=0) no longer fails. (Reported by
Herv'e Pag`es.)
o read.dcf() removes trailing blanks: unfortunately on some
platforms this included \xa0 (non-breaking space) which is the
trailing byte of a UTF-8 character. It now only considers ASCII
space and tab to be 'blank'.
o There was a sign error in part of the calculations for the
variance returned by KalmanSmooth(). (PR#14738)
o pbinom(10, 1e6, 0.01, log.p = TRUE) was NaN thanks to the buggy
fix to PR#14320 in R 2.11.0. (PR#14739)
o RweaveLatex() now emulates auto-printing rather than printing, by
calling methods::show() when auto-printing would.
o duplicated() ignored fromLast for a one-column data frame.
(PR#14742)
o source() and related functions did not put the correct timestamp
on the source references; srcfilecopy() has gained a new argument
timestamp to support this fix. (PR#14750)
o LaTeX conversion of Rd files did not correctly handle
preformatted backslashes. (PR#14751)
o HTML conversion of Rd files did not handle markup within tabular
cells properly. (PR#14708)
o source() on an empty file with keep.source = TRUE tried to read
from stdin(), in R 2.14.0 only. (PR#14753)
o The code to check Rd files in packages would abort if duplicate
description sections were present.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.14.1 is released
|
Peter Dalgaard
| 410 |
|
From pd@me@ @end|ng |rom cb@@dk Thu Mar 12 13:30:35 2020
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Thu, 12 Mar 2020 12:30:35 +0000
Subject: [Rd] R 4.0.0 scheduled for April 24
Message-ID: <[email protected]>
Full schedule is available on developer.r-project.org.
Notice that Copenhagen Business School, like all Danish educational institutions, is physically locked down for two weeks due to COVID-19. The schedule is automated, but there may be irregularities with the nightly builds, if things act up and I can't get to the machine.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
|
[Rd] R 4.0.0 scheduled for April 24
|
Peter Dalgaard
| 617 |
|
From kmullen at nist.gov Mon Feb 1 20:31:12 2010
From: kmullen at nist.gov (Katharine Mullen)
Date: Mon, 1 Feb 2010 14:31:12 -0500 (EST)
Subject: Abstract submission deadline, useR! 2010
Message-ID: <[email protected]>
The abstract submission deadline for the R Users Conference, useR! 2010,
is just one month away.
Submission deadline: 2010-03-01
Early registration will also close on 2010-03-01.
Now is the perfect time to prepare an abstract presenting innovations or
exciting applications of R. The call for abstracts along with the link for
submission is available at:
http://www.R-project.org/useR-2010/#Call
This meeting of the R user community will take place at the Gaithersburg,
Maryland, USA campus of the National Institute of Standards and Technology
(NIST), July 21-23, 2010.
The conference schedule is comprised of invited lectures and
user-contributed sessions as well as half-day tutorials presented by R
experts on July 20, 2010, prior to the conference.
Invited speakers will include
Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer,
Richard Stallman, Luke Tierney, and Diethelm Wuertz.
The full spectrum of conference information is available from the webpage:
http://www.R-project.org/useR-2010/
We hope to meet you in Gaithersburg!
Kate Mullen, for the organizing committee
|
Abstract submission deadline, useR! 2010
|
Katharine Mullen
| 358 |
|
From mikalzet at libero.it Tue Jul 3 12:54:45 2001
From: mikalzet at libero.it (mikalzet at libero.it)
Date: Tue, 3 Jul 2001 12:54:45 +0200 (CEST)
Subject: R-1.3.0 RPM for Mandrake 8.0 (correct version)
Message-ID: <[email protected]>
The RPM of R-1.3.0 for Mandrake 8.0 is now available on CRAN
in the complete and correct version.
Sorry to all those who had problems with the previous version
because of absent linking against the readline library.
--
Michele Alzetta
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
R-1.3.0 RPM for Mandrake 8.0 (correct version)
|
mikalzet at libero.it
| 258 |
|
From p.murrell at auckland.ac.nz Tue Dec 18 04:52:36 2001
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Tue, 18 Dec 2001 16:52:36 +1300
Subject: new versions of grid and lattice
Message-ID: <[email protected]>
Hi
New versions of the grid and lattice packages will be available with the
release of R 1.4 (in a couple of days):
grid_0.5
lattice_0.3-1
These packages will no longer be in the "development" directory (i.e., they
will be in CRAN/src/contrib).
The changes in this release are mostly to grid, with lattice modified just
to take account of those changes.
Some important points about the grid changes are ...
(i) grid_0.5 will only work with R version 1.4 or later.
(ii) The main new features are support for clipping to viewports and
support for multiple devices. See the file grid/doc/changes_0.5.txt for
other changes.
(iii) There is a known bug on Windows; turning on plot history recording
while producing grid graphics will crash R. Adding individual plots to the
plot history seems to work ok.
(iv) Some things still missing are: vector fonts, mathematical annotation,
compatibility with base graphics, and many helpful suggestions from users
that I still haven't found time to get to! :)
Paul Murrell
Deepayan Sarkar
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
new versions of grid and lattice
|
Paul Murrell
| 282 |
|
From Achim.Zeileis at wu-wien.ac.at Mon Mar 22 20:49:42 2004
From: Achim.Zeileis at wu-wien.ac.at (Achim Zeileis)
Date: Mon, 22 Mar 2004 20:49:42 +0100
Subject: useR! 2004 program online
Message-ID: <[email protected]>
Dear useRs,
the program for the first R user conference useR! 2004 (taking place in
Vienna, May 20-22) is now available online at the conference web page:
http://www.ci.tuwien.ac.at/Conferences/useR-2004/program.html
We received many exciting abstracts about a wide spectrum of
applications in which R is used. This is reflected in the program and I
think we can look forward to a very interesting useR! conference.
Note that the early registration deadline is 2004-03-31 so that you can
still register as an early bird if you want to visit this event.
For the organizing committee,
Achim Zeileis, Torsten Hothorn, and David Meyer
|
useR! 2004 program online
|
Achim Zeileis
| 376 |
|
From murdoch at stats.uwo.ca Tue Oct 5 21:52:22 2004
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 05 Oct 2004 15:52:22 -0400
Subject: [R] R 2.0.0 is released
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
On 04 Oct 2004 17:29:39 +0200, Peter Dalgaard
<p.dalgaard at biostat.ku.dk> wrote :
>
>I've rolled up R-2.0.0.tar.gz a short while ago. This is a new version
>with a number of new features. See below for the details.
>
>As was the case with R 1.0.0, this new version represents a coming of
>age more than a radical change to R. We do plan to celebrate the new
>major version with press releases and such.
>
>The release will be available from
>
>http://cran.r-project.org/src/base/R-2/R-2.0.0.tar.gz
>
>or you might wait for it to be mirrored at a CRAN site nearer to you.
>Binaries for various platforms will appear in due course.
The Windows binary build is now on CRAN at
http://cran.r-project.org/bin/windows/base
and the mirrors, e.g. the U.S. mirror
http://cran.us.r-project.org/bin/windows/base
A few of the links on the page are broken today, but should be fixed
tomorrow.
Duncan Murdoch
|
[R] R 2.0.0 is released
|
Duncan Murdoch
| 384 |
|
From bates at stat.wisc.edu Mon Feb 26 15:41:09 2001
From: bates at stat.wisc.edu (Douglas Bates)
Date: 26 Feb 2001 08:41:09 -0600
Subject: R-1.2.2 via rsync
Message-ID: <[email protected]>
R-1.2.2 is now available via rsync as rsync.r-project.org::r-release
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
R-1.2.2 via rsync
|
Douglas Bates
| 224 |
|
From P.Dalgaard at biostat.ku.dk Fri Jun 26 16:20:07 2009
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Fri, 26 Jun 2009 16:20:07 +0200
Subject: R 2.9.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.9.1.tar.gz a few hours ago.
This is a maintenance release and fixes a number of mostly minor issues.
See the full list of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.9.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
11a746c387c5a94f172a27939b96dd4c NEWS
7abcbbc7480df75a11a00bb09783db90 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
8ea34a9306ef5cf5dc03b45883586129 FAQ
54a79eebdf0cec3fd2c489fc94d99b00 R-2.9.1.tar.gz
54a79eebdf0cec3fd2c489fc94d99b00 R-latest.tar.gz
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.9.1
NEW FEATURES
o New function anyDuplicated(x) returns 0 (= FALSE) or the index
of the first duplicated entry of x.
o matplot(), matlines() and matpoints() now also obey a 'lend'
argument, determining line end styles. (Wish of PR#13619).
o bw.SJ(), bw.bcv() and bw.ucv() now gain an optional 'tol'
argument allowing more accurate estimates.
o new.packages() no longer regards packages with the same name
as a member of an installed bundle as 'new' (this is now
consistent with the dependency checks in install.packages()).
It no longer reports on partially installed bundles (since
members can be updated individually if a bundle is unbundled).
o old.packages() and hence updates.packages() will look for
updates to members of package bundles before updates to the
whole bundle: this allow bundles to be split and installations
updated.
o nlminb() gives better non-convergence messages in some cases.
o S3 method dispatch will support S4 class inheritance for S3
methods, for primitives and via UseMethod(), if the argument
S3methods=TRUE is given to setClass(). S4 method dispatch
will use S3 per-object inheritance if S3Class() is set on the
object. See ?Methods and the paper referenced there.
o R CMD INSTALL is more tolerant of (malformed) packages with a
'man' directory but no validly named .Rd files.
o R CMD check now reports where options are used that cause some
of the checks to be skipped.
o RSiteSearch has been updated to be consistent with the new
layout of the search site itself, which now includes separate
options for vignettes, views, and r-sig-mixed-models, as well
as changed names for r-help. (Contributed by Jonathan Baron.)
o That R CMD check makes use of a
<pkg>/tests/Examples/<pkg>-Ex.Rout.save file as a reference
result is now documented in 'Writing R Extensions'.
DEPRECATED & DEFUNCT
o print.atomic() (defunct since 1.9.0) has been removed since it
caused confusion for an S4 class union "atomic".
o png(type="cairo1") is deprecated -- it was only needed for
platforms with 1.0 <= cairo < 1.2.
BUG FIXES
o The ... argument was not handled properly when ... was found
in the enclosure of the current function, rather than in the
function header itself. (This caused integrate() to fail in
certain cases.)
o col2rgb("#00000080", TRUE) would return the background colour.
(Reported by Hadley Wickham.)
o interaction() now ensures that the levels of the result are unique.
o packageDescription() and hence sessionInfo() now report the correct
package version also for a non-attached loaded namespace of
a version different from the default lib.loc.
o smoothScatter() now also works when e.g. xlim[2] < xlim[1].
o Invalid use of sprintf() such as sprintf("%S%") now give an error
instead of a segmentation fault, as do very unusual cases such as
sprintf("%s", tryCatch(stop(), error=identity)). (It was
always documented that misuse could crash R in
platform-dependent ways.)
o parse_Rd() would mishandle braces when they occurred at
the start of a line within an R string in an Rd file (reported
by Alex Couture-Beil) or when they occurred in an R comment
(reported by Mark Bravington).
o readNEWS() missed version numbers with more than one digit.
o building R --without-x no longer fails (PR#13665)
o printCoefmat(cbind(0,1)) now works too (PR#13677)
o bw.SJ(c(1:99, 1e6)) now works too.
o Rd2txt() could not handle empty descriptions of items in an Rd
file (reported by Mark Bravington), and did not wrap long lists
of arguments if they were given in a single item.
o stars() would do a partial plot when called with plot = FALSE;
it now consistently returns the locations of the stars.
o Rd2latex() could not handle empty sections.
o old.packages() and hence update.packages() would fail on a
repository which contained only one package but with multiple
versions of that package.
o as.character.Rd() added extra braces when displaying two-argument
macros. (Report and fix by Manuel Eugster.)
o unsplit() was misbehaving in the case of single-column data
frames. (Reported by Will Gray.)
o as(I(1), "vector") and similar coercions from objects of
"unregistered" S3 classes now work.
o srcref records produced by parse() and parse_Rd() did not record
the encoding of the source file. (Reported by Romain Francois.)
o The X11 version of View() was misbehaving in MBCS locales, and
PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama.
o R CMD check looked at the environment variable PDFLATEX, but
as from R 2.8.1 R CMD Rd2dvi used R_PDFLATEXCMD in
preference, and that was set by R CMD (and not PDFLATEX). Now
R CMD check looks at R_PDFLATEXCMD.
o sprintf() now signals an error when the result of single format
specification would be longer than the limit (8192 bytes); it would
return "somewhat random" results or segfault previously. (PR#13667)
Further, arguments of type "language" or "symbol" are no longer
allowed, as these, e.g., sprintf("%s", quote(list())), typically
lead to unexpected results or hard to understand error messages.
o The new (in 2.9.0) 'stringsAsFactors' argument to expand.grid()
was not working: it now does work but has default TRUE for
backwards compatibility.
o tcrossprod(<1d-array>, <matrix>) now does work when the arguments
are of compatible dimensions.
o qbinom() now is accurate also in (large size, small prob)
cases. (PR#13711)
o The calculation of the Spearman p-value in cor.test() is
slightly more accurate in some cases. (PR#13574)
o The digamma(), trigamma() and psigamma() functions could be
inaccurate for values of x around 1e-15 due to cancellation.
(PR#13714).
o median.default() was altered in 2.8.1 to use sum() rather
than mean(), although it was still documented to use mean().
This caused problems for POSIXt objects, for which mean() but
not sum() makes sense, so the change has been reverted.
o Assigning an extra 0-length column to a data frame by
DF$foo <- value gave a corrupt data frame rather than failing.
(PR#13724) This also happened for DF[["foo"]] <- value.
o R CMD INSTALL no longer gives a spurious warning about old R
versions ignoring multiple dependencies, if the conditions are
known to be satisfied.
o The test for setting dim() allowed a value with two or more
NAs to be set on a 0-length object. (PR#13729) Also, it
allowed an even number of negative values.
o xtfrm(), rank(), sort() and order() did not always make use of
custom comparison methods specific to the class of elements
being sorted.
o Increase NAMED value on 'seq' value in for() loop so loop code
cannot modify 'seq' value.
o Prevent rectangles of size < 0.5 pixel from disappearing in
Quartz when using rastered backend. (PR#13744)
o Printing _NA_complex_ had a low-level thinko; patch thanks to
Bill Dunlap.
o CP1257 encoding for postscript/PDF has been corrected. (PR#13736)
o aov() with an error term was evaluating the ... arguments in
2.9.0 whilst checking their names, so could fail by evaluating
them in the wrong place. (PR#13733)
o The print() method for arima() failed if all coefs were fixed.
o R CMD INSTALL --no-latex was not implemented in 2.9.0 (only).
o Added a needed PROTECT call in RunFinalizers to handle cases where
the routine is called recursively from a GC in a finalizer.
o Constructing error messages about unused arguments in calls to
closures no longer evaluates the arguments.
o qr(x, LAPACK=TRUE) did not coerce integer x to numeric.
o qr.coef() misbehaved in the LAPACK case with a matrix RHS, so
that solve(qr(x, LAPACK=TRUE)) gave wrong results. (Found by
Avraham Adler, PR#13762 by Ravi Varadhan.)
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.9.1 is released
|
Peter Dalgaard
| 657 |
|
From Kurt.Hornik at ci.tuwien.ac.at Wed Apr 23 17:13:22 1997
From: Kurt.Hornik at ci.tuwien.ac.at (Kurt Hornik)
Date: Wed, 23 Apr 1997 17:13:22 +0200
Subject: R-FAQ v0.1-0
Message-ID: <[email protected]>
A much updated R FAQ is now available at the URL
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
The plain text version is appended below.
-k
*****************************************************************************
* Kurt Hornik * *
* Dept of Statistics TU Wien * tel: +43 (1) 58801-4542 *
* Wiedner Hauptstr 8-10/1071 * fax: +43 (1) 504-1498 *
* A-1040 Wien * email: Kurt.Hornik at ci.tuwien.ac.at *
* Austria * WWW: http://www.ci.tuwien.ac.at/~hornik *
*****************************************************************************
*****************************************************************************
R FAQ
Kurt Hornik
v0.1-0, 1997/04/23
This document contains answers to some of the most frequently asked
questions about R. Feedback is welcome.
______________________________________________________________________
Table of Contents:
1. Introduction
1.1 Legalese
1.2 Obtaining this Document
1.3 Notation
1.4 Feedback
2. R Basics
2.1 What Is R?
2.2 What Machines Does R Run on?
2.3 What Is the Current Version of R?
2.4 How Can R Be Obtained?
2.5 How Can R Be Installed?
2.5.1 How Can R Be Installed (Unix)
2.5.2 How Can R Be Installed (Windows)
2.5.3 How Can R Be Installed (Macintosh)
2.6 Are there Unix Binaries for R?
2.7 Which Documentation Exists for R?
2.8 Which Mailing Lists Exist for R?
2.9 What is CRAN?
3. R and S
3.1 What Is S?
3.2 What Is S-PLUS?
3.3 What Are the Differences between R and S?
4. R Add-On Packages
4.1 Which Add-on Packages Exist for R?
4.2 How Can Add-on Packages Be Installed?
4.3 How Can Add-on Packages Be Used?
4.4 How Can I Contribute to R?
5. R and Emacs
5.1 Is there Emacs Support for R?
5.2 Should I Run R from Within Emacs?
6. R Miscellania
6.1 How Can I Read a Large Data Set into R?
6.2 Why Can't R Source a `Correct' File?
6.3 How Can I Set Components of a List to NULL?
6.4 How Can I Save My Workspace?
6.5 How Can I Clean Up My Workspace?
7. Acknowledgments
______________________________________________________________________
11..
This document contains answers to some of the most frequently asked
questions about R.
11..11..
This document is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
If you do not have a copy of the GNU General Public License, write to
the Free Software Foundation, 59 Temple Place - Suite 330, Boston, MA
02111-1307, USA.
11..22..
The latest version of this document is always available from
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html.
From there, you can also obtain versions converted to plain ASCII
text, GNU info, DVI, and PostScript, as well as the SGML source used
for creating all these formats using the SGML-Tools (formerly
Linuxdoc-SGML) system. (Note that right now cross-references don't
work in the translation to plain ASCII.)
11..33..
Everything should be pretty standard. `R>' is used for the R prompt,
and a `$' for the shell prompt (where applicable).
11..44..
Feedback is of course most welcome.
In particular, note that I do not have access to Windows or Mac
systems. If you have information on these systems that you think
should be added to this document, please let me know.
22..
22..11..
R is a system for statistical computation and graphics. It consists
of a language plus a run-time environment with graphics, a debugger,
access to certain system functions, and the ability to run programs
stored in script files.
The design of R has been heavily influenced by two existing languages:
Becker, Chambers & Wilks' S (see question ``What is S?'') and
Sussman's Scheme. Whereas the resulting language is very similar in
appearance to S, the underlying implementation and semantics are
derived from Scheme. See question ``What Are the Differences between
R and S?'' for a discussion of the differences between R and S.
R is being developed by Ross Ihaka and Robert Gentleman, who are
Senior Lecturers at the Department of Statistics of the University of
Auckland in Auckland, New Zealand.
R is free software distributed under a GNU-style copyleft.
22..22.. WWhhaatt MMaacchhiinneess DDooeess RR RRuunn oonn??
R is being developed for the Unix, Windows and Mac platforms.
R will configure and build under a number of common Unix platforms
including dec-alpha-osf, freebsd, hpux, linux-elf, sgi-irix, solaris,
and sunos. If you know about other platforms, please drop me a note.
22..33.. WWhhaatt IIss tthhee CCuurrrreenntt VVeerrssiioonn ooff RR??
The current Unix version is 0.49, the previous one was 0.16.1. The
jump in the version number reflects the fact that this version
represents quite a jump towards what is hoped to be in the eventual
1.0 release. (However, it fell a little short of what was wanted for
0.50.) Version 0.49 added group methods and complex numbers, and
hence more or less provides a full implementation of S as described in
``The New S Language''.
The versions for Windows and Mac are pre-alpha. With some good luck,
the Windows version will soon catch up with the Unix version.
22..44..
Sources, binaries and documentation for R can be obtained via CRAN,
the ``Comprehensive R Archive Network'' (see question ``What is
CRAN?'').
22..55.. HHooww CCaann RR BBee IInnssttaalllleedd??
22..55..11..
If binaries are available for your platform (see question ``Are there
Unix Binaries for R?''), you can use these, following the instructions
that come with them.
Otherwise, you can compile and install R yourself, which can be done
very easily under a number of common Unix platforms (see question
``What Machines Does R Run on?''). The file INSTALL that comes with
the R distribution contains instructions.
Choose a place to install the R tree (R is not just a binary, but has
additional data sets, help files, font metrics etc). Let's call this
place RHOME (given appropriate permissions, a natural choice would be
`/usr/local/lib/R'). Untar the source code, and issue the following
commands (at the shell prompt):
$ ./configure
$ make
$ make install-help
You can also build a LaTeX version of the manual entries with
$ make install-latex
and an HTML version of the manual with
$ make install-html
If these commands execute successfully, the R binary will be copied to
the `$RHOME/bin' directory. In addition, a shell script font-end
called `R' will be created and copied to the same directory. You can
copy this script to a place where users can invoke it, for example to
`/usr/local/bin'. You could also copy the man page `R.1' to a place
where your man reader finds it, such as `/usr/local/man/man1'.
22..55..22..
Get the file `Rexe.zip' from the `bin/ms-windows' directory of a CRAN
site. This archive contains a binary Windows 3.xx distribution for R
and installation instructions.
Robert Gentleman has recently made an updated pre-alpha Windows
executable file available for ftp at
ftp://stat.auckland.ac.nz/pub/research/rgentlem/rbeta.zip. This
binary should be more compatible with Windows 95 than the other (he
does not know about 3.1). You still need all the other extra files
from the previous Windows distribution, it is only an executable.
22..55..33..
CRAN sites have a directory `bin/macintosh' which contains
`R.sea.hqx', a binhexed self-extracting archive, and installation
instructions in `README.MACINTOSH'.
22..66.. AArree tthheerree UUnniixx BBiinnaarriieess ffoorr RR??
Experimental `.deb' packages for installation under Debian GNU/Linux
can be found in `bin/ix86-linux'. No other binaries distributions for
Unix systems have thus far been made publically available.
22..77.. WWhhiicchh DDooccuummeennttaattiioonn EExxiissttss ffoorr RR??
Currently, there is no R manual. Online documentation for most of the
functions and variables in R exists, and can be printed on-screen by
typing help(_n_a_m_e) (or ?_n_a_m_e) at the R prompt, where _n_a_m_e is the name
of the R object help is sought for. (In the case of unary and binary
operators and control-flow special forms, the name may need to be be
quoted.)
This documentation can also be made available as HTML, and as hardcopy
via LaTeX, see question ``How Can R Be Installed?''. An up-to-date
HTML version is always available for web browsing at
http://www.stat.math.ethz.ch/R-manual
In the absence of a systematic introduction to R, one can mostly get
along with introductions to S or S-PLUS, such as ``Notes on S-PLUS: A
Programming Environment for Data Analysis and Graphics'' by Bill
Venables <venables at stats.adelaide.edu.au> and David Smith
<D.M.Smith at lancaster.ac.uk>. This document talks mostly about plain S
features, and does not concentrate on features specific to S-PLUS, and
is available from the Statlib S repository at
http://lib.stat.cmu.edu/S/SplusNotes/ (LaTeX source and PostScript).
An introduction to R based on it will soon be available.
Last, but not least, Ross' and Robert's experience in designing and
implementing R is described in:
@Article{,
author = {Ross Ihaka and Robert Gentleman},
title = {R: A Language for Data Analysis and Graphics},
journal = {Journal of Computational and Graphical Statistics},
year = 1996,
volume = 5,
number = 3,
pages = {299--314}
}
This is also the reference for R to use in publications.
22..88..
Thanks to Martin Maechler <maechler at stat.math.ethz.ch>, there are
three mailing lists devoted to R.
rr--aannnnoouunnccee
This list is for announcements about the development of R and
the availability of new code.
rr--ddeevveell
This list is for discussions about the future of R and pre-
testing of new versions. It is meant for those who maintain an
active position in the development of R.
rr--hheellpp
The `main' R mailing list, for announcements about the
development of R and the availability of new code, questions and
answers about problems and solutions using R, enhancements and
patches to the source code and documentation of R, comparison
and compatibility with S and S-plus, and for the posting of nice
examples and, benchmarks.
To send a message to everyone on the r-help mailing list, send email
to
r-help at stat.math.ethz.ch
To subscribe (or unsubscribe) to this list send subscribe (or unsub-
scribe) in the BODY of the message (not in the subject!) to r-help-
request at stat.math.ethz.ch. Information about the list can be obtained
by sending an email with info as its contens to r-help-
request at stat.math.ethz.ch.
Subscription and posting to the other lists is done analogously, with
`r-help' replaced by `r-announce' and `r-devel', respectively. Note
that the r-announce list is gatewayed into r-help, so you don't need
to subscribe to both of them.
It is recommended that you send mail to r-help rather than only to the
R developers (who are also subscribed to the list, of course). This
may save them precious time they can use for constantly improving R,
and will typically also result in much quicker feedback for yourself.
Of course, in the case of bug reports it would be very helpful to have
code which reliably reproduces the problem.
22..99.. WWhhaatt iiss CCRRAANN??
The ``Comprehensive R Archive Network'' (CRAN) is a collection of
sites which carry identical material, consisting of the R
distribution(s), the contributed extensions, documentation for R, and
binaries.
The CRAN master site can be found at the URL
ftp://ftp.ci.tuwien.ac.at/pub/R/
and is currently being mirrored daily at
http://lib.stat.cmu.edu/R/CRAN/
ftp://franz.stat.wisc.edu/pub/R/
ftp://ftp.stat.math.ethz.ch/R-CRAN/
Please use the CRAN site closest to you to reduce network load.
The structure of the CRAN tree is as follows.
``src/base'
contains the official R distribution as provided by Ross Ihaka
and Robert Gentleman.
``src/contrib'
contains code for extension packages.
``doc'
is for additional documentation and information on R.
``bin'
is for prebuilt R binaries (the base distribution and
extensions), grouped according to platforms. Currently, there
are only experimental packages for Debian GNU/Linux. I hope
that `.tar.gz' files with contents relative to an installation
tree (e.g. `bin', `lib/R/', and `man/man1/R.1') can be made
available soon for all major supported Unix platforms.
The process of ``submitting'' to CRAN currently is very simple: upload
to ftp://ftp.ci.tuwien.ac.at/incoming and send email to Kurt Hornik
<Kurt.Hornik at ci.tuwien.ac.at>. Please indicate the copyright
situation (GPL, ...) in your submission.
33..
33..11.. WWhhaatt IIss SS??
S is a very high level language and an environment for data analysis
and graphics. S was written by Richard A. Becker, John M. Chambers,
and Allan R. Wilks of AT&T Bell Laboratories Statistics Research
Department.
The primary references for S are two books by the creators of S.
+o Richard A. Becker, John M. Chambers and Allan R. Wilks (1988),
``The New S Language,'' Chapman & Hall, London.
This book is often called the ``_B_l_u_e _B_o_o_k''.
+o John M. Chambers and Trevor J. Hastie (1992), ``Statistical Models
in S,'' Chapman & Hall, London.
This is also called the ``_W_h_i_t_e _B_o_o_k''.
There is a huge amount of user-contributed code for S, available at
the S Repository at CMU.
See the ``Frequently Asked Questions about S''
(http://lib.stat.cmu.edu/S/faq) for further information about S.
33..22.. WWhhaatt IIss SS--PPLLUUSS??
S-PLUS is a value-added version of S sold by Statistical Sciences,
Inc. (now a division of Mathsoft, Inc.) S is a subset of S-PLUS, and
hence anything which may be done in S may be done in S-PLUS. In
addition S-PLUS has extended functionality in a wide variety areas,
including robust regression, modern nonparametric regression, time
series, survival analysis, multivariate analysis, classical
statistical tests, quality control, and graphics drivers. Add-on
modules add additional capabilities for wavelet analysis, spatial
statistics, and design of experiments.
See the MathSoft S-PLUS page (http://www.mathsoft.com/splus.html) for
further information.
33..33.. WWhhaatt AArree tthhee DDiiffffeerreenncceess bbeettwweeeenn RR aanndd SS??
Whereas the developers of R have tried to stick to the S language as
defined in ``The New S Language'' (Blue Book, see question ``What is
S?''), they have adopted the evaluation model of Scheme.
This difference becomes manifest when _f_r_e_e variables occur in a
function. Free variables are those which are neither formal
parameters (occurring in the argument list of the function) nor local
variables (created by assigning to them in the body of the function).
Whereas S (like C) by default uses _s_t_a_t_i_c scoping, R (like Scheme) has
adopted _l_e_x_i_c_a_l scoping. This means the values of free variables are
determined by a set of global variables in S, but in R by the bindings
that were in effect at the time the function was created.
Consider the following function:
cube <- function(n) {
sq <- function() n * n
n * sq()
}
Under S, sq() does not ``know'' about the variable n unless it is
defined globally:
S> cube(2)
Error in sq(): Object "n" not found
Dumped
S> n <- 3
S> cube(2)
[1] 18
In R, the ``environment'' created when cube() was invoked is also
looked in:
R> cube(2)
[1] 8
Lexical scoping allows using function closures and maintaining local
state. A simple example (taken from Abelson and Sussman) can be found
in the `demos/language' subdirectory of the R distribution. Further
information is provided in the standard R reference ``R: A Language
for Data Analysis and Graphics'' (see question ``Which Documentation
Exists for R?'') and a paper on ``Lexical Scope and Statistical
Computing'' by Robert Gentleman and Ross Ihaka which can be obtained
from the `doc/misc' directory of a CRAN site.
Lexical scoping also implies a further major difference. Whereas S
stores all objects as separate files in a directory somewhere (usually
`.Data' under the current directory), R does not. All objects in R
are stored internally. When R is started up it grabs a very large
piece of memory and uses it to store the objects. R performs its own
memory management of this piece of memory. Having everything in
memory is necessary because it is not really possible to externally
maintain all relevant ``environments'' of symbol/value pairs. This
difference also seems to make R _m_u_c_h _f_a_s_t_e_r than S.
The down side is that if R crashes you will lose all the work for the
current session. Saving and restoring the memory ``images'' (the
functions and data stored in R's internal memory at any time) can be a
bit slow, especially if they are big. In S this does not happen,
because everything is saved in disk files and if you crash nothing is
likely to happen to them. R is still in an alpha stage, and does
crash from time to time. Hence, for important work you should
consider saving often, see question ``How Can I Save My Workspace?''
(other possibilities are logging your sessions, or have your R
commands stored in text files which can be read in using source()).
(Note that if you run R from within Emacs (see question ``R and
Emacs''), you can save the contents of the interaction buffer to a
file and conveniently manipulate it using S-transcript-mode, as well
as save source copies of all functions and data used.)
Apart from lexical scoping and its implications, R follows the S
language definition in the Blue Book as much as possible, and hence
really is an ``implementation'' of S. There are some intentional
differences where the behavior of S is considered ``not clean''. In
general, the rationale is that R should help you detect programming
errors, while at the same time being as compatible as possible with S.
Some known differences are the following.
+o In R, if x is a list, then x[sub] <- NULL and x[[sub]] <- NULL
remove the specified elements from x. The first of these is
incompatible with S, where it is a no-op.
+o In S, the functions named .First and .Last in the `.Data' directory
can be used for customizing, as they are executed at the very
beginning and end of a session, respectively. R looks for files
called `.Rprofile' in the user's home directory and the current
directory, and sources these. (It also loads a saved image from
`.RData' in case there is one.) If a .First function exists then,
it is executed. The .Last mechanism is not supported yet.
+o Attaching library sections works differently. In S, library(_n_a_m_e)
adds the data directory for the library section _n_a_m_e to the search
list. If a function object named `.First.lib' exists in the
directory, it is executed; this is typically used to dynamically
load compiled code required by the functions in the section. In R,
library(_n_a_m_e) currently simply sources the file
$RHOME/library/_n_a_m_e, and compiled code can be loaded by calling
library.dynam() in this file. The .First.lib mechanism is not
really supported. (Note that a library file is only loaded once,
so that any code in the library that is not in a function is
executed the first time the library is loaded.)
+o R does not try as hard as S to preserve dimnames attributes
(examples are apply, rbind, and cbind, but also arithmetic ops).
+o R presently does not support IEEE Inf and NaN.
+o In R, attach currently only works for lists and data frames (not
for directories).
+o Categories do not exist in R, and never will as they are deprecated
now in S. Use factors instead.
+o In R, For() loops are not necessary and hence not supported.
+o In R, assign() uses the argument envir= rather than where= as in S.
+o The random number generators are different, and the seeds have
different length.
+o The glm family objects are implemented differently in R and S. The
same functionality is available but the components have different
names.
+o terms objects are stored differently. In S a terms object is an
expression with attributes, in R it is a formula with attributes.
The attributes have the same names but are mostly stored
differently. The major difference in functionality is that a terms
object is subscriptable in S but not in R. If you can't imagine
why this would matter then you don't need to know.
There are also differences which are not intentional, and result from
missing or incorrect code in R. The developers would appreciate
hearing about any deficiencies you may find (in a written report fully
documenting the difference as you see it). Of course, it would be
useful if you were to implement the change yourself and make sure it
works.
44..
44..11..
The R distribution comes with the following extra libraries:
eeddaa
Exploratory Data Analysis. Currently only contains functions
for robust line fitting, and median polish and smoothing.
mmvvaa
Multivariate Analysis. Currently contains code for principal
components (prcomp), canonical correlations (cancor),
hierarchichal clustering (hclust), and metric multidimensional
scaling (cmdscale). More functions for clustering and scaling,
biplots, profile and star plots, and code for ``real''
discriminant analysis will be added soon.
The following packages are available from the CRAN `src/contrib' area.
aacceeppaacckk
ace (Alternating Conditional Expectations) and avas (Additivity
and VAriance Stabilization for regression) for selecting
regression transformations.
bboooottssttrraapp
Software (bootstrap, cross-validation, jackknife), data and
errata for the book ``An Introduction to the Bootstrap'' by B.
Efron and R. Tibshirani, 1993, Chapman and Hall.
cctteesstt
A library of classical tests, including the Bartlett, Fisher,
Kruskal-Wallis, Kolmogorov-Smirnov, and Wilcoxon tests.
ddaattee
Functions for dealing with dates. The most useful of them
accepts a vector of input dates in any of the forms 8/30/53,
30Aug53, 30 August 1953, ..., August 30 53, or any mixture of
these.
ee11007711
Miscellaneous functions used at the Department of Statistics at
TU Wien (E1071).
ffrraaccddiiffff
Maximum likelihood estimation of the parameters of a
fractionally differenced ARIMA(p,d,q) model (Haslett and
Raftery, Applied Statistics, 1989).
ggeeee
An implementation of the Liang/Zeger generalized estimating
equation approach to GLMs for dependent data.
jjppnn
A function to plot Japan's coast-line and prefecture boundaries.
oozz Functions for plotting Australia's coastline and state
boundaries.
ssnnnnss
An R interface to the Stuttgart Neural Networks Simulator
(SNNS).
sspplliinneess
Regression spline functions.
ssuurrvviivvaall44
Functions for survival analysis (requires sspplliinneess).
See CRAN `src/contrib/INDEX' for more information.
Paul Gilbert <pgilbert at bank-banque-canada.ca> has a written a
multivariate time series library for S called ttiimmee..sseerriieess that is
mostly converted to run in R. He will make this port generally
available when complex numbers are implemented (see question ``What is
the current version of R?'').
According to Paul, the PADI interface from the Bank of Canada also
works with minor changes. PADI can be used to access Fame time series
data bases and potentially other databases, even remotely over the
Internet. For further information see http://www.bank-banque-
canada.ca/pgilbert.
According to Arne Kovac <A.Kovac at Bristol.ac.uk>, Guy Nason's
WaveThresh package for S worked with only minor modifications under R
version 0.12.
More code has been posted to the r-help mailing list, and can be
obtained from the mailing list archive.
44..22..
(Unix only.) Untar the add-on packages in $RHOME/src/library/ and
type
$ make libs
$ cd ../..
$ ./etc/install-libhelp
at the shell prompt.
44..33..
To find out which add-ons have already been installed, type
R> library()
at the R prompt. This produces something like
NAME DESCRIPTION
acepack ace() and avas() for selecting regression transformations
bootstrap Functions for the book "An Introduction to the Bootstrap"
ctest Classical Tests
date Functions for handling dates
eda Exploratory Data Analysis
fracdiff Fractionally differenced ARIMA (p,d,q) models
gee Generalized Estimating Equation models
mva Classical Multivariate Analysis
splines Regression spline functions
survival4 Survival analysis [needs library(splines)]
You can ``load'' an add-on with name _n_a_m_e by
R> library(_n_a_m_e)
You can then find out which functions it provides by typing
R> help(library = _n_a_m_e)
44..44..
R is currently still in alpha (or pre-alpha) state, so simply using it
and communicating problems is certainly of great value.
One place where functionality is still missing is the modeling
software as described in ``Statistical Models in S'' (see question
``What is S?''. The functions
add1 kappa alias labels drop1 proj
are missing; many of these are interpreted functions so anyone that is
bored and wants to have a go at implementing them it would be appreci-
ated. In addition, only linear and generalized linear models are cur-
rently available, aov, gam, loess, tree, and the nonlinear modelling
code are not there yet.
Many of the packages available at the Statlib S Repository might be
worth porting to R.
If you are interested in working on any of these projects, please
notify Kurt Hornik.
55.. RR aanndd EEmmaaccss
55..11.. IIss tthheerree EEmmaaccss SSuuppppoorrtt ffoorr RR??
There is an Emacs-Lisp interface to S/S-PLUS called S-mode. Its
current version is 4.8 and can be obtained at
http://www.maths.lancs.ac.uk:2080/~maa036/elisp/S-mode/. The earlier
versions which can be found at the Statlib S repository (gnuemacs3 and
gnuemacs4) are outdated.
It contains code for interacting with an inferior S process from
within Emacs including an interface to the help system, editing S
source code, and transcript manipulation, and comes with detailed
instructions for installation.
Martin Maechler <maechler at stat.math.ethz.ch> and Tony Rossini
<rossini at math.sc.edu> have integrated support for R into this package.
The current version is at
ftp://ftp.math.sc.edu/rossini/S-mode-4.8.MM6.XE2.tar.gz
and runs under both GNU Emacs and XEmacs.
To install, put the byte-compiled `.el' files into a place where Emacs
can find them, and add
(if (not (assoc "\\.R$" auto-mode-alist)
(add-to-list 'auto-mode-alist (cons "\\.R$" 'R-mode))))
(autoload 'R "S" "Run an inferior R process" t)
(autoload 'R-mode "S" "Mode for editing R source" t)
(autoload 'r-mode "S" "Mode for editing R source" t)
to one of your Emacs startup files, typically `~/.emacs'. You can
then fire up R from within Emacs by typing `M-x R' (note however that
many interface functions will not work), and if you use the extension
`.R' for your files with R code, Emacs will automagically turn on R
edit mode whenever you visit such a file.
Tony Rossini, Martin Maechler and Kurt Hornik have officially taken
over the development of S-mode. Version 4.9 (based on the current
4.8.MM series) will be released shortly; version 5.0 (codenamed
``istat'') should be out by the end of 1997.
55..22..
Yes. Inferior R mode provides a readline/history mechanism, object
name completion, and syntax-based highlighting of the interaction
buffer using Font Lock mode, as well as a very convenient interface to
the R help system.
Of course, it also integrates nicely with the mechanisms for editing R
source using Emacs. One can write code in one Emacs buffer and send
whole or parts of it for execution to R; this is helpful for both data
analysis and programming. One can also seamlessly integrate with a
revision control system, in order to maintain a log of changes in your
programs and data, as well as to allow for the retrieval of past
versions of the code.
In addition, it allows you to keep a record of your session, which can
also be used for error recovery through the use of the transcript
mode.
66..
66..11..
R (currently) uses a _s_t_a_t_i_c memory model. This means that when it
starts up, it asks the operating system to reserve a fixed amount of
memory for it. The size of this chunk cannot be changed subsequently.
Hence, it can happen that not enough memory was allocated.
In these cases, you should restart R with more memory available, using
the command line options -n and -v. To understand these options, one
needs to know that R maintains separate areas for fixed and variable
sized objects. The first of these is allocated as an array of
SEXPRECs assembled in a list using ``cons cells'' (ordered pairs each
containing an element of the list and a pointer to the next cell), and
the second as an array of VECRECs. The -n option can be used to
specify the number of cons cells (each occupying 16 bytes) which R is
to use (the default is 200000), and the -v option to specify the size
of the vector heap in megabytes (the default is 2). Only integers are
allowed for both options.
E.g., to read in a table of 5000 observations on 40 numeric variables,
R -v 6 should do.
Note that the information where to find vectors and strings on the
heap is stored using cons cells. Thus, it may also be necessary to
allocate more space for cons cells in order to perform computations
with very ``large'' variable-size objects.
You can find out the current memory comsumption by typing gc() at the
R prompt.
66..22..
R sometimes has problems parsing a file which does not end in a
newline. This can happen for example when Emacs is used for editing
the file and next-line-add-newlines is set to nil. To avoid the
problem, either set require-final-newline to a non-nil value in one of
your Emacs startup files, or make sure R-mode (see question ``Is there
Emacs Support for R?'') is used for editing R source files (which
locally ensures this setting).
Earlier R versions had a similar problem when reading in data files,
but this should have been taken care of now.
66..33..
You can use
x[i] <- list(NULL)
to set component i of the list x to NULL, similarly for named compo-
nents. Do not set x[i] or x[[i]] to NULL, because this will remove
the corresponding component from the list.
For dropping the row names of a matrix x, it may be easier to use
rownames(x) <- NULL, similarly for column names.
66..44.. HHooww CCaann II SSaavvee MMyy WWoorrkkssppaaccee??
The expression
save(list = ls(), file = ".RData")
saves the objects in the currently active environment (typically the
user's .GlobalEnv) to the file `.RData' in the R startup directory.
66..55..
To remove all objects in the currently active environment (typically
the user's .GlobalEnv), you can do
rm(list = ls())
77..
Of course, many many thanks to Robert and Ross for the R system, and
to the package writers and porters for adding to it.
Special thanks go to Peter Dalgaard, Paul Gilbert, Martin Maechler,
and Anthony Rossini for their comments which helped me improve this
FAQ.
More to some soon ...
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
|
R-FAQ v0.1-0
|
Kurt Hornik
| 567 |
|
From p.dalgaard at biostat.ku.dk Wed Apr 7 19:44:09 1999
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 07 Apr 1999 19:44:09 +0200
Subject: R-0.64.0 oops
Message-ID: <[email protected]>
> For those who *are* desperate, I've left a copy in
> ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.64.0.tgz
> (Be gentle, that's my desktop PC!)
Well, *now* it's there anyway...
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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Send "info", "help", or "[un]subscribe"
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_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-0.64.0 oops
|
Peter Dalgaard BSA
| 472 |
|
From pd.mes at cbs.dk Mon Mar 10 15:54:50 2014
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 10 Mar 2014 15:54:50 +0100
Subject: 3.1.0 on April 10
Message-ID: <[email protected]>
We intend to release R 3.1.0 on April 10. Prerelease versions will appear starting March 13 (for the source version, binaries may come a little later). See developer.r-project.org for details.
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
3.1.0 on April 10
|
Peter Dalgaard
| 347 |
|
From keitt at nceas.ucsb.edu Sun Nov 21 22:59:02 1999
From: keitt at nceas.ucsb.edu (Timothy H. Keitt)
Date: Sun, 21 Nov 1999 13:59:02 -0800
Subject: PostgreSQL package
Message-ID: <[email protected]>
I've made some small updates to my postgres access package for R. Its
been renamed to rpgsql. It also now allows you to specify the host,
database name, etc. from within R instead of relying on environment
variables.
It can be downloaded from http://www.nceas.ucsb.edu/~keitt/R/rpgsql.tgz
(Someone was going to send me an example package make file, but I've
lost their email. I would be grateful for a copy if someone has some
pre-made make files for R packages.)
Cheers,
Tim
--
Timothy H. Keitt
National Center for Ecological Analysis and Synthesis
735 State Street, Suite 300, Santa Barbara, CA 93101
Phone: 805-892-2519, FAX: 805-892-2510
http://www.nceas.ucsb.edu/~keitt/
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
PostgreSQL package
|
Timothy H. Keitt
| 505 |
|
From pd.mes at cbs.dk Thu Mar 15 09:59:19 2018
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 15 Mar 2018 08:59:19 +0000
Subject: R 3.4.4 is released
Message-ID: <[email protected]>
The build system rolled up R-3.4.4.tar.gz (codename "Someone to Lean On") this morning.
This is intended to be the last of the 3.4.x release series. The list below details the changes.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.4.4.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = f12a9c3881197b20b08dd3d1f9d005e6
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 32a94aba902b293cf8b8dbbf4113f2ab
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = f0ddf36639951987249a206fd4295da9
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 591dcf615162127f904e4e461f330ce9
MD5 (R-latest.tar.gz) = 9d6f73be072531e95884c7965ff80cd8
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = f60d286bb7294cef00cb0eed4052a66f
MD5 (VERSION-INFO.dcf) = 00f5b3721b3b72360c92fbd9dc8c7411
MD5 (R-3/R-3.4.4.tar.gz) = 9d6f73be072531e95884c7965ff80cd8
6474d9791fff6a74936296bde3fcb569477f5958e4326189bd6e5ab878e0cd4f AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
7936facb07e752869342808b9c8879d0e270b1a9ec92b67ef4dd87496abfef0a FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
6c231ff2da54f9a39ab1cf754c692d69b80f6004a6d28dbf29286b0d5bc0a109 NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
ca04f78ffe54afa326fe3ed40e7e1411aca0000ed2fa5ead97ddf51c6aa5b7bc NEWS.2
b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337 R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
52f934a4e8581945cbc1ba234932749066b5744cbd3b1cb467ba6ef164975163 THANKS
03e5641c23de903c0a3c379bc0d4c5857805051954011da0d41271ab02a6db2f VERSION-INFO.dcf
b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337 R-3/R-3.4.4.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 3.4.4:
NEW FEATURES:
* Sys.timezone() tries more heuristics on Unix-alikes and so is
more likely to succeed (especially on Linux). For the slowest
method, a warning is given recommending that TZ is set to avoid
the search.
* The version of LAPACK included in the sources has been updated to
3.8.0 (for the routines used by R, a very minor bug-fix change).
* parallel::detectCores(logical = FALSE) is ignored on Linux
systems, since the information is not available with virtualized
OSes.
INSTALLATION on a UNIX-ALIKE:
* configure will use pkg-config to find the flags to link to jpeg
if available (as it should be for the recently-released jpeg-9c
and libjpeg-turbo). (This amends the code added in R 3.3.0 as
the module name in jpeg-9c is not what that tested for.)
DEPRECATED AND DEFUNCT:
* Sys.timezone(location = FALSE) (which was a stop-gap measure for
Windows long ago) is deprecated. It no longer returns the value
of environment variable TZ (usually a location).
* Legacy support of make macros such as CXX1X is formally
deprecated: use the CXX11 forms instead.
BUG FIXES:
* power.prop.test() now warns when it cannot solve the problem,
typically because of impossible constraints. (PR#17345)
* removeSource() no longer erroneously removes NULL in certain
cases, thanks to D'enes T'oth.
* nls(`NO [mol/l]` ~ f(t)) and nls(y ~ a) now work. (Partly from
PR#17367)
* R CMD build checks for GNU cp rather than assuming Linux has it.
(PR#17370 says 'Alpine Linux' does not.)
* Non-UTF-8 multibyte character handling fixed more permanently
(PR#16732).
* sum(<large ints>, <stuff>) is more consistent. (PR#17372)
* rf() and rbeta() now also work correctly when ncp is not scalar,
notably when (partly) NA. (PR#17375)
* R CMD INSTALL now correctly sets C++ compiler flags when all
source files are in sub-directories of src.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.4.4 is released
|
Peter Dalgaard
| 682 |
|
From d|cook@rj @end|ng |rom gm@||@com Wed Aug 11 09:29:32 2021
From: d|cook@rj @end|ng |rom gm@||@com (Dianne Cook)
Date: Wed, 11 Aug 2021 17:29:32 +1000
Subject: Volume 13/1, June 2021 now available
Message-ID: <[email protected]>
Dear R Community,
The first issue of the R Journal for 2021 is now available at https://journal.r-project.org/.
There is also a dev version of rending articles in html at https://journal.r-project.org/dev/. Particularly look at articles by Earo Wang for embedded interactive graphics, and by Mike Kane for html rendering. Feedback and suggestions are welcome.
Happy reading, and coding!
Regards,
Di
%>%>%>%>%
Professor Dianne Cook
Editor-in-Chief, R Journal
dicook.rj at gmail.com
|
Volume 13/1, June 2021 now available
|
Dianne Cook
| 639 |
|
From ht @end|ng |rom he@therturner@net Mon Mar 14 20:11:42 2022
From: ht @end|ng |rom he@therturner@net (Heather Turner)
Date: Mon, 14 Mar 2022 19:11:42 +0000
Subject: Call for proposals to organize useR! 2023 as a global online
conference
Message-ID: <[email protected]>
Dear All,
The R Foundation Conference Committee invites proposals to organize useR! 2023 as a global online conference:
https://www.r-project.org/conferences/useR_2023_call.html
The call is open to teams worldwide and the deadline for outline proposals is **Friday 22 April 2022**.
Any queries should be sent to R-conferences at r-project.org (after a careful read of the call!).
Best wishes,
Heather Turner
on behalf of the R Foundation Conference Committee
|
Call for proposals to organize useR! 2023 as a global online conference
|
Heather Turner
| 588 |
|
From gregory_r_warnes at groton.pfizer.com Wed Oct 30 20:16:33 2002
From: gregory_r_warnes at groton.pfizer.com (Warnes, Gregory R)
Date: Wed, 30 Oct 2002 14:16:33 -0500
Subject: gregmisc version 0.7.3 now available
Message-ID: <[email protected]>
Version 0.7.3 of the gregmisc package is now available on CRAN. A compiled
windows package has also been sent to Brian Ripley for inclusion in the
windows package directory.
This version of gregmisc fixes a number of bugs and introduces several new
functions.
Highlights of this version:
===========================
New Features:
- Introduction of pdirichlet() and rdirichlet() functions.
- Addition of fast.prcomp() and fast.svd(), are more efficient than
the built-in versions on very wide matrixes. (Short term solution
until patches are integrated into the R source.)
- Add permute() function as a convenience wrapper for sample()
Bug Fixes:
- Fixed bug in barplot2() when log scale axes are used.
- Fixed contrasts.lm() to allow use on aov objects
- Other miscellaneous bug fixes.
- Removed enhanced version of plot.lm() which has been broken by
recent changes to R base packages.
Documentation Enhancements:
- make.contrasts(), which allows easy creation of user specified
contrasts, is now fully documented.
- Help files for make.contrasts and contrast.lm now show how to
compute and test contrasts, including SSQ decompositions, in
analysis of variance models
Description:
============
Package: gregmisc
Description: Misc Functions written/maintained by Gregory R. Warnes
Title: Greg's Miscellaneous Functions
Version: 0.7.3
Date: 2002/10/29
Maintainer: Gregory R. Warnes <Gregory_R_Warnes at groton.pfizer.com>
Author: Gregory R. Warnes. Includes code provided by Ben Bolker,
Bendix Carstensen, Don MacQueen, William Venables, and Marc
Schwartz, Ben Bolker, and Ian Wilson
License: GPL (version 2 or later)
Depends: MASS
Built: R 1.6.0; sparc-sun-solaris2.8; Tue Oct 29 21:40:30 EST 2002
Index:
CrossTable Cross Tabulation with Tests for Factor
Independence
aggregate.table Create 2-Way Table of Summary Statistics
bandplot Plot x-y Points with Locally Smoothed Mean and
Standard Deviation
barplot2 Enhanced Bar Plots
boxplot.n Produce a Boxplot Annotated with the Number of
Observations
ci Compute Confidence Intervals
combinations Enumerate the Combinations or Permutations of
the Elements of a Vector
combine Combine R Objects With a Column Labeling the
Source
contrast.lm Compute and test arbitrary contrasts for
regression objects
rdirichlet Functions for the Dirichlet Distribution
estimable Compute and test estimable linear functions of
the fitted coefficients (including contrasts)
of regression objects
factorial Compute factorial function
fast.prcomp Efficient computation of principal components
and singular value decompositions.
glh.test Test a General Linear Hypothesis for a
Regression Model
hist2d Compute and Plot a 2-Dimensional Histogram
interleave Interleave Rows of Data Frames or Matrices
lowess Scatter Plot Smoothing
make.contrasts Construct a User-Specified Contrast Matrix
nobs Compute the Number of Non-missing Observations
permute Randomly Permute the Elements of a Vector
plotCI Plot Error Bars
plotmeans Plot Group Means and Confidence Intervals
quantcut Create a Factor Variable Using the Quantiles of
a Continuous Variable
rename.vars Rename variables in a dataframe
reorder Reorder the Levels of a Factor
running Apply a Function Over Adjacent Subsets of a
Vector
space Space points in an x-y plot so they don't
overlap.
undocumented Undocumented functions
wapply Compute the Value of a Function Over a Local
LEGAL NOTICE
Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
gregmisc version 0.7.3 now available
|
Warnes, Gregory R
| 85 |
|
From jago at mclink.it Sat Apr 28 17:05:09 2001
From: jago at mclink.it (Stefano)
Date: Sat, 28 Apr 2001 17:05:09 +0200
Subject: R 1.2.3 for MacOS/X available
Message-ID: <[email protected]>
From release 1.2.3, R can run different Macintosh platforms.
Two versions are currently available that are non concurrent.
One version runs on MacOS Systems from 8.6 to 9.1 and MacOSX using the
standard MacOS/MacOSX interface, that means that is behaves like any
usual Macintosh application. (This is mantained by Stefano M. Iacus)
The other version is a Darwin/X11 that means a Unix-like version taking
advantages of the X11 server (to be installed separately) and of the BSD
kernel of MacOS X. (This version is mantained by Jan de Leeuw).
About the Carbon version
This new version of R fixes may bugs of the previous Macintosh release
and adopt Apple's Carbon technology to let R run natively under both
MacOS 8.6 to 9.1 and MacOS X. This means that under MacOS X when you
double click on the R icon, the System no longer launches the Classic
Compatibility environment. Under MacOS X the Carbon R take advantages of
the new Aqua look/interface and memory management.
More informations on this version can be found at:
http://www.eco-dip.unimi.it/R/rmac-FAQ.html
You can download the carbon distribution at:
http://cran.r-project.org/bin/macos
About the Darwin/X11 version
There are two builds for Mac OS X, more precisely for Darwin/X11, of the
R-patched and R-devel distributions of 04/14/01.
They were build using the native cc compiler, with help from f2c,
dlcompat, libjpeg, libpng, libz, OS X versions of tcl/tk., and Tenon's
Xtools distribution.
The dynamic libraries you need are included, except for the X11
libraries, which you have to install anyway along with an X11 server.
In order to install one of these builds, su root, move to /, and unpack.
Everything installs in /usr/local/lib, except for the R driver which
goes to /usr/local/bin. The R-devel tarball contains most of the
contributed R packages.
You can find this distribution on Jan's page :
http://www.stat.ucla.edu/~deleeuw/R
For more information read the following r-announce msg
http://www.r-project.org/nocvs/mail/r-announce/latest/0026.html
Stefano
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R 1.2.3 for MacOS/X available
|
Stefano
| 242 |
|
From e.pebesma at geog.uu.nl Wed Mar 12 11:46:12 2003
From: e.pebesma at geog.uu.nl (Edzer J. Pebesma)
Date: Wed, 12 Mar 2003 11:46:12 +0100
Subject: Gstat: multivariable geostatistics for S (R and S-Plus)
Message-ID: <[email protected]>
The majority of the functionality present in the gstat stand-alone
program (http://www.gstat.org/) is now available as a package/library for
the S language (R, S-Plus), again called gstat. The package provides
multivariable geostatistical modelling, prediction and simulation, as
well as several visualisation functions. Gstat was started 10 years
ago and was released under the GPL in 1996; the original stand-alone
program is closely linked to several GIS systems. Gstat was not initially
written for teaching purposes, but for research purposes, emphasizing
flexibility, scalability and portability. It can deal with a large number
of practical issues in geostatistics, including change of support (block
kriging), simple/ordinary/universal (co)kriging, fast local neighbourhood
selection, flexible trend modelling, variables with different sampling
configurations, and efficient simulation of large spatially correlated
random fields, indicator kriging and simulation, and (directional)
variogram and cross variogram modelling. The S formula/models interface
is used to define multivariable geostatistical models.
The source and windows package for R are available from CRAN. The page on
http://www.gstat.org/s.html has links to R and S-Plus (6.x) source code,
as well as examples, graphs, and a longer list of features. (A binary
Win32 S-Plus library is planned later this year.)
On http://www.ci.tuwien.ac.at/Conferences/DSC-2003/ you can find a
draft paper further describing the package.
Any feedback is appreciated.
--
Edzer
|
Gstat: multivariable geostatistics for S (R and S-Plus)
|
Edzer J. Pebesma
| 159 |
|
From p.dalgaard at biostat.ku.dk Tue Mar 17 14:52:44 1998
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 17 Mar 1998 14:52:44 +0100
Subject: R-0.61.2 released
Message-ID: <[email protected]>
R-0.61.2.tgz is now available from the Auckland FTP site, from where
it should spread to the CRAN sites during the next day or two. Unless
you're in a big hurry or actually living in New Zealand, please don't
get it from Auckland.
There is also an R-0.61.1-0.61.2.diff.gz which can be used to patch an
existing R-0.61.1. Instructions for patching are in the VERSION file
in same directory.
This release mainly fixes a number of trivial bugs (segfaults from
strange constructions and the like). One major change is that the
changes to factor coercion that was introduced previously was deemed
to be buggy after all, so now as.numeric(factor(100,200)) == 1:2
again. A few features was also allowed to trickle down from the 0.62
as-yet-unreleased version.
Jim Lindsey will probably be disappointed in finding that his
favourite model formula bugs are still there. This is not because we
disagree that they are bugs or have forgotten all about them, but
fixing it turned out to require more substantial changes than we cared
to introduce in a patch release.
This release was made primarily to be included in the Debian Linux 2.0
release. For this reason the problems with non-GNU make programs have
not been touched at all.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-0.61.2 released
|
Peter Dalgaard BSA
| 524 |
|
From deleeuw at stat.ucla.edu Fri May 10 00:48:07 2002
From: deleeuw at stat.ucla.edu (Jan de Leeuw)
Date: Thu, 9 May 2002 15:48:07 -0700
Subject: R-1.5.0 for Darwin
Message-ID: <[email protected]>
ftp://gifi.stat.ucla.edu/pub/R
Currently it only has the base distribution. Unpack in /usr/local. In
addition you may need many dylibs from fink. This version has
support for gnome, but not for atlas yet. It also has libR.dylib.
Recommended packages will come later.
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
homepage: http://www.stat.ucla.edu/~deleeuw
========================================================
No matter where you go, there you are. --- Buckaroo Banzai
http://www.stat.ucla.edu/~deleeuw/sounds/nomatter.au
========================================================
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
R-1.5.0 for Darwin
|
Jan de Leeuw
| 35 |
|
From ripley at stats.ox.ac.uk Wed Jun 24 10:07:56 1998
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 24 Jun 1998 09:07:56 +0100 (BST)
Subject: Packages: KernSmooth logspline ppr rpart tree
Message-ID: <[email protected]>
The following are now on CRAN:
KernSmooth: version 2.2 of the code for Wand & Jones book on kernel smoothing.
logspline: spline fits to log denisites, with automatic choice of smoothing.
ppr: projection pursuit regression.
rpart: recursive partitioning (CART-like)
VR: Venables & Ripley libraries 5.3pl021 for 0.62.1
and in the devel section
tree: a clone of tree, prune.tree, cv.tree ...
which is fully operational but not much documented. Use your V&R2!
You can find out about KernSmooth, logspline, ppr and rpart in the
on-line statistics complements to Venables & Ripley at
http://www.stats.ox.ac.uk/pub/MASS2
The final release of the VR libraries is yet to come: it will follow
the bug-fixes in 0.62.2. If you really want to experiment, the current
version will be at http://www.stats.ox.ac.uk/pub/R, but do use this with
the latest R-release.tar.gz or R-snapshot.tar.gz.
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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|
Packages: KernSmooth logspline ppr rpart tree
|
Prof Brian Ripley
| 540 |
|
From jfox at mcmaster.ca Mon May 26 16:27:53 2003
From: jfox at mcmaster.ca (John Fox)
Date: Mon, 26 May 2003 10:27:53 -0400
Subject: new cross-platform basic-statistics GUI
Message-ID: <[email protected]>
Dear R-announce list members,
I've submitted a new package to CRAN, Rcmdr, which provides a
cross-platform basic-statistics GUI for R. Rcmdr is based on the tcltk
package and uses only standard Tk widgets. It therefore runs under Windows
if Tcl/Tk support is installed with R, although it requires the
single-document interface (SDI). I've tested Rcmdr with Windows and Red Hat
Linux; others have reported that it works on other Linux/Unix and Macintosh
systems (the latter under X11).
The R-Commander GUI consists of a window containing several menus, buttons,
and information fields. The Commander window also contains a log/script
box. The R-Commander menus are easily configurable through a text file. The
menu tree and additional information are available at
<http://www.socsci.mcmaster.ca/jfox/Misc/Rcmdr/>.
The menus lead to simple dialog boxes, the general contents of which are
more or less obvious from the names of the menu items. These boxes have a
common structure, including a help button leading to the help page for a
relevant function.
Commands generated via dialogs are posted to the R session window, along
with printed output, and to the log window. Lines in the log window may be
edited and (re)submitted for execution. Logs can be saved and reloaded.
My object in designing and implementing this GUI was to cover the content
of a basic-statistics course. The target text was Moore's The Basic
Practice of Statistics, Second Edition (Freeman, 2000), which is the text
that I currently use for a two-semester introduction to statistics for
undergraduate sociology majors. The R Commander implements the content of
this text plus some additional material (e.g., linear and generalized
linear models). As a result of several suggestions that I received, the
coverage is now larger than originally envisaged, and I'm happy to
entertain suggestions for further additions -- keeping in mind, however,
the intended limited scope of the project.
Until the package appears on CRAN, you can download the package source and
a Windows binary from my web site. The Rcmdr package mostly uses functions
in the base and recommended packages; it also uses some functions in my car
package.
John
-----------------------------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
email: jfox at mcmaster.ca
phone: 905-525-9140x23604
web: www.socsci.mcmaster.ca/jfox
|
new cross-platform basic-statistics GUI
|
John Fox
| 170 |
|
From pd@|gd @end|ng |rom gm@||@com Fri Apr 22 10:19:36 2022
From: pd@|gd @end|ng |rom gm@||@com (peter dalgaard)
Date: Fri, 22 Apr 2022 10:19:36 +0200
Subject: [Rd] R 4.2.0 is released
Message-ID: <[email protected]>
The build system rolled up R-4.2.0.tar.gz (codename "Vigorous Calisthenics") this morning.
This is a major update, notably containing extensive rework on the Windows port and its toolchain, including UTF-8 support.
The list below details the changes in this release.
You can get the source code from
https://cran.r-project.org/src/base/R-4/R-4.2.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = 320967884b547734d6279dedbc739dd4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = f593bc2137bcb005337630ca5611a26f
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = c154effcc08d4202851e282bbac50859
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = b38d94569700664205a76a7de836ba83
MD5 (NEWS.3) = e55ed2c8a547b827b46e08eb7137ba23
MD5 (R-latest.tar.gz) = f1d4b7fec9e15835fdcfb8369ef039c0
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = a79b9b338cab09bd665f6b62ac6f455b
MD5 (THANKS) = 45b6d2e88a6ecb5b24fa33a781351cd5
MD5 (VERSION-INFO.dcf) = 3adb7939bc77f583d2472a43824072cd
MD5 (R-4/R-4.2.0.tar.gz) = f1d4b7fec9e15835fdcfb8369ef039c0
60a0d150e6fc1f424be76ad7b645d236b56e747692a4679f81ce6536c550e949 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
1b1f962382ff185e14b6b5b9b40dc87360399466c7d7ce928ae443261e3955c9 FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
faab2a0cdd10fa456fcdbbb409e2fd6fd0afe8d3d5172ce13fbed176976a3633 NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
cde079b6beab7d700d3d4ecda494e2681ad3b7f8fab13b68be090f949393ec62 NEWS.2
1910a2405300b9bc7c76beeb0753a5249cf799afe175ce28f8d782fab723e012 NEWS.3
38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488 R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
8b7d3856100220f4555d4d57140829f2e81c27eccec5b441f5dce616e9ec9061 RESOURCES
8319c5415de58ee10d4bc058d79c370fd8e6b2ad09e25d7a1e04b74ca5f380a6 THANKS
b4aa7d9d51ed8145caa4490012cc8e33033b761c4e8eead49136b69cd481fc2f VERSION-INFO.dcf
38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488 R-4/R-4.2.0.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 4.2.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* The formula method of aggregate() now matches the generic in
naming its first argument x (resolving PR#18299 by Thomas
Soeiro).
This means that calling aggregate() with a formula as a named
first argument requires name formula in earlier versions of R and
name x now, so portable code should not name the argument (code
in many packages did).
* Calling && or || with either argument of length greater than one
now gives a warning (which it is intended will become an error).
* Calling if() or while() with a condition of length greater than
one gives an error rather than a warning. Consequently,
environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has
any effect.
* Windows users should consult the WINDOWS section below for some
profound changes including
* Support for 32-bit builds has been dropped.
* UTF-8 locales are used where available.
* The default locations for the R installation and personal
library folder have been changed.
Thanks to Tomas Kalibera for months of work on the Windows port
for this release.
NEW FEATURES:
* matrix(x, n, m) now warns in more cases where length(x) differs
from n * m, as suggested by Abby Spurdle and Wolfgang Huber in
Feb 2021 on the R-devel mailing list.
This warning can be turned into an error by setting environment
variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran
does so unless it is already set.
* Function file_test() in package utils gains tests for symlinks,
readability and writability.
* capabilities("libxml") is now false.
The description of capabilities("http/ftp") now reflects that it
refers to the default method, no longer the internal one.
* simplify2array() gains an except argument for controlling the
exceptions used by sapply().
* Environment variables R_LIBS_USER and R_LIBS_SITE are both now
set to the R system default if unset or empty, and can be set to
NULL to indicate an empty list of user or site library
directories.
* The warning for axis()(-like) calls in cases of relatively small
ranges (typically in log-scale situations) is slightly improved
_and_ suppressed from explicit calls to .axisPars() as has always
been the intention.
* The contrasts setter function `contrasts<-` gains an explicit
default how.many = NULL rather than just using missing(how.many).
* grid.pretty() gains a new optional argument n = 5.
* There is a new function .pretty() with option bounds as a
technical-utility version of pretty(). It and pretty() gain a
new argument f.min with a better than back-compatible default.
* Function grDevices::axisTicks() and related functions such as
graphics::axis() work better, notably for the log scale; partly
because of the pretty() improvements, but also because care is
taken e.g., when ylim is finite but diff(ylim) is infinite.
* nclass.FD() gains a digits option.
* The R Mathlib internal C function bd0() (called indirectly from a
dozen probability density and distribution functions such as
dpois(), dbinom(), dgamma(), pgamma() _etc_) has been
complemented by a more sophisticated and (mostly) more accurate C
function ebd0(), currently called only by internal dpois_raw()
improving accuracy for R level dpois() and potentially others
calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to
Morten Welinder's PR#15628.)
* write.ftable() gains sep = " " argument as suggested by Thomas
Soeiro.
* The names of the locale categories supported by R's
Sys.getlocale() and Sys.setlocale() are now provided by variable
.LC.categories in the base namespace.
* The Date and POSIXt methods for hist() and the histogram method
for plot() now also use the new default col = "lightgray" in
consistency with the corresponding change to hist()'s default for
R 4.0.0.
* hist.default() gains new fuzz argument, and the histogram plot
method no longer uses fractional axis ticks when displaying
counts ("Frequency").
* mapply() and hence Map() now also obey the "max-or-0-if-any"
recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid
now.
* as.character(<obj>) for "hexmode" or "octmode" objects now
fulfils the important basic rule as.character(x)[j] ===
as.character(x[j]).
* The set utility functions, notably intersect() have been tweaked
to be more consistent and symmetric in their two set arguments,
also preserving a common mode.
* substr(ch, start,end) <- new now e.g., preserves names(ch); ditto
for substring(), thanks to a patch from Brodie Gaslam.
* plot(<lm>) gains a extend.ylim.f argument, in partial response to
PR#15285; further PR#17784 is fixed thanks to several
contributors and a patch by Elin Waring. The Cook's dist
contours get customizable via cook.col and cook.lty with a
different default color and their legend is nicer by default and
customizable via cook.legendChanges.
* Attempting to subset an object that is not subsettable now
signals an error of class notSubsettableError. The
non-subsettable object is contained in the object field of the
error condition.
* Subscript-out-of-bounds errors are now signaled as errors of
class subscriptOutOfBoundsError.
* Stack-overflow errors are now signaled as errors inheriting from
class stackOverflowError. See ?stackOverflowError for more
details.
* New partly experimental Sys.setLanguage() utility, solving the
main problem of PR#18055.
* gettext() and gettextf() get a new option trim = TRUE which when
set to false allows translations for strings such as "Execution
halted\n" typical for C code.
* An experimental implementation of hash tables is now available.
See ?hashtab for more details.
* identical() gains a extptr.as.ref argument for requesting that
external pointer objects be compared as reference objects.
* reorder() gets an argument decreasing which it passes to sort()
for level creation; based on the wish and patch by Thomas Soeiro
in PR#18243.
* as.vector() gains a data.frame method which returns a simple
named list, also clearing a long standing 'FIXME' to enable
as.vector(<data.frame>, mode="list"). This breaks code relying
on as.vector(<data.frame>) to return the unchanged data frame.
* legend() is now vectorized for arguments cex, x.intersp, and
text.width. The latter can now also be specified as a vector
(one element for each column of the legend) or as NA for
computing a proper column wise maximum value of strwidth(legend).
The argument y.intersp can be specified as a vector with one
entry for each row of the legend.
legend() also gains new arguments title.cex and title.font.
Thanks to Swetlana Herbrandt.
* Deparsing no longer remaps attribute names dim, dimnames, levels,
names and tsp to historical S-compatible names (which structure()
maps back).
* sample() and sample.int() have additional sanity checks on their
size and n arguments.
all.equal.numeric() gains a sanity check on its tolerance
argument - calling all.equal(a, b, c) for three numeric vectors
is a surprisingly common error.
mean(na.rm =), rank(na.last =), barplot(legend.text =),
boxplot(), contour(drawlabels =), polygon(border =) and
methods::is(class2 =) have more robust sanity checks on their
arguments.
R CMD Rd2pdf (used by R CMD check) has a more robust sanity check
on the format of \alias{} commands.
* psigamma(x, deriv) for negative x now also works for deriv = 4
and 5; their underlying C level dpsifn() is documented in
'Writing R Extensions'.
* The HTML help system now uses HTML5 (wish of PR#18149).
* ks.test() now provides exact p-values also with ties and MC
p-values in the two-sample (Smirnov) case. By Torsten Hothorn.
* ks.test() gains a formula interface, with y ~ 1 for the
one-sample (Kolmogorov) test and y ~ group for the two-sample
(Smirnov) test. Contributed by Torsten Hothorn.
* The return value from ks.test() now has class c("ks.test",
"htest") - packages using try() need to take care to use
inherits() and not == on the class.
* New functions psmirnov(), qsmirnov() and rsmirnov() in package
stats implementing the asymptotic and exact distributions of the
two-sample Smirnov statistic.
* iconv() now allows sub = "c99" to use C99-style escapes for UTF-8
inputs which cannot be converted to encoding to.
* In a forward pipe |> expression it is now possible to use a named
argument with the placeholder _ in the rhs call to specify where
the lhs is to be inserted. The placeholder can only appear once
on the rhs.
* The included LAPACK sources have been updated to version 3.10.0,
except for the four Fortran 77 routines which 3.10.0 has
re-implemented in Fortran 90 (where the older versions have been
retained as the R build process does not support Fortran 90).
* path.expand() and most other uses of tilde expansion now warn if
a path would be too long if expanded. (An exception is
file.exists(), which silently returns false.)
* trunc(<Date>, *) now supports units = "months" or "years" for
consistency with the POSIXt method, thanks to Dirk Eddelbuettel's
proposal in PR#18099.
* list2DF() now checks that its arguments are of the same length,
rather than use recycling.
* The HTML help system has several new features: LaTeX-like math
can be typeset using either KaTeX or MathJax, usage and example
code is highlighted using Prism, and for dynamic help the output
of examples and demos can be shown within the browser if the
knitr package is installed. These features can be disabled by
setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to
a false value.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 15
and so packages that provide graphics devices should be
reinstalled.
* The grid package now allows the user to specify a "vector" of
pattern fills. The fill argument to gpar() accepts a list of
gradients and/or patterns and the functions linearGradient(),
radialGradient(), and pattern() have a new group argument.
Points grobs (data symbols) can now also have a pattern fill.
The grobCoords() function now returns a more informative and
complex result.
* The grid package has new functions for drawing isolated groups:
grid.group(), grid.define(), and grid.use(). These functions add
compositing operators and affine transformations to R's graphics
capabilities.
The grid package also has new functions for stroking and filling
paths: grid.stroke(), grid.fill(), and grid.fillStroke().
A new function as.path() allows the user to specify the fill rule
for a path that is to be used for clipping, stroking, or filling;
available options are "winding" and "evenodd". A new function
as.mask() allows the user to specify the type of a mask;
available options are "alpha" and "luminance".
These new features are only supported so far (at most) on the
Cairo-based graphics devices and on the pdf() device.
* dev.capabilities() reports on device support for the new
features.
* par() now warns about unnamed non-character arguments to prevent
misuse such as {usr <- par("usr"); par(usr)}.
WINDOWS:
* R uses UTF-8 as the native encoding on recent Windows systems (at
least Windows 10 version 1903, Windows Server 2022 or Windows
Server 1903). As a part of this change, R uses UCRT as the C
runtime. UCRT should be installed manually on systems older than
Windows 10 or Windows Server 2016 before installing R.
* The default personal library on Windows, folder R\win-library\x.y
where x.y stands for R release x.y.z, is now a subdirectory of
Local Application Data directory (usually a hidden directory
C:\Users\username\AppData\Local). Use shell.exec(.libPaths()[1])
from R to open the personal library in Explorer when it is first
in the list (PR#17842).
* R uses a new 64-bit Tcl/Tk bundle. The previous 32-bit/64-bit
bundle had a different layout and can no longer be used.
* Make files and installer scripts for Windows have been tailored
to Rtools42, the newly recommended 64-bit gcc 10.3 MinGW-W64 UCRT
toolchain.
* Rtools42 by default uses the Windows security features ASLR and
DEP; hence CRAN builds of R and packages also do.
* R now supports files Makevars.ucrt, Makefile.ucrt, configure.ucrt
and cleanup.ucrt in packages, which are used in preference to the
.win variants. This allows keeping the .win files around to
support older versions of R. This feature will be removed in the
future once support for older versions of R would no longer be
needed.
* R.version gains a new field crt (only on Windows) to denote the C
runtime. The value is "ucrt".
* On Windows, download.file(method = "auto") and url(method =
"default") now follow Unix in using "libcurl" for all except
file:// URIs.
* Rtools42 includes an unpatched Msys2 build of GNU tar. Paths
including drive letters can be made to work by adding
--force-local to environment variable TAR_OPTIONS. (Rtools40 and
earlier included a patched version which defaulted to this
option.)
* Installer builds of R automatically find the Rtools42 software
collection as well as the compiler toolchain. No PATH setting is
required from the user.
* The default installation directory of R for a user-only
installation has been changed to the User Program Files directory
(usually a hidden directory
C:\Users\username\AppData\Local\Programs) to follow Windows
conventions. Use shell.exec(R.home()) from R to open the R
installation directory in Explorer (PR#17842).
* R now supports installation-time patching of packages. Patches
may be installed from a supplied URL or a local directory or
disabled. Patches are included into the installed packages for
reference. This experimental feature may be removed in the
future.
* libcurl is now required for building from source.
* The clipboard connection now works also with text in other than
the current native encoding (PR#18267, with Hiroaki Yutani).
Text is always pasted to the clipboard in UTF16-LE and the
encoding argument is ignored.
* The internal case-changing functions are now used by default on
Windows - this circumvents problems (for example with E acute) of
the UCRT Windows' runtime.
* R on Windows now uses the system memory allocator. Doug Lea's
allocator was used since R 1.2.0 to mitigate performance
limitations seen with system allocators on earlier versions of
Windows.
* memory.limit() and memory.size() are now stubs on Windows (as on
Unix-alikes).
* Applications embedding R on Windows can now use additional
callbacks, which have so far only been available only on Unix
(PR#18286).
INSTALLATION:
* Facilities for accessing ftp:// sites are no longer tested
(except _pro tem_ for curlGetHeaders()) as modern browsers have
removed support.
* R can now be built with DEFS = -DSTRICT_R_HEADERS .
PACKAGE INSTALLATION:
* R CMD INSTALL no longer tangles vignettes. This completes an R
CMD build change in R 3.0.0 and affects packages built before R
3.0.2. Such packages should be re-made with R CMD build to have
the tangled R code of vignettes shipped with the tarball.
* USE_FC_LEN_T will become the default: this uses the correct
prototypes for Fortran BLAS/LAPACK routines called from C/C++,
and requires adjustment of most such calls - see 'Writing R
Extensions' SS6.6.2. (This has been supported since R 3.6.2.)
* Package installation speed for packages installed with
keep.source has been improved. This resolve the issue reported by
Ofek Shilon in PR#18236.
UTILITIES:
* R CMD check can optionally report files/directories left behind
in home, /tmp (even though TMPDIR is set) and other directories.
See the "R Internals" manual for details.
* R CMD check now reports byte-compilation errors during
installation. These are not usually fatal but may result in
parts of the package not being byte-compiled.
* _R_CHECK_DEPENDS_ONLY_ can be applied selectively to examples,
tests and/or vignettes in R CMD check: see the "R Internals"
manual.
* _R_CHECK_SRC_MINUS_W_IMPLICIT_ now defaults to true: recent
versions of Apple clang on macOS have made implicit function
declarations in C into a compilation error.
* R CMD check --as-cran makes use of the environment variable
AUTORECONF. See the "R Internals" manual SS8 for further details.
* R CMD check --use-valgrind also uses valgrind when re-building
vignettes as some non-Sweave vignettes unhelpfully comment out
all their code when R CMD check runs vignettes.
* Errors in re-building vignettes (unless there are LaTeX errors)
are reported by R CMD check as ERROR rather than WARNING when
running vignettes has been skipped (as it frequently is in CRAN
checks and by --as-cran).
* R CMD Rd2pdf gains a --quiet option that is used by R CMD build
when building the PDF package manual.
* R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with
Texinfo >= 6.7. The --batch option is ignored.
* R CMD build and R CMD check now include the Rd file name and line
numbers in the error message of an \Sexpr evaluation failure.
* For packages using the \doi Rd macro (now an install-time \Sexpr)
but no other dynamic Rd content, R CMD build now produces a
smaller tarball and is considerably faster - skipping temporary
package installation.
C-LEVEL FACILITIES:
* The non-API header R_ext/R-ftp-http.h is no longer provided, as
the entry points it covered are now all defunct.
* A number of non-API declarations and macro definitions have been
moved from the installed header Rinternals.h to the internal
header Defn.h. Packages that only use entry points and
definitions documented to be part of the API as specified in
'Writing R Extensions' SS6 should not be affected.
* The macro USE_RINTERNALS no longer has any effect when compiling
package code. Packages which also use R_NO_REMAP will need to
ensure that the remapped names are used for calls to API
functions that were formerly also made available as macros.
* The deprecated legacy S-compatibility macros PROBLEM, MESSAGE,
ERROR, WARN, WARNING, RECOVER, ... are no longer defined in
R_exts/RS.h (included by R.h). Replace these by calls to
Rf_error and Rf_warning (defined in header R_ext/Error.h included
by R.h).
Header R_ext/RS.h no longer includes R_ext/Error.h.
* Header R_ext/Constants.h (included by R.h) when included from C++
now includes the C++ header cfloat rather than the C header
float.h (now possible as C++11 is required).
* The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h
(included by R.h) are deprecated.
* The deprecated S-compatibility macros SINGLE_* in
R_ext/Constants.h (included by R.h) have been removed.
* R_Calloc, R_Free and R_Realloc are preferred to their unprefixed
forms and error messages now use the prefix. These forms were
introduced in R 3.4.0 and are available even when
STRICT_R_HEADERS is defined.
* rmultinom has been documented in 'Writing R Extensions' SS6 so is
now part of the R API.
* Similarly, Rtanpi, called from R level tanpi() is now part of the
R API.
* The long-deprecated, undocumented and non-API entry point call_R
is no longer declared in R_ext/RS.h (included by R.h).
* The header S.h which has been unsupported since Jan 2016 has been
removed. Use R.h instead.
DEPRECATED AND DEFUNCT:
* The (non-default and deprecated) method = "internal" for
download.file() and url() no longer supports http:// nor ftp://
URIs. (It is used only for file:// URIs.)
On Windows, download.file(method = "wininet") no longer supports
ftp:// URIs. (It is no longer the default method, which is
"libcurl" and does.)
On Windows, the deprecated method = "wininet" now gives a warning
for http:// and https:// URIs for both download.file() and url().
(It is no longer the default method.)
* On Windows, the command-line option --max-mem-size and
environment variable R_MAX_MEM_SIZE are defunct. The memory
allocation limit was important for 32-bit builds, but these are
no longer supported.
* default.stringsAsFactors() is now formally deprecated, where that
was only mentioned on its regular help page, previously. So it
now gives a warning if called.
* unix.time() is defunct now; it had been deprecated since R 3.4.0.
BUG FIXES:
* Setting digits = 0 in format(), print.default() (and hence
typically print()) or options() is again invalid. Its behaviour
was platform-dependent, and it is unclear what "zero significant
digits" should mean (PR#18098).
* Messages from C code in the cairo section of package grDevices
are now also offered for translation, thanks to Michael Chirico's
PR#18123.
* mean(x) with finite x now is finite also without "long.double"
capability.
* R CMD Rd2pdf no longer leaves an empty build directory behind
when it aborts due to an already existing output file. (Thanks
to Sebastian Meyer's PR#18141.)
* density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now
removes weights "in parallel" to x, fixing PR#18151, reported by
Matthias Gondan. Additionally, it gets a subdensity option.
* Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer
produces long blocks of empty lines when <expR> itself contains
several lines all producing empty output. Thanks to a report and
patch by Ivan Krylov posted to R-devel.
* R CMD build no longer fails if a package vignette uses child
documents and inst/doc exists. (Thanks to Sebastian Meyer's
PR#18156.)
* When an R documentation ('help' source) file man/foo.Rd in a
package has \donttest{..} examples with a syntax error, it is now
signalled as ERROR and with correct line numbers relating to the
*-Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's
reports and patch proposals in PR#17501.
* Improved determination of the correct translation domain in
non-base packages, addressing the combination of PR#18092 and
PR#17998 (#c6) with reports and _augmented_ patch #2904 by
Suharto Anggono.
Note that "R-base" is no longer the default domain e.g., for
top-level calls to gettext(); rather translation needs explicit
domain = * specification in such cases.
* identical(attrib.as.set=FALSE) now works correctly with data
frames with default row names (Thanks to Charlie Gao's PR#18179).
* txtProgressBar() now enforces a non-zero width for argument char,
without which no progress can be visible.
* dimnames(table(d)) is more consistent in the case where d is a
list with a single component, thanks to Thomas Soeiro's report to
R-devel.
Further, table(d1, d2) now gives an error when d1 and d2 are data
frames as suggested by Thomas in PR#18224.
* Fix for drawing semi-transparent lines and fills on the native
Windows graphics device (PR#18219 and PR#16694). Thanks to Nick
Ray for helpful diagnosis on Bugzilla.
* The deparser now wraps sub-expressions such as if(A) .. with
parentheses when needed; thanks to Duncan Murdoch's PR#18232 and
Lionel Henry's patches there.
* remove.packages() no longer tries to uninstall Priority: base
packages, thanks to a report and suggestions by Colin Fay in
PR#18227.
* win.metafile() now has xpinch and ypinch arguments so that the
user can override Windows' (potentially wrong) guess at device
dimensions.
* x[i] and x[[i]] for non-integer i should now behave in all cases
as always documented: the index used is equivalent to
as.integer(i) unless that would overflow where trunc(i) is used
instead; thanks to Suharto Anggono's report and patch proposals
in PR#17977.
* asOneSidedFormula() now associates the resulting formula with the
global environment rather than the evaluation environment created
for the call.
* <bibentry>$name now matches the field name case-insensitively,
consistent with bibentry() creation and the replacement method.
* cbind() failed to detect some length mismatches with a mixture of
time-series and non-time-series inputs.
* The default LaTeX style file Sweave.sty used by the RweaveLatex
driver no longer loads the obsolete ae package; thanks to a
report by Thomas Soeiro in PR#18271. Furthermore, it now skips
\usepackage[T1]{fontenc} for engines other than pdfTeX (if
detected) or if the new [nofontenc] option is used.
* smooth.spline() now stores its logical cv argument more safely,
fixing a rare bug when printing, and also stores n.
* smooth.spline(x,y,*) now computes the cv.crit statistic
correctly, also when is.unsorted(x), fixing PR#18294.
* The data.frame method of rbind() now warns when binding
not-wholly-recycling vectors, by analogy to the default method
(for matrices).
* setAs() finds the correct class for name to when multiple
packages define a class with that name. Thanks to Gabor Csardi
for the report.
* Fix for detaching a package when two classes of the same name are
present in method signatures for the same generic. Thanks to
Gabor Csardi for the report.
* match.arg("", c("", "a", "B")) gives a better error message, in
part from PR#17959, thanks to Elin Waring.
* R CMD Sweave --clean no longer removes pre-existing files or
subdirectories (PR#18242).
* The quartz() device no longer splits polylines into subpaths.
That has caused narrowly-spaced lines with many points to always
look solid even when dashed line type was used due to dash phase
restarts.
* Deparsing constructs such as quote(1 + `!`(2) + 3) works again as
before R 3.5.0, thanks to the report and patch in PR#18284 by
Suharto Anggono.
* as.list(f) for a factor f now keeps names(f), fixing PR#18309.
* qbeta(.001, .9, .009) and analogous qf() calls now return a
correct value instead of NaN or wrongly 1, all with a warning;
thanks to the report by Ludger Goeminne in PR#18302.
* plot.lm() failed to produce the plot of residuals vs. factor
levels (i.e., which=5 when leverages are constant) for models
with character predictors (PR#17840).
* interaction.plot(..., xtick = TRUE) misplaced the x-axis line
(PR#18305).
* Not strictly fixing a bug, format()ing and print()ing of
non-finite Date and POSIXt values NaN and +/-Inf no longer show
as NA but the respective string, e.g., Inf, for consistency with
numeric vector's behaviour, fulfilling the wish of PR#18308.
* R CMD check no longer runs test scripts generated from
corresponding .Rin files twice and now signals an ERROR if
processing an .Rin script fails.
* tools::Rd2txt() used for plain-text help pages now renders \hrefs
(if tools::Rd2txt_options(showURLs = TRUE)) and \urls with
percent-encoding and standards-compliant delimiting style (angle
brackets and no URL: prefix). \email is now rendered with a
mailto: prefix.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
|
[Rd] R 4.2.0 is released
|
peter dalgaard
| 590 |
|
From p.dalgaard at biostat.ku.dk Sun Dec 21 21:00:08 1997
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 21 Dec 1997 21:00:08 +0100
Subject: New version available
Message-ID: <[email protected]>
A new version is available from
ftp.stat.auckland.ac.nz:/pub/R/R-0.61.tgz
and soon from CRAN mirrors everywhere.
As usual, there is at least one unfixed bug in the release, but this
time, we hope that we have set things up so that future bugfixes can
be released more or less immediately.
Merry Christmas!
The R core team.
**********************************************************************
Here's the top of the CHANGES file:
CHANGES IN VERSION R VERSION 0.61
We try to make development more flexible by creating a "CVS branch".
This should make it easier to produce patches for obvious bugs in the
releases, without having to wait for changes in other areas to
stabilize.
NEW FEATURES
o New functions "all.vars" and "all.names" added.
o There has been a small change in the include file structure.
All include files now live in RHOME/src/include and are
copied to RHOME/include when needed.
o The "noquote" functions are now documented.
o A new `language' demo, "is.things", is provided.
o symnum(.) function
o The files in R/library/base/data have had a .R suffix added.
BUG_FIXES
o A nasty bug which showed when attempt was made to create
a zero length call has been fixed.
o model.matrix(.) now allows a contrasts argument.
o barplot(.) now also works for barplot(table(rpois(100,3))).
o make clean ; make now should work; ./Makefile.in eliminated
o format(.) is now generic; the default method has a `digits' argument.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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Send "info", "help", or "[un]subscribe"
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_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
New version available
|
Peter Dalgaard BSA
| 582 |
|
From P.Dalgaard at biostat.ku.dk Fri Apr 17 10:56:19 2009
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Fri, 17 Apr 2009 10:56:19 +0200
Subject: R 2.9.0 is released
Message-ID: <[email protected]>
I've rolled up R-2.9.0.tar.gz a short while ago. This is a development
release which contains a number of new features.
Also, a number of mostly minor bugs have been fixed. See the full list
of changes below.
You can get it (later today) from
http://cran.r-project.org/src/base/R-2/R-2.9.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. In case of
impatience, try http://www.biostat.ku.dk/~pd/R-release
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
7861f511a3f8e8598c9b84d65e93c389 NEWS
7abcbbc7480df75a11a00bb09783db90 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
b96e9596f947794c5628712f8016aa90 FAQ
a5b79a2bc1372136cda4674b5f46d146 R-2.9.0.tar.gz
a5b79a2bc1372136cda4674b5f46d146 R-latest.tar.gz
This is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.9.0
SIGNIFICANT USER-VISIBLE CHANGES
o expand.grid() by default no longer coerces strings into factors.
NEW FEATURES
o Package 'Matrix' is now a recommended package contained in the
basic R distribution. It provides S4 classes and methods for
dense and sparse matrices, often by using the numerical
libraries Lapack and from the SuiteSparse collection CHOLMOD,
CSparse, and SPQR among others.
o pdf() and postscript() gain a 'useKerning' argument to place
strings using kerning (which had previously been ignored in
display but not in strwidth), based in part on an idea and
code from Ei-ji Nakama. The default is TRUE.
Kerning involving spaces is now ignored (it was previously
only used in the computation of string widths).
o seq.default() and seq.int() ensure that the result is within the
interval [from, to] even when the last value would previously
have been slightly out of range because of the allowance for
rounding error in computing the number of elements.
o boxplot() gains a simple 'matrix' method, enabling boxplot(mat)
instead of boxplot(data.frame(mat)).
o zip.file.extract() gains an optional 'dir' argument (but use
unzip() instead).
o source() with 'encoding' specified (and not as "unknown") marks
the encoding of character strings in Latin-1 and UTF-8
locales.
o parse(text=z) now marks the encoding of character strings in
Latin-1 and UTF-8 locales if 'z' is of known encoding (that is
all elements are either ASCII or marked as Latin-1 or UTF-8).
o sprintf() does stricter error checking on input formats to
avoid passing invalid formats to the OS (which have a tendency
to crash under such inputs).
o expand.grid() gains a 'stringsAsFactor' argument to ask for
automatic conversion of character vectors to factors (which
happened for many years but was not previously documented, and
is no longer the default).
o bxp() now coputes the 'ylim' including the outliers only if
'outline = TRUE'. (Wish of PR#13196)
o barplot() gains a 'args.legend' argument. (Wish of PR#13265).
o RweaveLatexSetup() now accepts all (and not just some) options
passed through from Sweave()
o cumsum(x) and cumprod(x) for double precision x now use a long
double accumulator where available and so more closely match
sum() and prod() in potentially being more accurate.
o plot() methods for "stepfun" (and hence "ecdf") gain an 'col'
argument, allowing to set all three colors simultaneously.
o Iterating over a factor in a for loop now coerces to a character
vector (rather than using the integer codes).
o data.frame() now recycles columns of list arguments, not just
vectors and factors.
o plot.ts(plot.type="multiple") now makes use of *.lab and
*.axis graphical parameters (wish of PR#13134 and 13135).
o Classes can be exported from a name space using the NAMESPACE
file directive 'exportClassPattern' which has the same syntax
as 'exportPattern'.
o strftime() now converts its first argument with as.POSIXlt()
and so is no longer an alias for format.POSIXLt.
o body<-() now treats list values consistently with other
types: they no longer need to be wrapped in a list() call.
o option("pdfbrowser") is now set on Windows as well as on
Unix-alikes.
o object.size() now returns an object of class "object_size" and
has a print() method.
o [col/row]Sums(), *Means() now have an additional '...' argument,
so that they can more easily be turned into generic functions.
o Package 'tools' contains dependsOnPkgs() to compute reverse
dependencies.
o Strict type checking is now turned on: this catches more
internal corruptions, and some badly written contributed code.
o There are new functions in package 'tcltk', tk_choose.files(),
tk_choose.dir() and tk_messageBox(), analogues of functions
available on Windows (the last is an analogue of winDialog).
o Sys.glob() now does tilde expansion on all platforms.
o read.table() and friends gain a 'fileEncoding' argument to
make re-encoding of input just a little bit simpler.
o grep() gains an 'invert' argument mimicking 'grep -v/--invert'.
o strwrap() now allows a separate prefix for the first line.
o grep() has a more efficient sibling grepl() that returns a
logical vector.
o xfig() has new arguments 'defaultFont' and 'textSpecial'
contributed by Sebastian Fischmeister.
o parse() and parse_Rd() now point to syntax errors in the
reported error context, and include the filename and line and
column numbers so smart text editors can jump to the error
location.
o str(<1d-array>) now writes "[1:n(1d)]" instead of the previous
less clear "[, 1:n]".
o New function testInstalledPackage() in package 'tools' allows
the examples (and if they were installed) any package-specific
tests to be run on an installed package.
testInstalledPackages() can run all the examples and tests in
the standard and/or recommended packages. Also
testInstalledBasic() can run the basic tests (if installed).
o file.copy() now has a 'recursive' argument.
o Errors in setOldClass() will cause a previous definition to be
restored.
o Ambiguities in class inheritance and method selection resulting
from duplicates in superclasses are now resolved by requiring
(if possible) consistency with all the superclass inheritance. The
rules for method selection have been revised to take advantage of
the improved ordering.
See ?Methods and the reference there related to inheritance.
o New function unzip() in package 'utils' to expand or list zip
archives.
o Replacement functions for class() and oldClass() will unset
the S4 bit when the replacement can't be an S4 object;
oldClass() will return the S3 class for S4 objects with slot
.S3Class.
o clip() takes extra steps to avoid the next graphics call
resetting the clip region.
o New function sample.int() to provide documented access to the
internal part of sample() (sampling from seq_len(n)).
o New version of withVisible() for better handling of cases like
withVisible(eval.parent(....)). Moved to package 'base' with a
view to replace .Internal(eval.with.vis) in source() later.
o showClass() which is also used to auto-print class definitions, now
mentions the package where the class comes from, if there is one.
o simulate(obj) now also works for "glm" objects and for weighted
fits, thanks in part to contributions from Ben Bolker and
Heather Turner. There is now a means to extend the methods
available for "glm" objects, as glm families can have an
optional 'simulate' component.
o S4 classes that inherit from any of the "structure" classes or
from "vector" will turn on methods for all the "Ops" group of
functions when the package containing the classes is
loaded. See class?structure.
o A mechanism now allows S4 classes to inherit from object types
"environment", "externalptr" and symbol ("name"). See ?setClass.
o demo() gains 'echo' and 'ask' arguments, with defaults similar
to example().
o library() no longer checks for the packages merged during the
re-organization of 1.9.0.
o New function poisson.test() in package 'stats' for exact test
of rates and rate ratios.
o New function isdebugged() indicates whether its argument has the
debug flag set or not.
o ls.str() [via print method] now also works when some objects in
the environment are missing().
o Subsetting S4-objects (without an explicit "[" method) no longer
preserves the class in cases like setClass("C",
contains="list"); This reverts a "bug fix" activated in R 2.8.0.
o .packages() and .find.packages() no longer check the package
info for installed packages with dumped metadata, since this
was checked when the package was installed. .packages() only
considers such packages to be validly installed (any others
were installed in a long-obsolete version of R). Both changes
speed up searches in libraries of thousands of packages().
o boxplot() uses butt line endings for its median line
(suggestion of Uwe Ligges, PR#13553).
o S4 objects passed to a non-default S3 method will be converted
to a valid S3 object with the S3 class. See the section on
inheriting from non-S4 classes in ?Classes.
o A new class "nonStructure" has been defined; classes that extend
a vector class but that should lose their slots under Math or
Ops functions should extend this class. See class?nonStructure.
o axis.POSIXct() now plots in the timezone marked for its inputs
(if any) rather than in the local time. The latter was a
deliberate choice, but is easy to select by removing the
'tzone' attribute. (Suggestion of Dan Kelley.)
o A new function classesToAM() returns an adjacency matrix
representing the inheritance of the classes specified. Allows
better human examination of the patterns, e.g. by using the
matrix as input to one of the graph packages (see the
documentation).
o X11options(antialias = "none") now works, for consistency with
X11().
o sprintf() now allows zero-length arguments (with a zero-length
result). (Suggestion of Bill Dunlap.)
o unlink() is now able to remove broken symbolic links on
Unix-alikes.
o New selectSuperClasses() utility.
o HoltWinters() now allows parameters alpha and beta to be fixed
at 0 and hence beta = FALSE and gamma = FALSE are used to
specify restricted models.
o A new function smoothScatter has been added to package
'graphics'. It is appropriate for very dense scatter plots
and uses density estimation and color to reflect density of
plotting.
DEPRECATED & DEFUNCT
o allGenerics() is defunct.
o Use of allocVector(CHARSXP ...) is defunct and gives an error.
o The compatibility define for graphics structure NewDevDesc in
GraphicsDevice.h has been removed.
o Support for versioned installs (R CMD INSTALL
--with-package-versions
and install.packages(installWithVers = TRUE)) has been removed.
Packages installed with versioned names will be ignored.
o The numeric and power(0.5) forms of argument to make.link()
which were deprecated in 2.4.0 are now defunct: use power()
directly.
o Conversion to Sd and Ssgm by R CMD Rdconv is now defunct.
o Support for R --gui=gnome is now defunct (and package
gnomeGUI has been withdrwan as it used a long-obsolete version
of GNOME).
o R CMD SHLIB on Windows will call the first target (not 'all') in
Makevars[.win] in future versions: so make 'all' the first
target if you have any.
UTILITIES
o R CMD build now also uses a Makevars[.win] file for cleaning
up src/.
o R CMD Rd2dvi and R CMD check are now able to cope with Cyrillic
characters in UTF-8 if environment variable _R_CYRILLIC_TEX_
is set to a non-empty value and the latex system has suitable
fonts (thanks to a hint from Alexey Shipunov).
o New function rtags() in package 'utils' that provides etags-like
indexing capabilities for R code files.
New front-end script R CMD rtags provides an interface to the
rtags() function (see R CMD rtags --help for details).
o New environment variable R_TEXI2DVICMD to hold the path (if any)
to 'texi2dvi' found at configure time: this now provides the
default to option("texi2dvi").
o massage-Examples.pl has been replaced by the R function
tools:::massageExamples().
o R CMD REMOVE now uses remove.packages() and hence removes all
members of a bundle.
o R CMD SHLIB is now an R script and has a new option -n aka
--dry-run to show what commands would be run. The same code
is used on Unix and Windows.
o R CMD Rdconv has new options --package and --version to set the
corresponding fields in HTML conversion.
o R CMD check runs the package tests with a custom startup file,
currently containing 'options(useFancyQuotes = FALSE)'.
Those tests are run by an R script: using a tests/Makefile
(undocumented) no longer works.
o R CMD config now knows about DYLIB_EXT and SHLIB_EXT, for use
in configure files.
o R CMD BATCH has a new option --no-timing to suppress printing
out the session timing.
o R CMD Rd2dvi can now work on an installed package.
o R CMD check no longer loads package 'tcltk' when checking for
code problems, so more problems may be reported.
o For R CMD SHLIB on Windows the default 'all' target only makes
the DLL, and no longer call targets 'before' and 'after'.
Rd CONVERSION
o Rd files have an optional \Rdversion{} section, which if
missing defaults to 1.0. There is support for version 1.1, a
slightly modified version with the following changes:
- The warnings for \code{} inside example are suppressed.
- Whitespace between arguments in \item and \section is
accepted without a warning (see below).
- $ is treated literally in text, even for latex conversions.
- \ is only an escape before % { } \ .
- \R, \dots and \ldots can be followed by {}, and it is
recommended that they when not followed by whitespace.
- The obsolete interpretation of \Alpha etc is no longer done.
o Rd conversion now handles ^ ~ < > | correctly in non-code
environments (such as \samp), and # and _ even in latex
conversion (but $ still needs to be escaped in version 1.0).
o Whitespace between first and second arguments is now accepted
for \item and \section, e.g. \item{foo} {some value}.
Previously arguments after whitespace were silently ignored,
and a warning is given for version 1.0 files.
o The Rd files created by prompt() and friends are declared to be
version 1.1.
o \alias now supports the escaping of { as well as of %, and this
is recommended.
o parse_Rd(), an experimental parser for Rd files, and Rd2txt(),
Rd2HTML(), Rd2latex() and Rd2ex(), even more experimental
converters, have been added to package 'tools'.
o R CMD check runs the package's Rd files through parse_Rd() for a
stricter syntax check. This can be suppressed by setting
_R_CHECK_RD_PARSE_ to FALSE.
o Added markup \verb, which displays like \code, but parses as
verbatim text. Currently only supported by parse_Rd() and
Rd2HTML().
INSTALLATION
o The shell used by the 'R' script and other shell scripts
intended to be run directly can be specified at installation
time by setting the (precious) configure variable R_SHELL.
o libtool has been updated to 2.2.6a.
o --with-ICU is now the default: this means that ICU will be
used for collation on Mac OS >= 10.4.
o make install-tests can be used to install the test files,
to allowed an installed version of R to be tested -- see the
R-admin manual. This is also supported by the function
testInstalledPackages() in package 'tools'.
o 'make install' using a parallel make should now work.
o 'make check' now always re-makes and re-runs the package
examples, which are now collated in the locale's order (and
not ASCII order).
o configure will now set the default optimization level for
gfortran on x86_64 Linux to -O as -O2 has caused problems with
gfortran 4.3.x.
PACKAGE INSTALLATION
o install.packages() is able to infer that repos=NULL was
intended from the extension on the file name specified as 'pkgs'.
On Mac OS X it now supports local binary packages with .tar.gz
extension. Nonetheless .tgz remains the preferred extension
and is expected in repositories.
It now checks >= version dependencies for dependent packages,
and so will install a newer version of a dependency if needed
and available on the repositories.
The library being installed into is considered when looking
for installed packages if it is not already part of
.libPaths() (as INSTALL already does).
It has a new argument 'Ncpus' to support parallel installs of
source packages.
o HTML links will be resolved first to the standard packages: this
avoids other installed packages diverting help on e.g. qr()
and plot() to themselves. The HTML files are only "touched" if
they have changed.
o A check is done that the R files can be parsed: this both
prevents a broken package without lazy-loading from being
installed and gives better diagnostics.
o install.packages() gains a 'configure.vars' argument, and both
this and 'configure.args' get their defaults from options().
o There is a unified R script for INSTALL on both Unix-alike and
Windows that takes option names used by either in the past.
It adds --no-multiarch to disable building other than the main
sub-architecture, and allows multiple instances of
--configure-args and --configure-vars (which will be
concatenated).
New option --install-tests will install any package-specific
tests.
o Times in the Packaged: and Built: fields are now recorded in
UTC, and in most cases in ISO 8601 format.
C-LEVEL FACILITIES
o A helper function, asCharacterFactor, converts from factors to
character vectors.
BUG FIXES
o The postscript() output for setting text is faster and smaller.
o Subsetting a data frame with duplicate column names without
selecting columns (e.g. z[i,]) no longer makes the column
names unique. This was never documented, but some packages
have assumed it.
o data.frame() no longer ignores row names on objects if the
first name is empty. (PR#13230: this has been the behaviour
for a long time, but apparently undocumented.)
o deparse(control="S_compatible") now never uses backticks.
o X-spline drawing is improved for cases where the control
points are located well off the edges of the device.
The symptom of this problem is the error "reached MAXNUMPTS".
o exists() with mode= "any" will no longer run an active binding's
function.
o format(c(1 + 2i, NA)) no longer has extraneous space in " NA".
o mood.test() could fail in 2.8.x on large samples because of
integer overflow.
o heatmap() without a dendrogram could fail. (PR#13512)
o Checks for missing values will no longer occasionally result in
an infinite loop or stack overflow error, depending on the
compiler. Active bindings are now always considered to be
non-missing.
o Rd conversion was not accepting \p (as in \pkg} or (when using
Perl 5.10.x) \k (as in \kbd) in any preamble text in a
\value{} section, since those are nowadays interpreted by
Perl. (PR#13575)
o if(as.raw(1)) TRUE now works as expected. (PR#13630)
Also, c(as.raw(12), TRUE) or c(raw(3), pi) do.
o duplicated(<data frame>, incomparables = NA) now gives the
intended error message.
o name handling of as.data.frame() has been sanitized somewhat
o Evaluating an assignment expression with a string on the left
hand side no longer destructively changes the string to a symbol
in the expression.
**************************************************
* *
* 2.8 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.8.1 patched
NEW FEATURES
o R CMD check has a new argument '--install-args' to pass
command-line arguments to INSTALL.
E.g. --install-args="--docs=normal" on Windows if the HTML
Help Workshop is not installed.
o R-Forge has been added to R_HOME/etc/repositories, so it will
be available interactively in setRepositories().
o The compiled loess() code has been updated to the current
version of dloess from Netlib. This includes patches from Ben
Tyner which correct some errors when degree = 0 and hence
solve PR#13570.
INSTALLATION
o --with-ICU is now supported (and recommended) on Mac OS X using
Apple's supplied port. Note however that the locale category
LC_COLLATE cannot be changed whilst R is running on Apple's
version of ICU.
Configure supports a wider range of ICU versions on other
OSes: version 3.0 should suffice, and 3.2, 3.8 and 4.0 have
been tested.
BUG FIXES
o grid-based plots no longer reset the base text size to the
default 96dpi in cairo-based bitmap devices.
o Rd conversion was incorrectly parsing \\\* and \\\{ (and other
cases with an odd number of backslashes greater than one).
Text conversion of \code{\ etc} was incorrect (a single
backslash stands for itself inside \code).
\code{} inside \examples{} is now fixed up (but the warning
remains, since it will be handled incorrectly in earlier
versions of R).
o as.matrix.data.frame() could fail if coercion changed the
dimension of one of the columns (as e.g. the coercion of a "Surv"
object to a character vector does).
o When extracting part of a complex list structure using [[]]
with a vector index, the extracted part was not marked for
duplication on change. (PR#13411)
o Assigning an additional element to a pairlist/language element
by x[["foo"]] <- value did not name the additional element.
o .Call() and .External() were not accepting "NativeSymbolInfo"
and "NativeSymbol" objects as claimed. (Patch from Olaf
Mersmann.)
o codoc() was missing some default value mismatches with
unescaped backslashes, e.g. final="\\" needs to be written as
final="\\\\" in the Rd file.
The reports on values now give strings in the original quoted
format (with \ and " escaped).
o The $<- method for pairlists (including language objects)
failed to duplicate if NAMED was 2.
o read.table(blank.lines.skip = FALSE) gave a final empty row on
files with less than 5 lines (PR#13433).
o Workaround for a bug in some versions of iconv that was seen
with output lines of more than 10,000 bytes and with
re-encoding requested on an output connection.
o The fullrefman.{dvi,pdf} duplicated part I in part II (at
least on some systems).
o cbind() could crash with a zero-length input and a list result.
o pdf(colormodel = "gray") was setting the stroke colour for fills.
o file.show() with multiple files would only show multiple
copies of the first one. (PR#13469)
o formatC(mode = "character") was documented to work, but
did not. (PR#13474)
o besselI(x,.., expon.scaled=TRUE) now gives accurate results for
x < 1e5 whereas it previously underflowed for x >~= 1500.
Further, besselJ(x,..) also computes up to 1e5 (instead of 1e4).
o str() was incorrectly warning about its option component
'formatNum' set by strOptions().
o nls(algorithm = "port") did not accept the [factor] notation.
(PR#13650)
o The relational (aka "comparison") operators are now binary, also in
a lower level sense, and an expression as "<"(1) is now erronous.
o The 'offset' argument for lm() and glm() is not longer
documented to be allowed to be of length 1: this has not been
true for a long time.
o format.info(x) is now also correct when x has no finite content.
o predict.lm() now works correctly when the fit had more than
one offset (possibly specified both in the formula and as an
argument). This function is called by predict.glm(), so the
same isses are corrected there.
o besselI(x, nu) with nu a negative integer (a singular case) is now
correct. (PR#13556)
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.9.0 is released
|
Peter Dalgaard
| 651 |
|
From jfox at mcmaster.ca Sun Nov 24 15:18:55 2002
From: jfox at mcmaster.ca (John Fox)
Date: Sun, 24 Nov 2002 09:18:55 -0500
Subject: Using XEmacs and ESS with R for MS/Windows
Message-ID: <[email protected]>
I've been working on a document describing the use of XEmacs and ESS with R
for Windows users, along with configuration files that are meant to make
things simple for Windows users. This was initially intended for my
students, but with recent discussions of Windows (and other) editors on the
the R-help list, I thought that I'd make the material more widely available.
The document describes how to install, configure, and use XEmacs and ESS
with R under Windows. The configuration files divide the XEmacs windows
into two sub-windows, one for R source files (with tabs when multiple files
are open), the other with the R process. A customized toolbar is provided
with buttons to send individual lines, "paragraphs," marked regions of
text, and functions from the source window to the R process; there are
other buttons to source the whole file silently, and to interrupt the R
process. Menus are provided to perform operations similar to those in the
standard Windows R GUI -- for example, to install, load, and update
packages. In general, I've tried to provide features available in the R GUI
and in Uwe Ligges's R plug-in for the shareware editor WinEdt. As well,
I've attempted to make XEmacs appear more Windows-like in its behaviour,
for example by defining standard Windows editing keys.
More information is available at
<http://www.socsci.mcmaster.ca/jfox/Books/Companion/ESS/>.
Comments and suggestions would be appreciated.
John
-----------------------------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
email: jfox at mcmaster.ca
phone: 905-525-9140x23604
web: www.socsci.mcmaster.ca/jfox
-----------------------------------------------------
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Using XEmacs and ESS with R for MS/Windows
|
John Fox
| 95 |
|
From maechler at stat.math.ethz.ch Tue Apr 1 11:48:02 1997
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 1 Apr 97 11:48:02 +0200
Subject: "R-announce", "R-help", "R-devel" : 3 mailing lists for R
Message-ID: <9704010948.AA00412@>
Upon proposal by Robert Gentleman,
and given the ``immediate'' release of R 0.50 beta (instead of alpha),
I have created three mailing lists concerned with R
where the 2nd one, "R-help", is the replacement for the current "R-testers".
For a while, "r-testers" will be kept as synonymous to "r-help".
The 3 mailing lists are
1) R-announce : Only announcement of new versions / important patches
2) R-help : Questions / Answers about ("released versions of") R
3) R-devel : The alpha-/ pre-testers list of "R-hackers".
People who get the newest release, try out patches,....
(maybe not much more than the R 0.50 prerelease testers)
where 1) is gatewayed to 2) i.e. all "R-announce" is forwarded to "R-help".
The intent is that "R-announce" would have less than one message per day,
typically rather only a few messages per month.
Note that I am sending this to "R-announce" and
everyone who has been on the "R-testers" list is getting this e-mail
since everything that is sent to "r-announce" is automatically forwarded to
"r-help".
- -------
AGAIN: For most of you nothing changes, you'll get all the announcements
and everything from "R-help".
However, if you are only interested in important announcements and new
releases, you should
- unsubscribe from "R-help"
- subscribe to "R-announce"
((by sending unsubscribe to R-help-request at stat.math.ethz.ch
subscribe to R-announce-request at stat.math.ethz.ch
in the message "body", not as "subject ..))
PS. Yes, this is the first post to any of these lists,
so there may be problems, even though I don't hope so.
PPS. In spite of the date, this is no "April's fool" joke....
Martin Maechler <maechler at stat.math.ethz.ch> <><
Seminar fuer Statistik, SOL F5
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1086
http://www.stat.math.ethz.ch/~maechler/
|
"R-announce", "R-help", "R-devel" : 3 mailing lists for R
|
<9704010948.AA00412@>
|
Martin Maechler
| 563 |
From stefano.iacus at unimi.it Sat Apr 28 17:25:22 2001
From: stefano.iacus at unimi.it (Stefano Iacus)
Date: Sat, 28 Apr 2001 17:25:22 +0200
Subject: R for Mac Special Interest Group
Message-ID: <[email protected]>
R for Mac Special Interest Group
Along with latest version 1.2.3 of R a new mailing list has been
activated. The list is intended to exchange ideas, impressions, give
suggestions etc on the portings of R for MacOS and MacOS X.
You can subscribe to the list going to its official page:
Go to the list page :
http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
To post a message to this list just send a mail to r-sig-
mac at stat.math.ethz.ch
Stefano
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R for Mac Special Interest Group
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Stefano Iacus
| 240 |
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From p.murrell at auckland.ac.nz Fri Oct 6 04:07:14 2006
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Fri, 06 Oct 2006 15:07:14 +1300
Subject: DSC final call
Message-ID: <[email protected]>
Hi
This is a final call for abstracts; the deadline for submitting
abstracts is October 15 2006.
Please forward and circulate to other interested parties.
[apologies for any cross-posting]
DSC 2007, a conference on systems and environments for statistical
computing, will take place in Auckland, New Zealand on February 15 & 16,
2007.
We invite abstracts on the development of software systems and computing
environments for interactive statistics. The workshop will focus on,
but is not limited to, open source statistical computing.
The deadline for early registration for the conference is
December 1st (2006-12-01)
Please visit the conference web page at
http://www.stat.auckland.ac.nz/dsc-2007/
and send abstracts (one page) to dsc2007 at stat.auckland.ac.nz
Paul
(on behalf of the Organising Committee)
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
|
DSC final call
|
Paul Murrell
| 460 |
|
From plummer at iarc.fr Thu Oct 29 09:02:48 1998
From: plummer at iarc.fr (Martyn Plummer)
Date: Thu, 29 Oct 1998 08:02:48 -0000 ()
Subject: R binaries for Red Hat Linux/SPARC
Message-ID: <[email protected]>
Thanks to Vin Everett and David Clayton <david.clayton at mrc-bsu.cam.ac.uk>,
an RPM package of R-0.62.4 for Red Hat Linux/SPARC 5.1 is now available
on CRAN. This means that RPMs are available for all three platforms
(Intel, Alpha, SPARC) currently supported by Red Hat.
Martyn
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R binaries for Red Hat Linux/SPARC
|
Martyn Plummer
| 553 |
|
From maechler at stat.math.ethz.ch Thu Sep 25 22:57:40 2008
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Thu, 25 Sep 2008 22:57:40 +0200
Subject: R Foundation adopts Certification/Validation document
In-Reply-To: <[email protected]>
References: <[email protected]>
<[email protected]>
<[email protected]>
<[email protected]>
<[email protected]>
Message-ID: <[email protected]>
The Board of the R Foundation would like to announce the unanimous
adoption of the document entitled:
"R: Regulatory Compliance and Validation Issues. A Guidance Document for
the Use of R in Regulated Clinical Trial Environments"
The updated version of the document, dated August 17, 2008, is available
from the main R web page (http://www.r-project.org/) via the
Certification link, listed under Documentation.
The document provides extensive background and detailed guidance for the
use of R within the regulated framework of human clinical trials,
covering GxP and 21 CFR Part 11 issues. This document should serve R
users as a key reference for their internal regulatory activities
relating to the use of statistical software for clinical trials.
We would like to thank all of those whose hard work has resulted in this
finished document!
- - - - -
For The R Foundation for Statistical Computing,
Martin Maechler
ETH Zurich
Note: As an exception, we are announcing this through R-announce.
|
R Foundation adopts Certification/Validation document
|
Martin Maechler
| 605 |
|
From naras at stanford.edu Wed Sep 9 17:46:36 2015
From: naras at stanford.edu (Balasubramanian Narasimhan)
Date: Wed, 9 Sep 2015 08:46:36 -0700
Subject: useR! 2016 Conference Announcement
Message-ID: <[email protected]>
We are happy to announce that the R user conference
useR! 2016
is scheduled for June 27-30, 2016, and will take place at the campus
of Stanford University, Stanford California, USA.
Following the formats of previous conferences, the program will
consist of a day of tutorials followed by three days of invited
lectures and user-contributed sessions.
The program will cover topics such as
* History of R and computing with data
* Bayesian Statistics
* Bioinformatics
* Economics, Finance and Insurance
* High Performance Computing
* Industrial Applications
* Statistical Learning with Big Data
* Spatial Statistics
* Teaching
* Visualization & Graphics
* and many more.
CONFERENCE WEBPAGE
The URL for the conference web page is:
http://www.R-project.org/useR-2016
It is minimal at the moment but details of invited speakers, tutorial
sessions, registration and abstract submission process will soon
appear. A follow-up announcement will be posted to announce important
details but please feel free to check the website periodically.
CALL FOR TUTORIAL SUBMISSIONS
We invite R users to submit proposals for three hour tutorials on
special topics on R. The proposals should give a brief description of
the tutorial, including goals, detailed outline, justification why the
tutorial is important, background knowledge required and potential
attendees. The proposals should be sent before January 3, 2016 to
useR-2016 at R-project.org.
IMPORTANT DATES
October 26, 2015 open submission of abstracts
December 1, 2015 open registration
January 3, 2016 tutorial submission deadline
March 1, 2016 early registration deadline
March 3, 2016 submission deadline for abstracts
March 28, 2016 notification of abstract acceptance
June 1, 2016 registration deadline
June 20, 2016 late registration deadline (space permitting)
June 27, 2016 tutorials
June 28, 2016 conference start
June 30, 2016 conference end
We hope to meet you in Stanford!
The organizing committee:
John Chambers, Sandrine Dudoit, Trevor Hastie, Susan Holmes,
Simon Jackman, Olivia Lau, Nicholas Lewin-Koh, Norman Matloff,
Balasubramanian Narasimhan, Karthik Ram, Joseph Rickert,
Duncan Temple Lang.
|
useR! 2016 Conference Announcement
|
Balasubramanian Narasimhan
| 206 |
|
From Torsten.Hothorn at rzmail.uni-erlangen.de Fri Jul 22 11:59:37 2005
From: Torsten.Hothorn at rzmail.uni-erlangen.de (Torsten Hothorn)
Date: Fri, 22 Jul 2005 11:59:37 +0200 (CEST)
Subject: useR! 2006
Message-ID: <Pine.LNX.4.51.0507221158070.4089@artemis.imbe.med.uni-erlangen.de>
We are happy to announce that the second R user conference
useR! 2006
is scheduled for June 15-17 2006 and will take place at the Vienna
University of Economics and Business Administration.
This second world-meeting of the R user community will focus on
- R as the `lingua franca' of data analysis and statistical computing,
- providing a platform for R users to discuss and exchange ideas how R can
be used to do statistical computations, data analysis, visualization and
exciting applications in various fields,
- giving an overview of the new features of the rapidly evolving R
project.
As for the predecessor conference, the program will consist of two parts:
keynote lectures and user-contributed sessions (abstract submission will be
available online starting from October 2005). Prior to the conference, there
will be tutorials on R (proposals for tutorials should be sent before
2005-09-30).
KEYNOTE LECTURES
R becomes the standard computing engine in more and more disciplines, both
in academia and the business world. How R is used in different areas will be
presented in keynote lectures addressing hot topics including
- Marketing
- Teaching
- R on Different Platforms
- Graphics
- History of S and R
Speakers will include John M. Chambers, John Fox, Stefan Iacus, Uwe
Ligges, Paul Murrell, Peter Rossi, Simon Urbanek and Sanford Weisberg.
USER-CONTRIBUTED SESSIONS
The sessions will be a platform to bring together R users, contributers,
package maintainers and developers in the S spirit that `users are developers'.
People from different fields will show us how they solve problems
with R in fascinating applications. The sessions are organized by
members of the program committee, including Claudio Agostinelli, Roger
Bivand, Peter Buehlmann, Ram?n D?az-Uriarte, Sandrine Dudoit, Dirk
Eddelbuettel, Frank Harrell, Simon Jackman, Roger Koenker, Uwe Ligges, Andrew
Martin, Balasubramanian Narasimhan, Peter Rossi, Anthony Rossini, Gerhard
Tutz and Antony Unwin and will cover topics such as
- Applied Statistics & Biostatistics
- Bayesian Statistics
- Bioinformatics
- Econometrics & Finance
- Machine Learning
- Marketing
- Robust Statistics
- Spatial Statistics
- Statistics in the Social and Political Sciences
- Teaching
- Visualization & Graphics
- and many more.
PRE-CONFERENCE TUTORIALS
Before the start of the official program, half-day tutorials will be offered
on Wednesday, June 14th, including a lecture on R graphics by Paul Murrell.
We invite R users to submit proposals for three hour tutorials on special
topics on R. The proposals should give a brief description of the tutorial,
including goals, detailed outline, justification why the tutorial is
important, background knowledge required and potential attendees. The
proposals should be sent before 2005-09-30 to useR-2006 at R-project.org.
After the official presentations, Vienna's famous wine and beer pubs, cafes
and restaurants proofed to be a very stimulating environment for fruitful
discussions at previous meetings of the R community like last year's `useR!
2004'.
We invite all R users to submit abstracts on topics presenting innovations or
exciting applications of R. A web page offering more information on the `useR!'
conference, abstract submission, registration and Vienna is available at
http://www.R-project.org/useR-2006/
IMPORTANT DATES
- registration: starting October 2005
- online abstract submission: starting October 2005
- submission deadline of tutorial proposals: 2005-09-30
- early registration deadline: 2006-01-31
- submission deadline of abstracts: 2006-02-28
- registration deadline: 2006-05-31
We hope to meet you in Vienna!
The organizing committee:
Torsten Hothorn, Achim Zeileis, David Meyer, Bettina Gruen,
Kurt Hornik and Friedrich Leisch
|
useR! 2006
|
<Pine.LNX.4.51.0507221158070.4089@artemis.imbe.med.uni-erlangen.de>
|
Torsten Hothorn
| 392 |
From pd.mes at cbs.dk Fri Feb 25 13:49:42 2011
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 25 Feb 2011 13:49:42 +0100
Subject: [R] R 2.12.2 is released
Message-ID: <[email protected]>
I've rolled up R-2.12.2.tar.gz a short while ago. This is an update release, which fixes a number of mostly minor issues, and one major issue in which complex arithmetic was being messed up on some compiler platform.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.12.2.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 72deeabefdf6fd14e83bf5703dce9176
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 30b55e4f34c155fcb2fafa7ebb55528e
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = bc70b51dddab8aa39066710624e55d5e
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655
MD5 (R-2/R-2.12.2.tar.gz) = bc70b51dddab8aa39066710624e55d5e
This is the relevant part of the NEWS file:
R News
CHANGES IN R VERSION 2.12.2:
SIGNIFICANT USER-VISIBLE CHANGES:
? Complex arithmetic (notably z^n for complex z and integer n) gave
incorrect results since R 2.10.0 on platforms without C99 complex
support. This and some lesser issues in trignometric functions
have been corrected.
Such platforms were rare (we know of Cygwin and FreeBSD).
However, because of new compiler optimizations in the way complex
arguments are handled, the same code was selected on x86_64 Linux
with gcc 4.5.x at the default -O2 optimization (but not at -O).
? There is a workaround for crashes seen with several packages on
systems using zlib 1.2.5: see the INSTALLATION section.
NEW FEATURES:
? PCRE has been updated to 8.12 (two bug-fix releases since 8.10).
? rep(), seq(), seq.int() and seq_len() report more often when the
first element is taken of an argument of incorrect length.
? The Cocoa back-end for the quartz() graphics device on Mac OS X
provides a way to disable event loop processing temporarily
(useful, e.g., for forked instances of R).
? kernel()'s default for m was not appropriate if coef was a set of
coefficients. (Reported by Pierre Chausse.)
? bug.report() has been updated for the current R bug tracker,
which does not accept emailed submissions.
? R CMD check now checks for the correct use of $(LAPACK_LIBS) (as
well as $(BLAS_LIBS)), since several CRAN recent submissions have
ignored ?Writing R Extensions?.
INSTALLATION:
? The zlib sources in the distribution are now built with all
symbols remapped: this is intended to avoid problems seen with
packages such as XML and rggobi which link to zlib.so.1 on
systems using zlib 1.2.5.
? The default for FFLAGS and FCFLAGS with gfortran on x86_64 Linux
has been changed back to -g -O2: however, setting -g -O may still
be needed for gfortran 4.3.x.
PACKAGE INSTALLATION:
? A LazyDataCompression field in the DESCRIPTION file will be used
to set the value for the --data-compress option of R CMD INSTALL.
? Files R/sysdata.rda of more than 1Mb are now stored in the
lazyload daabase using xz compression: this for example halves
the installed size of package Imap.
? R CMD INSTALL now ensures that directories installed from inst
have search permission for everyone.
It no longer installs files inst/doc/Rplots.ps and
inst/doc/Rplots.pdf. These are almost certainly left-overs from
Sweave runs, and are often large.
DEPRECATED & DEFUNCT:
? The ?experimental? alternative specification of a name space via
.Export() etc is now deprecated.
? zip.file.extract() is now deprecated.
? Zip-ing data sets in packages (and hence R CMD INSTALL
--use-zip-data and the ZipData: yes field in a DESCRIPTION file)
is deprecated: using efficiently compressed .rda images and
lazy-loading of data has superseded it.
BUG FIXES:
? identical() could in rare cases generate a warning about
non-pairlist attributes on CHARSXPs. As these are used for
internal purposes, the attribute check should be skipped.
(Reported by Niels Richard Hansen).
? If the filename extension (usually .Rnw) was not included in a
call to Sweave(), source references would not work properly and
the keep.source option failed. (PR#14459)
? format.data.frame() now keeps zero character column names.
? pretty(x) no longer raises an error when x contains solely
non-finite values. (PR#14468)
? The plot.TukeyHSD() function now uses a line width of 0.5 for its
reference lines rather than lwd = 0 (which caused problems for
some PDF and PostScript viewers).
? The big.mark argument to prettyNum(), format(), etc. was inserted
reversed if it was more than one character long.
? R CMD check failed to check the filenames under man for Windows'
reserved names.
? The "Date" and "POSIXt" methods for seq() could overshoot when to
was supplied and by was specified in months or years.
? The internal method of untar() now restores hard links as file
copies rather than symbolic links (which did not work for
cross-directory links).
? unzip() did not handle zip files which contained filepaths with
two or more leading directories which were not in the zipfile and
did not already exist. (It is unclear if such zipfiles are valid
and the third-party C code used did not support them, but
PR#14462 created one.)
? combn(n, m) now behaves more regularly for the border case m = 0.
(PR#14473)
? The rendering of numbers in plotmath expressions (e.g.
expression(10^2)) used the current settings for conversion to
strings rather than setting the defaults, and so could be
affected by what has been done before. (PR#14477)
? The methods of napredict() and naresid() for na.action =
na.exclude fits did not work correctly in the very rare event
that every case had been omitted in the fit. (Reported by Simon
Wood.)
? weighted.residuals(drop0=TRUE) returned a vector when the
residuals were a matrix (e.g. those of class "mlm"). (Reported
by Bill Dunlap.)
? Package HTML index files <pkg>/html/00Index.html were generated
with a stylesheet reference that was not correct for static
browsing in libraries.
? ccf(na.action = na.pass) was not implemented.
? The parser accepted some incorrect numeric constants, e.g. 20x2.
(Reported by Olaf Mersmann.)
? format(*, zero.print) did not always replace the full zero parts.
? Fixes for subsetting or subassignment of "raster" objects when
not both i and j are specified.
? R CMD INSTALL was not always respecting the ZipData: yes field of
a DESCRIPTION file (although this is frequently incorrectly
specified for packages with no data or which specify lazy-loading
of data).
R CMD INSTALL --use-zip-data was incorrectly implemented as
--use-zipdata since R 2.9.0.
? source(file, echo=TRUE) could fail if the file contained #line
directives. It now recovers more gracefully, but may still
display the wrong line if the directive gives incorrect
information.
? atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms
without C99 complex support.
? library() failed to cache S4 metadata (unlike loadNamespace())
causing failures in S4-using packages without a namespace (e.g.
those using reference classes).
? The function qlogis(lp, log.p=TRUE) no longer prematurely
overflows to Inf when exp(lp) is close to 1.
? Updating S4 methods for a group generic function requires
resetting the methods tables for the members of the group (patch
contributed by Martin Morgan).
? In some circumstances (including for package XML), R CMD INSTALL
installed version-control directories from source packages.
? Added PROTECT calls to some constructed expressions used in C
level eval calls.
? utils:::create.post() (used by bug.report() and help.request())
failed to quote arguments to the mailer, and so often failed.
? bug.report() was naive about how to extract maintainer email
addresses from package descriptions, so would often try mailing
to incorrect addresses.
? debugger() could fail to read the environment of a call to a
function with a ... argument. (Reported by Charlie Roosen.)
? prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work
correctly.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[R] R 2.12.2 is released
|
Peter Dalgaard
| 397 |
|
From pd@me@ @end|ng |rom cb@@dk Wed Mar 1 13:04:56 2023
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Wed, 1 Mar 2023 12:04:56 +0000
Subject: [Rd] R 4.2.3 scheduled for March 15
Message-ID: <[email protected]>
Full schedule available on developer.r-project.org in a short while.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[Rd] R 4.2.3 scheduled for March 15
|
Peter Dalgaard
| 583 |
|
From guido at hal.stat.unipd.it Fri Jan 19 08:59:23 2001
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Fri, 19 Jan 2001 08:59:23 +0100
Subject: R 1.2.1 for Windows
Message-ID: <[email protected]>
Windows binaries at CRAN (http://cran.r-project.org) have been updated
to R-1.2.1. See below for the list of Windows-specific changes.
guido masarotto
(for the R-core team)
Windows-specific changes to R
=============================
Pipe connections now work under RGui and embedded R.dll, although
slower than under Rterm, and as they run with no stdin or stdout to
inherit what you can do with them is limited. They work better for
reading than writing.
The installer will no longer crash trying to install addons with a
long PATH and R_HOME not set. Similarly, Rcmd accepts long paths.
Using Rcmd INSTALL with an incorrect path specification ending in \ no
longer runs amok.
Internal pager no longer fails when given a file of one line and no
line ending.
Hyperlinks to other packages in CHTML files launched by help() will
now work irrespective of the working directory (but like HTML, only
to packages in the same library). The .chm files do need to be
re-built under this version.
help(, winhelp=TRUE) will now find alias topics as well as main items.
Hitting the total memory allocation limit set by --max-mem-size will
give a warning (and will usually also lead to an error, and that may
suppress printing out the warning).
There is a new make target test-Reg to run the regression tests (which
now do I/0, so might give different results on Windows).
Rcmd build with the latest tar.exe will exclude files as intended.
There are further improvements in the GUI console receiving output
(e.g. from tcltk interactive functions) during input. If you can,
arrange to send output in a single piece, or at least a whole line at
a time (although partial lines will now work). For example, don't use
print() but capture the output in a text connection and use something
like cat(paste(outlines, "", collapse="\n)) to output a single string.
The initial rescaling is no longer done for windows(rescale="fixed"),
and the scrollbars in that mode are more responsive but move the
viewport 20 pixels at a time.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R 1.2.1 for Windows
|
Guido Masarotto
| 217 |
|
From deepayan at stat.wisc.edu Tue Jan 15 04:12:42 2002
From: deepayan at stat.wisc.edu (Deepayan Sarkar)
Date: Mon, 14 Jan 2002 21:12:42 -0600 (CST)
Subject: new version of lattice
Message-ID: <[email protected]>
A new version of the Lattice package is now available on CRAN. A list of
the (mostly minor) changes are given below. The documentation is probably
still a bit shaky at places, and suggestions for improvement would be
appreciated.
-----------------------------------------------------------------------
Changes in lattice 0.4
======================
Some of the implementation details have changed a lot (mainly in
print.trellis). This might cause some old code to fail, though no such
instances are known.
No significant new features have been added, but there are several
bugfixes (notably in levelplot). The important changes are:
o documentation restructured. There is no topic called `trellis.args'
any more. The detailed description of the arguments common to all
high level trellis functions can be found under help(xyplot)
o once trellis.device() is called, Lattice graphics and base R
graphics should mix more or less seamlessly. There is an optional
argument in trellis.device() that can deal with the first blank
page problem, with certain restrictions.
o a (as yet very small) demo, called by demo("lattice")
o Clipping: whatever is drawn by the panel function is now clipped to
inside the panel region. Strip texts are clipped to inside the
strips.
o Axis tick labels by default do not overlap, some tick marks are
left unlabelled if necessary.
o The argument list for strip.default changed to be like S
o levels() and nlevels() give sensible answers for shingles. new
print methods for shingles and levels of shingles
o colorkey (currently used only in levelplot) can now be placed to
the left, top or bottom as well
o new ``lines'' component in the par.strip.text argument that can be
used to change the height of strips
o xlab, main etc can be double height strings (containing "\n"-s),
the spaces allocated for these would be automatically adjusted
o strip.default now has style=5
o new panel.superpose.2 (suggested by Neil Klepeis)
o the default colour settings sometimes seem too light on a white
background. To deal with this, there is a new setting with some
darker colours that can be set by calling lset(theme =
"white.bg"). see ?lset for details. This is currently in a
proof-of-concept stage (the colors in "white.bg" were chosen just
because I liked their names) and suggestions for better color
schemes would be most welcome.
o show.settings() added
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
new version of lattice
|
Deepayan Sarkar
| 4 |
|
From pd@me@ @end|ng |rom cb@@dk Sat Feb 29 10:14:22 2020
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Sat, 29 Feb 2020 09:14:22 +0000
Subject: R 3.6.3 is released
Message-ID: <[email protected]>
The build system rolled up R-3.6.3.tar.gz (codename "Holding the Windsock") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.6.3.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 28a3942a7129877e9af1d5ea16202052
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 2b364f6eaef28e069ab8ed779ee5859d
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 591dcf615162127f904e4e461f330ce9
MD5 (R-latest.tar.gz) = 506c9576ba33e1262ad5b5624db9d96a
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = bb45f89c01d509721c47fd41f147da60
MD5 (VERSION-INFO.dcf) = d97d382dc5583f9385461d8a4b0ff091
MD5 (R-3/R-3.6.3.tar.gz) = 506c9576ba33e1262ad5b5624db9d96a
2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
38219d9c6221ccfbf075ef03711b420a1aa8731f890c8f2337148b602a217c2d FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
50381062bad9aeb4b0c8c4695cb6955c5ff70699fcc821a8e1b340229100278c NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
ca04f78ffe54afa326fe3ed40e7e1411aca0000ed2fa5ead97ddf51c6aa5b7bc NEWS.2
89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
2a8dca916cd92229ef9e328f3610ca204809c262823b860252b42072dac2473a THANKS
20f8bfdfc6302bb2cf9b0fc5424c9a10ac0953096b6c32768ffd106a3fdd4589 VERSION-INFO.dcf
89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f R-3/R-3.6.3.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 3.6.3:
NEW FEATURES:
* The included LAPACK has been updated to version 3.9.0 (for the
included routines, just bug fixes).
BUG FIXES:
* Fixed a C level integer overflow in rhyper(); reported by
Benjamin Tyner in PR#17694.
* Uses of url(gzcon(.)) needing to extend buffer size have failed
(with HTTP/2 servers), reported by G'abor Cs'ardi.
* predict(loess(..), se=TRUE) now errors out (instead of
seg.faulting etc) for large sample sizes, thanks to a report and
patch by Benjamin Tyner in PR#17121.
* tools:assertCondition(., "error") and hence assertError() no
longer return errors twice (invisibly).
* update(form, new) in the case of a long new formula sometimes
wrongly eliminated the intercept from form, or (more rarely)
added a garbage term (or seg.faulted !); the fix happened by
simplifying the C-level logic of terms.formula(). Reported by
Mathias Amb"uhl in PR#16326.
* The error message from stopifnot(.., <error producing call>)
again contains the full "stopifnot(.......)" call: Its attempted
suppression did not work consistently.
* On Windows, download.file(., , "wininet", headers=character())
would fail; reported with patch proposal by Kevin Ushey in
PR#17710.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.6.3 is released
|
Peter Dalgaard
| 616 |
|
From king at solzhenitsyn.ens.gu.edu.au Wed Aug 19 01:00:40 1998
From: king at solzhenitsyn.ens.gu.edu.au (Robert King)
Date: Wed, 19 Aug 1998 09:00:40 +1000 (EST)
Subject: HTML version of R mailing list archives
Message-ID: <Pine.LNX.3.93.980819085630.947A-100000@solzhenitsyn.ens.gu.edu.au>
The HTML version of the R-help mailing list archives has been moved
slightly. The new address is
http://www.ens.gu.edu.au/robertk/R/help/98b/index.htm
for the present section and
http://www.ens.gu.edu.au/robertk/R/
is a page containing links to all the sections.
The move has taken place because they have been expanded to include
r-devel and r-announce archives as well. (at present these archives only
contain from August 1998 onwards, but I will also convert the earlier
archives).
----
Robert King, || The Society for the Preservation of Tithesis commends your
Environmental|| ebriated and scrutable use of "delible" and "defatigable",
Science, || which are gainly, sipid and couth. We are gruntled and
Griffith Uni,|| consolate that you have the ertia and eptitude to choose such
Australia || putably pensible tithesis, which we parage. - Evan Kirshenbaum
Robert.King at ens.gu.edu.au http://www.ens.gu.edu.au/robertk/index.htm
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
HTML version of R mailing list archives
|
<Pine.LNX.3.93.980819085630.947A-100000@solzhenitsyn.ens.gu.edu.au>
|
Robert King
| 546 |
From maechler at stat.math.ethz.ch Tue Nov 26 18:39:45 2002
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 26 Nov 2002 18:39:45 +0100
Subject: R-announce moved from majordomo to [procmail+mailman]
Message-ID: <[email protected]>
I have moved the R-announce mailing list from the Majordomo
software to a combination of procmail & mailman an hour or so ago.
You find a link in the footer of this message giving an URL
where you can modify your subscription, look at the archives
(everything from the beginning in 1997) and more.
CHANGE: Postings to R-announce are now moderated, ie.
they have to be approved by a list maintainer
unless they come from one of a small set of R developers.
Note that *everyone* subscribed to R-help also gets R-announce
messages without a need to subscribe.
Notice that the "Sender:" field of these e-mails has changed
from owner-r-announce to r-announce-admin. Those who use
mail-filtering rules may wish to adapt.
We expect faster mail delivery and an easier user (and
maintainer!) interface. Feedback welcome, to me privately or R-help.
The R-help mailing list (and its "digest") version will move to
mailman too.
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
|
R-announce moved from majordomo to [procmail+mailman]
|
Martin Maechler
| 98 |
|
From Friedrich.Leisch at ci.tuwien.ac.at Thu Jul 10 15:10:35 1997
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Thu, 10 Jul 1997 15:10:35 +0200
Subject: New Packages in CRAN
Message-ID: <[email protected]>
The following packages have been contributed to CRAN by Thomas Lumley:
integrate-1.0.tar.gz:
S function and supporting C and Fortran code for adaptive
quadrature. The underlyling fortran code is purported to
work in from 2 to 20 dimensions.
S original by Michael Meyer (mikem at andrew.cmu.edu).
R port by Thomas Lumley <thomas at biostat.washington.edu>.
[1997/07/10]
leaps-1.0.tar.gz:
This library performs an exhaustive search for the best
subsets of a given set of potential regressors, using a
branch-and-bound algorithm, and also performs searches using
a number of less time-consuming techniques. It is designed to
replace the "leaps()" command in S.
Packaged for R by Thomas Lumley <thomas at biostat.washington.edu>
and based on FORTRAN77 code by Alan Miller
<Alan.Miller at vic.cmis.csiro.au>.
[1997/07/10]
The tar files are available from the CRAN main site at
ftp://ftp.ci.tuwien.ac.at/pub/R/
in the directory
src/contrib
and from the mirror sites (tomorrow):
http://lib.stat.cmu.edu/R/CRAN/ (U.S./Pennsylvania)
ftp://franz.stat.wisc.edu/pub/R/ (U.S./Wisconsin)
ftp://ftp.stat.math.ethz.ch/R-CRAN/ (Switzerland)
http://www.stat.unipg.it/pub/stat/statlib/R/CRAN/ (Italy)
If you want your server being added to the list of mirrors, please let
us know.
Best,
Fritz
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 4541
Technische Universit?t Wien Fax: (+43 1) 504 14 98
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
PGP public key http://www.ci.tuwien.ac.at/~leisch/pgp.key
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|
New Packages in CRAN
|
Friedrich Leisch
| 573 |
|
From pd.mes at cbs.dk Mon Oct 31 10:56:33 2011
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 31 Oct 2011 10:56:33 +0100
Subject: R 2.14.0 is released
Message-ID: <[email protected]>
The byte pixies have rolled up R-2.14.0.tar.gz (codename "Great Pumpkin") at 9:00 this morning. This is a development release with several new features; see the list below for details.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.14.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 7d14b4be550f30d8a73a830ab272e4f4
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 98ef8b3497d12fd43b56d3732c34f9cc
MD5 (NEWS.html) = 3ec485820148d22864b9b7990347bf2c
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = 98cf8fe74e512e1061caf1ee0c2043a8
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc
MD5 (R-2/R-2.14.0.tar.gz) = 98cf8fe74e512e1061caf1ee0c2043a8
This is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.14.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o All packages must have a namespace, and one is created on
installation if not supplied in the sources. This means that any
package without a namespace must be re-installed under this
version of R (but previously-installed data-only packages without
R code can still be used).
o The yLineBias of the X11() and windows() families of devices has
been changed from 0.1 to 0.2: this changes slightly the vertical
positioning of text in the margins (including axis annotations).
This is mainly for consistency with other devices such as
quartz() and pdf(). (Wish of PR#14538.)
There is a new graphics parameter "ylbias" which allows the
y-line bias of the graphics device to be tweaked, including to
reproduce output from earlier versions of R.
o Labeling of the p-values in various anova tables has been
rationalized to be either "Pr(>F)" or "Pr(>Chi)" (i.e. the
"Pr(F)", "Pr(Chi)" and "P(>|Chi|)" variants have been
eliminated). Code which extracts the p value _via_ indexing by
name may need adjustment.
o :: can now be used for datasets made available for lazy-loading
in packages with namespaces (which makes it consistent with its
use for data-only packages without namespaces in earlier versions
of R).
o There is a new package parallel.
It incorporates (slightly revised) copies of packages multicore
and snow (excluding MPI, PVM and NWS clusters). Code written to
use the higher-level API functions in those packages should work
unchanged (apart from changing any references to their namespaces
to a reference to parallel, and links explicitly to multicore or
snow on help pages).
It also contains support for multiple RNG streams following
L'Ecuyer _et al_ (2002), with support for both mclapply and snow
clusters. This replaces functions like clusterSetupRNG() from
snow (which are not in parallel).
The version released for R 2.14.0 contains base functionality:
higher-level convenience functions are planned (and some are
already available in the 'R-devel' version of R).
o Building PDF manuals (for R itself or packages, e.g. _via_ R CMD
check) by default requires the LaTeX package inconsolata: see the
section on 'Making the manuals' in the 'R Installation and
Administration Manual'.
o axTicks(*, log=TRUE) has changed in some cases to satisfy the
documented behavior and be consistent.
NEW FEATURES:
o txtProgressBar() can write to an open connection instead of the
console.
o Non-portable package names ending in . are no longer allowed.
Nor are single-character package names (R was already
disallowed).
o regexpr() and gregexpr() with perl = TRUE allows Python-style
named captures. (Wish and contribution of PR#14518.)
o The placement of 'plotmath' text in the margins of plots done by
base graphics now makes the same vertical adjustment as ordinary
text, so using ordinary and plotmath text on the same margin line
will seem better aligned (but not exactly aligned, since ordinary
text has descenders below the baseline and plotmath places them
on the baseline). (Related to PR#14537.)
o sunflowerplot() now has a formula interface. (Wish of PR#14541.)
o iconv() has a new argument toRaw to handle encodings such as
UTF-16 with embedded nuls (as was possible before the CHARSXP
cache was introduced).
It will also accept as input the type of list generated with
toRaw = TRUE.
o Garbage-collecting an unused input text connection no longer
gives a warning (since it 'connects' to nothing outside R).
o read.table() and scan() have gained a text argument, to allow
reading data from a (possibly literal) character string.
o optim(*, method = .) now allows method = "Brent" as an interface
to optimize(), for use in cases such as mle() where optim() is
used internally.
o mosaicplot() gains a border argument. (Wish of PR#14550.)
o smooth.spline() gains a tol argument which controls how different
x values need to be to be treated as distinct. The default has
been changed to be more reliable for inputs whose range is small
compared to their maximum absolute value. (Wish of PR#14452.)
o gl() runs faster by avoiding calling factor().
o The print() method for object.size() accepts B as well as b as an
abbreviation for 'bytes'.
o unlink() gains a force argument to work like rm -f and if
possible override restrictive permissions.
o pbirthday() and qbirthday() now use exact calculations for
coincident = 2.
o unzip() and unz() connections have been updated with support for
more recent Zip64 features (including large file sizes and bzip2
compression, but not UTF-8 file names).
unzip() has a new option to restore file times from those
recorded (in an unknown timezone) in the zip file.
o update.packages() now accepts a character vector of package names
for the oldPkgs argument. (Suggestion of Tal Galili.)
o The special reference class fields .self and .refClassDef are now
read-only to prevent corrupting the object.
o decompose() now returns the original series as part of its value,
so it can be used (rather than reconstructed) when plotting.
(Suggestion of Rob Hyndman.)
o Rao's efficient score test has been implemented for glm objects.
Specifically, the add1, drop1, and anova methods now allow test =
"Rao".
o If a saved workspace (e.g. .RData) contains objects that cannot
be loaded, R will now start with an warning message and an empty
workspace, rather than failing to start.
o strptime() now accepts times such as 24:00 for midnight at the
end of the day, for although these are disallowed by POSIX
1003.1-2008, ISO 8601:2004 allows them.
o Assignment of names() to S4 objects now checks for a
corresponding "names" slot, and generates a warning or an error
if that slot is not defined. See the section on slots in
?Classes.
o The default methods for is.finite(), is.infinite() and is.nan()
now signal an error if their argument is not an atomic vector.
o The formula method for plot() no longer places package stats on
the search path (it loads the namespace instead).
o There now is a genuine "function" method for plot() rather than
the generic dispatching internally to graphics::plot.function().
It is now exported, so can be called directly as plot.function().
o The one-sided ks.test() allows exact = TRUE to be specified in
the presence of ties (but the approximate calculation remains the
default: the 'exact' computation makes assumptions known to be
invalid in the presence of ties).
o The behaviour of curve(add = FALSE) has changed: it now no longer
takes the default x limits from the previous plot (if any):
rather they default to c(0, 1) just as the "function" method for
plot(). To get the previous behaviour use curve(add = NA), which
also takes the default for log-scaling of the x-axis from the
previous plot.
o Both curve() and the plot() method for functions have a new
argument xname to facilitate plots such as sin(t) _vs_ t.
o The local argument to source() can specify an environment as well
as TRUE (parent.env()) and FALSE (.GlobalEnv). It gives better
error messages for other values, such as NA.
o vcov() gains methods for classes "summary.lm" and "summary.glm".
o The plot() method for class "profile.nls" gains ylab and lty
arguments, and passes ... on to plot.default.
o Character-string arguments such as the mode argument of vector(),
as.vector() and is.vector() and the description argument of
file() are required to be of length exactly one, rather than any
further elements being silently discarded. This helps catch
incorrect usage in programming.
o The length argument of vector() and its wrappers such as
numeric() is required to be of length exactly one (other values
are now an error rather than giving a warning as previously).
o vector(len) and length(x) <- len no longer acccept TRUE/FALSE for
len (not that they were ever documented to, but there was
special-casing in the C code).
o There is a new function Sys.setFileTime() to set the time of a
file (including a directory). See its help for exactly which
times it sets on various OSes.
o The file times reported by file.info() are reported to sub-second
resolution on systems which support it. (Currently the POSIX
2008 and FreeBSD/Darwin/NetBSD methods are detected.)
o New function getCall(m) as an abstraction for m$call, enabling
update()'s default method to apply more universally. (NB: this
can be masked by existing functions in packages.)
o Sys.info() gains a euser component to report the 'effective' user
on OSes which have that concept.
o The result returned by try() now contains the original error
condition object as the "condition" attribute.
o All packages with R code are lazy-loaded irrespective of the
LazyLoad field in the DESCRIPTION file. A warning is given if
the LazyLoad field is overridden.
o Rd markup has a new \figure tag so that figures can be included
in help pages when converted to HTML or LaTeX. There are
examples on the help pages for par() and points().
o The built-in httpd server now allows access to files in the
session temporary directory tempdir(), addressed as the /session
directory on the httpd server.
o Development versions of R are no longer referred to by the number
under which they might be released, e.g. in the startup banner, R
--version and sessionUtils(). The correct way to refer to a
development version of R is 'R-devel', preferably with the date
and SVN version number.
E.g. R-devel (2011-07-04 r56266)
o There is a new function texi2pdf() in package tools, currently a
convenience wrapper for texi2dvi(pdf = TRUE).
o There are two new options for typesetting PDF manuals from Rd
files. These are beramono and inconsolata, and used the named
font for monospaced output. They are intended to be used in
combination with times, and times,inconsolata,hyper is now the
default for the reference manual and package manuals. If you do
not have that font installed, you can set R_RD4PF to one of the
other options: see the 'R Installation and Administration
Manual'.
o Automatic printing for reference classes is now done by the
$show() method. A method is defined for class envRefClass and
may be overriden for user classes (see the ?ReferenceClasses
example). S4 show() methods should no longer be needed for
reference classes.
o tools::Rdiff (by default) and R CMD Rdiff now ignore differences
in pointer values when comparing printed environments, compiled
byte code, etc.
o The "source" attribute on functions created with keep.source=TRUE
has been replaced with a "srcref" attribute. The "srcref"
attribute references an in-memory copy of the source file using
the "srcfilecopy" class or the new "srcfilealias" class.
o New items User Manuals and Technical Papers have been added to
the HTML help main page. These link to vignettes in the base and
recommended packages and to a collection of papers about R
issues, respectively.
o Documentation and messages have been standardized to use
"namespace" rather than "name space".
o setGeneric() now looks in the default packages for a non-generic
version of a function if called from a package with a namespace.
(It always did for packages without a namespace.)
o Setting the environment variable _R_WARN_ON_LOCKED_BINDINGS_ will
give a warning if an attempt is made to change a locked binding.
o \SweaveInput is now supported when generating concordances in
Sweave().
o findLineNum() and setBreakpoint() now allow the environment to be
specified indirectly; the latter gains a clear argument to allow
it to call untrace().
o The body of a closure can be one of further types of R objects,
including enviroments and external pointers.
o The Rd2HTML() function in package tools now has a stylesheet
argument, allowing pages to be displayed in alternate formats.
o New function requireNamespace() analogous to require(), returning
a logical value after attempting to load a namespace.
o There is a new type of RNG, "L'Ecuyer-CMRG", implementing
L'Ecuyer (1999)'s 'combined multiple-recursive generator'
MRG32k3a. See the comments on ?RNG.
o help.search() and ?? can now display vignettes and demos as well
as help pages. The new option "help.search.types" controls the
types of documentation and the order of their display.
This also applies to HTML searches, which now give results in all
of help pages, vignettes and demos.
o socketConnection() now has a timeout argument. It is now
documented that large values (package snow used a year) do not
work on some OSes.
o The initialization of the random-number generator now uses the
process ID as well as the current time, just in case two R
processes are launched very rapidly on a machine with
low-resolution wall clock (some have a resolution of a second;
modern systems have microsecond-level resolution).
o New function pskill() in the tools package to send a terminate
signal to one or more processes, plus constants such as SIGTERM
to provide a portable way to refer to signals (since the numeric
values are OS-dependent).
o New function psnice() in the tools package to return or change
the 'niceness' of a process. (Refers to the 'priority class' on
Windows.)
o list.dirs() gains a recursive argument.
o An Authors at R field in a package DESCRIPTION file can now be used
to generate Author and Maintainer fields if needed, and to
auto-generate package citations.
o New utility getElement() for accessing either a list component or
a slot in an S4 object.
o stars() gains a col.lines argument, thanks to Dustin Sallings.
(Wish of PR#14657.)
o New function regmatches() for extracting or replacing matched or
non-matched substrings from match data obtained by regexpr(),
gregexpr() and regexec().
o help(package = "pkg_name", help_type = "HTML") now gives HTML
help on the package rather than text help. (This gives direct
access to the HTML version of the package manual shown _via_
help.start()'s 'Packages' menu.)
o agrep() gains a fixed argument to optionally allow approximate
regular expression matching, and a costs argument to specify
possibly different integer match costs for insertions, deletions
and substitutions.
o read.dcf() and write.dcf() gain a keep.white argument to indicate
fields where whitespace should be kept as is.
o available.packages() now works around servers that fail to return
an error code when PACKAGES.gz does not exist. (Patch submitted
by Seth Schommer.)
o readBin() can now read more than 2^31 - 1 bytes in a single call
(the previously documented limitation).
o New function regexec() for finding the positions of matches as
well as all substrings corresponding to parenthesized
subexpressions of the given regular expression.
o New function adist() in package utils for computing 'edit'
(generalized Levenshtein) distances between strings.
o Class "raster" gains an is.na method to avoid confusion from the
misuse of the matrix method (such as PR#14618).
o The identical() function gains an ignore.bytecode argument to
control comparison of compiled functions.
o pmin and pmax now warn if an argument is partially recycled (wish
of PR#14638).
o The default for image(useRaster=) is now taken from option
"preferRaster": for the small print see ?image.
o str() now displays reference class objects and their fields,
rather than treating them as classical S4 classes.
o New function aregexec() in package utils for finding the
positions of approximate string matches as well as all substrings
corresponding to parenthesized subexpressions of the given
regular expression.
o download.file() has an extra argument to pass additional
command-line options to the non-default methods using
command-line utilities.
cacheOK = FALSE is now supported for method = "curl".
o interaction.plot(*, type = .) now also allows type "o" or "c".
o axTicks(*, log=TRUE) did sometimes give more values than the
ticks in the corresponding graphics::axis(). By default, it now
makes use of the new (graphics-package independent) axisTicks()
which can make use of a new utility .axisPars(). Further, it now
returns a decreasing sequence (as for log=FALSE) when usr is
decreasing.
o Using fix() or edit() on a R object (except perhaps a matrix or
data frame) writes its temporary file with extension .R so
editors which select their mode based on the extension will
select a suitable mode.
GRAPHICS DEVICES:
o The pdf() device makes use of Flate compression: this is
controlled by the new logical argument compress, and is enabled
by default.
o Devices svg(), cairo_pdf() and cairo_ps() gain a family argument.
On a Unix-alike X11() gains a family argument. This is one of
the x11.options() and so can be passed as an argument to the
bmp(), jpeg(), png() and tiff() devices.
Analogous changes have been made on Windows, so all built-in R
graphics devices now have a family argument except pictex()
(which has no means to change fonts).
o The bmp(), jpeg(), png() and tiff() devices now make use of the
antialias argument for type = "quartz".
o There are several new built-in font mappings for X11(type =
"Xlib"): see the help on X11Fonts().
o There is a new type X11(type = "dbcairo") which updates the
screeen less frequently: see its help page.
o The X11() device now makes use of cursors to distinguish its
states. The normal cursor is an arrow (rather than a crosshair);
the crosshair is used when the locator is in use, and a watch
cursor is shown when plotting computations are being done.
(These are the standard names for X11 cursors: how they are
actually displayed depends on the window manager.)
o New functions dev.hold() and dev.flush() for use with graphics
devices with buffering. These are used for most of the
high-level graphics functions such as boxplot(), so that the plot
is only displayed when the page is complete.
Currently implemented for windows(buffered = TRUE), quartz() and
the cairographics-based X11() types with buffering (which are the
default on-screen devices).
o New function dev.capture() for capture of bitmap snapshots of
image-based devices (a superset of the functionality provided by
grid.cap() in grid).
o The default colormodel for pdf() and postscript() is now called
"srgb" to more accurately describe it. (Instead of "rgb", and in
the case of postscript() it no longer switches to and from the
gray colorspace, by default.)
The colormodel for postscript() which does use both gray and sRGB
colorspaces is now called "srgb+gray".
Plots which are known to use only black/white/transparent can
advantageously use colormodel = "gray" (just as before, but there
is now slightly more advantage in doing so).
o postscript() with values colormodel = "rgb" and colormodel =
"rgb-nogray" give the behaviour prior to R 2.13.0 of uncalibrated
RGB, which under some circumstances can be rendered much faster
by a viewer.
pdf(colormodel = "rgb") gives the behaviour prior to R 2.13.0 of
uncalibrated RGB, which under some circumstances can be rendered
faster by a viewer, and the files will be smaller (by about 9KB
if compression is not used).
o The postscript() device only includes the definition of the sRGB
colorspace in the output file for the colormodels which use it.
o The postscript() and pdf() devices now output greyscale raster
images (and not RGB) when colormodel = "gray".
o postscript(colormodel = "gray") now accepts non-grey colours and
uses their luminance (as pdf() long has).
o colormodel = "grey" is allowed as an alternative name for
postscript() and pdf().
o pdf() in the default sRGB colorspace outputs many fewer changes
of colorspace, which may speed up rendering in some viewing
applications.
o There is a new function dev.capabilities() to query the
capabilities of the current device. The initial set of
capabilities are support for semi-transparent colours, rendering
and capturing raster images, the locator and for interactive
events.
o For pdf(), maxRasters is increased as needed so the argument is
no longer used.
SWEAVE & VIGNETTES:
o Options keep.source = TRUE, figs.only = FALSE are now the
default.
o The way the type of user-defined options is determined has
changed. Previously they were all regarded as logical: now the
type is determined by the value given at first use.
o The allowed values of logical options are now precisely those
allowed for character inputs to as.logical(): this means that t
and f are no longer allowed (although T and F still are).
o The preferred location for vignette sources is now the directory
vignettes and not inst/doc: R CMD build will now re-build
vignettes in directory vignettes and copy the .Rnw (etc) files
and the corresponding PDFs to inst/doc. Further files to be
copied to inst/doc can be specified _via_ the file
vignettes/.install_extras.
o R CMD Sweave now supports a --driver option to select the Sweave
driver: the default is equivalent to --driver=RweaveLatex.
o R CMD Sweave and R CMD Stangle support options --encoding and
--options.
o The Rtangle() driver allows output = "stdout" or output =
"stderr" to select the output or message connection. This is
convenient for scripting using something like
R CMD Stangle --options='output="stdout"' foo.Rnw > foo2.R
o There is a new option pdf.compress controlling whether PDF
figures are generated using Flate compression (they are by
default).
o R CMD Sweave now has a --pdf option to produce a PDF version of
the processed Sweave document.
o It is no longer allowed to have two vignettes with the same
vignette basename (e.g. vig.Rnw and vig.Snw). (Previously one
vignette hid the other in the vignette() function.)
C-LEVEL FACILITIES:
o Function R_tmpnam2 has been added to the API to allow a temporary
filename to include a specified extension.
PACKAGE INSTALLATION:
o Package DESCRIPTION file field KeepSource forces the package to
be installed with keep.source = TRUE (or FALSE). (Suggestion of
Greg Snow. Note that as all packages are lazy-loaded, this is
now only relevant at installation.)
There are corresponding options --with-keep.source and
--without-keep.source for R CMD INSTALL.
o R CMD INSTALL has a new option --byte-compile to byte-compile the
packages during installation (since all packages are now
lazy-loaded). This can be controlled on a per-package basis by
the optional field ByteCompile in the DESCRIPTION file.
o A package R code but without a NAMESPACE file will have a default
one created at R CMD build or R CMD INSTALL time, so all packages
will be installed with namespaces. A consequence of this is that
.First.lib() functions need to be copied to .onLoad() (usually)
or .onAttach(). For the time being, if there is an
auto-generated NAMESPACE file and no .onLoad() nor .onAttach()
function is found but .First.lib() is, it will be run as the
attach hook (unless the package is one of a list of known
exceptions, when it will be run as the load hook).
o A warning is given if test-loading a package changes a locked
binding in a package other than itself. It is likely that this
will be disallowed in future releases. (There are _pro tem_ some
exceptions to the warning.)
o A dependency on SVN revision is allowed for R, e.g. R (>=
r56550). This should be used in conjunction with a version
number, e.g. R (>= 2.14.0), R (>= r56550) to distinguish beteen
R-patched and R-devel versions with the same SVN revision.
o installed.packages() now hashes the names of its cache files to
avoid very rare problems with excessively long path names.
(PR#14669)
o A top-level COPYING file in a package is no longer installed
(file names LICENSE or LICENCE having long been preferred).
UTILITIES:
o R CMD check now gives an error if the R code in a vignette fails
to run, unless this is caused by a missing package.
o R CMD check now unpacks tarballs in the same way as R CMD
INSTALL, including making use of the environment variable
R_INSTALL_TAR to override the default behaviour.
o R CMD check performs additional code analysis of package startup
functions, and notifies about incorrect argument lists and
(incorrect) calls to functions which modify the search path or
inappropriately generate messages.
o R CMD check now also checks compiled code for symbols
corresponding to functions which might terminate R or write to
stdout/stderr instead of the console.
o R CMD check now uses a pdf() device when checking examples
(rather than postscript()).
o R CMD check now checks line-endings of makefiles and
C/C++/Fortran sources in subdirectories of src as well as in src
itself.
o R CMD check now reports as a NOTE what look like methods
documented with their full names even if there is a namespace and
they are exported. In almost all cases they are intended to be
used only as methods and should use the \method markup. In the
other rare cases the recommended form is to use a function such
as coefHclust which would not get confused with a method,
document that and register it in the NAMESPACE file by
s3method(coef, hclust, coefHclust).
o The default for the environment variable _R_CHECK_COMPACT_DATA2_
is now true: thus if using the newer forms of compression
introduced in R 2.10.0 would be beneficial is now checked (by
default).
o Reference output for a vignette can be supplied when checking a
package by R CMD check: see 'Writing R Extensions'.
o R CMD Rd2dvi allows the use of LaTeX package inputenx rather than
inputenc: the value of the environment variable RD2DVI_INPUTENC
is used. (LaTeX package inputenx is an optional install which
provides greater coverage of the UTF-8 encoding.)
o Rscript on a Unix-alike now accepts file names containing spaces
(provided these are escaped or quoted in the shell).
o R CMD build on a Unix-alike (only) now tries to preserve dates on
files it copies from its input directory. (This was the
undocumented behaviour prior to R 2.13.0.)
DEPRECATED AND DEFUNCT:
o require() no longer has a save argument.
o The gamma argument to hsv(), rainbow(), and rgb2hsv() has been
removed.
o The --no-docs option for R CMD build --binary is defunct: use
--install-args instead.
o The option --unsafe to R CMD INSTALL is defunct: use the
identical option --no-lock instead.
o The entry point pythag formerly in Rmath.h is defunct: use
instead the C99 function hypot.
o R CMD build --binary is formally defunct: R CMD INSTALL --build
has long been the preferred alternative.
o zip.file.extract() is now defunct: use unzip() or unz() instead.
o R CMD Rd2dvi without the --pdf option is now deprecated: only PDF
output will be supported in future releases (since this allows
the use of fonts only supported for PDF), and only R CMD Rd2pdf
will be available.
o Options such as --max-nsize and the function mem.limits() are now
deprecated: these limits are nowadays almost never used, and are
reported by gc() when they are in use.
o Forms like binomial(link = "link") for GLM families deprecated
since R 2.4.0 are now defunct.
o The declarativeOnly argument to loadNamespace() (not relevant
since R 2.13.0) has been removed.
o Use of library.dynam() without specifying all the first three
arguments is deprecated. (It is often called from a namespace,
and the defaults are only appropriate to a package.)
Use of chname in library.dynam() with the extension .so or .dll
(which is clearly not allowed according to the help page) is
deprecated. This also applies to library.dynam.unload() and
useDynLib directives in NAMESPACE files.
o It is deprecated to use mean(x) and sd(x) directly on data frames
(or also matrices, for sd) x, instead of simply using sapply.
In the same spirit, median(x) now gives an error for a data frame
x (it often gave nonsensical results).
o The keep.source argument to library() and require() is
deprecated: it was only used for packages installed without
lazy-loading, and now all packages are lazy-loaded.
o Using a false value for the DESCRIPTION field LazyLoad is
deprecated.
INSTALLATION:
o The base and recommended packages are now byte-compiled
(equivalent to make bytecode in R 2.13.x).
o Configure option --with-system-zlib now only makes use of the
basic interface of zlib and not the C function gzseek which has
shown erroneous behaviour in zlib 1.2.4 and 1.2.5.
o The zlib in the R sources is now version 1.2.5. (This is safe
even on 32-bit Linux systems because only the basic interface is
now used.)
o The .afm files in package grDevices are now installed as
compressed files (as long done on Windows), saving ca 2MB on the
installed size.
o The non-screen cairo-based devices are no longer in the X11
module and so can be installed without X11. (We have never seen
a Unix-alike system with cairographics installed but not X11, but
a user might select --without-x.)
o Configure will try to use -fobjc-exceptions for the Objective-C
compiler (if present) to ensure that even compilers that do not
enable exceptions by default (such as vanilla gcc) can be used.
(Objective-C is currently only used on Mac OS X.)
o The system call times is required.
o The C99 functions acosh, asinh, atanh, snprintf and vsnprintf are
now required.
o There is no longer support for making DVI manuals _via_ make dvi,
make install-dvi and similar. Only PDF manuals are supported (to
allow the use of fonts which are only available for PDF.)
o The configure arguments used during configuration of R are
included as a comment in Makeconf for informative purposes on
Unix-alikes in a form suitable for shell execution. Note that
those are merely command-line arguments, they do not include
environment variables (one more reason to use configure variables
instead) or site configuration settings.
o Framework installation now supports DESTDIR (Mac OS X only).
o Java detection (R CMD javareconf) works around bogus
java.library.path property in recent Oracle Java binaries.
BUG FIXES:
o The locale category LC_MONETARY was only being set on startup on
Windows: that is now done on Unix-alikes where supported.
o Reference class utilities will detect an attempt to modify
methods or fields in a locked class definition (e.g., in a
namespace) and generate an error.
o The formula methods for lines(), points() and text() now work
even if package stats is not on the search path.
o In principle, S4 classes from different packages could have the
same name. This has not previously worked. Changes have now
been installed that should allow such classes and permit methods
to use them. New functions className() and multipleClasses() are
related tools for programming.
o Work around an issue in Linux (a system select call resetting tv)
which prevented internet operations from timing out properly.
o Several stack trampling and overflow issues have been fixed in
TRE, triggered by agrep and friends with long patterns.
(PR#14627.)
o ("design infelicity") Field assignments in reference classes are
now consistent with slots in S4 classes: the assigned value must
come from the declared class (if any) for the field or from a
subclass.
o The methods objects constructed for "coerce" and "coerce<-" were
lacking some essential information in the generic, defined and
target slots; as() did not handle duplicate class definitions
correctly.
o The parser no longer accepts the digit 8 in an octal character
code in a string, nor does it accept unterminated strings in a
file. (Reported by Bill Dunlap.)
o The print() method for class "summary.aov" did not pass on
argument digits when summary() was called on a single object, and
hence used more digits than documented.
o The X11() device's cairo back-end produced incorrect capture
snapshot images on big-endian machines.
o loglin() gave a spurious error when argument margin consisted of
a single element of length one. (PR#14690)
o loess() is better protected against misuse, e.g. zero-length
span. (PR#14691)
o HoltWinters() checks that the optimization succeeded. (PR#14694)
o The (undocumented) inclusion of superclass objects in default
initializing of reference classes overwrote explicit field
arguments. The bug is fixed, the feature documented and a test
added.
o round(x, -Inf) now does something sensible (return zero rather
than NA).
o signif(x, -Inf) now behaves as documented (signif(x, 1)) rather
than giving zero.
o The "table" method for Axis() hardcoded side = 1, hence calls to
plot(<vector>, <table>) labelled the wrong axis. (PR#14699)
o Creating a connection might fail under gctorture(TRUE).
o stack() and unstack() converted character columns to factors.
unstack() sometimes produced incorrect results (a list or a
vector) if the factor on which to un-split had only one level.
o On some systems help(".C", help_type = "pdf") and similar
generated file names that TeX was unable to handle.
o Non-blocking listening socket connections continued to report
isIncomplete() as true even when the peer had closed down and all
available input had been read.
o The revised HTML search system now generates better hyperlinks to
help topics found: previously it gave problems with help pages
with names containing e.g. spaces and slashes.
o A late change in R 2.13.2 broke \Sexpr expressions in Rd files.
o The creation of ticks on log axes (including axTicks() sometimes
incorrectly omitted a tick at one end
o The creation of ticks on log axes (including by axTicks())
sometimes incorrectly omitted a tick at one end of the range by
rounding error in a platform-dependent way. This could be seen
in the examples for axTicks(), where with axis limits c(0.2, 88)
the tick for 0.2 was sometimes omitted.
o qgamma() for small shape underflows to 0 rather than sometimes
giving NaN. (PR#8528, PR#14710)
o mapply() now gives an explicit error message (rather than an
obscure one) is inputs of zero and positive length are mixed.
o Setting a Hershey font family followed by string height query
would crash R.
o R CMD javareconf -e would fail for some shells due to a shift
error. Also the resulting paths will no longer contain
$(JAVA_HOME) as that can result in an unintended substitution
based on Makeconf instead of the shell setting.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.14.0 is released
|
Peter Dalgaard
| 406 |
|
From bates at stat.wisc.edu Fri Nov 12 17:28:36 1999
From: bates at stat.wisc.edu (Douglas Bates)
Date: 12 Nov 1999 10:28:36 -0600
Subject: New domain - r-project.org
Message-ID: <[email protected]>
The R Project now has its own internet domain, r-project.org. The
preferred addresses for various services related to R have become:
www.r-project.org # basic information regarding R
cran.r-project.org # home site for CRAN - Comprehensive R Archive Network
cran.at.r-project.org # CRAN mirror in Austria
cran.ch.r-project.org # CRAN mirror in Switzerland
cran.dk.r-project.org # CRAN mirror in Denmark
cran.uk.r-project.org # CRAN mirror in the United Kingdom (Great Britain)
cran.us.r-project.org # CRAN mirror in the U.S.A.
lists.r-project.org # mailing lists related to R
rsync.r-project.org # anonymous rsync access to the source trees
E-mail to members of the R Development Core Group can be sent to
Firstname.Lastname at r-project.org
For example, Kurt.Hornik at r-project.org is a valid e-mail address.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
New domain - r-project.org
|
Douglas Bates
| 502 |
|
From deleeuw at stat.ucla.edu Wed Jun 19 22:26:04 2002
From: deleeuw at stat.ucla.edu (Jan de Leeuw)
Date: Wed, 19 Jun 2002 13:26:04 -0700
Subject: R-1.5.1 for Darwin/X11
Message-ID: <[email protected]>
The file
ftp://gifi.stat.ucla.edu/pub/R-1.5.1.dmg
has grown to 60 MB. It consists of a meta-package and its packages and
it will allow you to install binaries for R-1.5.1 and about 300
packages, just by
clicking the R-1.5.1.mpkg file. It also install quite a few dylibs in
/sw, but not
the ones for X11R6 and gnome yet. You can choose which of the packages
to install,
of course.
The same directory also contains the same files in tar.gz form.
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics
US mail: 8142 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
www: http://www.stat.ucla.edu/~deleeuw
==========================================================================
==
Remember, wherever you go, there you are. --- Buckaroo Banzai
==========================================================================
==
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|
R-1.5.1 for Darwin/X11
|
Jan de Leeuw
| 47 |
|
From rossini at blindglobe.net Thu May 2 17:19:45 2002
From: rossini at blindglobe.net (A.J. Rossini)
Date: 02 May 2002 08:19:45 -0700
Subject: BioConductor 1.0
Message-ID: <[email protected]>
The Bioconductor development team would like to announce the first release of
Bioconductor packages for the analysis of genomic data. Bioconductor is an
open source bioinformatics software project based on R.
TOOLS:
======
The released packages include tools which facilitate:
1. annotation (AnnBuilder, annotate).
2. data management and organization through the use of the S4 class
structure (Biobase, marrayClasses).
3. identification of differentially expressed genes and clustering
(edd, genefilter, geneplotter, multtest, ROC)
4. analysis of Affymetrix expression array data (affy)
5. diagnostic plots and normalization for cDNA array data (marrayInput,
marrayNorm, marrayPlots)
6. storage and retrieval of large datasets (rhdf5).
7. facilitate user interaction (tkWidgets)
PACKAGES:
=========
Biobase : Base functions for Bioconductor
annotate : Annotation for microarrays
AnnBuilder : Bioconductor annotation data builder
genefilter : Genefilter: filter genes
geneplotter : Geneplotter: plot microarray data
edd : expression density diagnostics
ROC : ROC analysis for differential expression in expression
arrays
affy : Methods for Affymetrix Oligonucleotide Arrays
marrayClasses : Classes and methods for cDNA microarray data
marrayInput : Data input for cDNA microarrays
marrayNorm : Location and scale normalization for cDNA microarray data
marrayPlots : Diagnostic plots for cDNA microarray data
multtest : Multiple hypothesis testing
rhdf5 : An HDF5 interface for R
tkWidgets : Useful tools for building graphical input widgets
The packages and more details may be found on the Bioconductor WWW
site:
http://www.bioconductor.org/
HELP AND RESOURCES:
===================
Information on subscribing to the mailing list and viewing its archives
can be found at:
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
Please use that list to discuss Bioconductor specific issues, bugs,
and problems. Note that every package has a vignette (a literate
program which provides an annotated example of the package's use) as
well as possibly some "HOWTO"s. These document the tool's usage, and
are provided in the "doc" subdirectory of each package library.
WHO:
====
For the Bioconductor development team:
Douglas Bates, University of Wisconsin, USA.
Vince Carey, Harvard Medical School, USA.
Marcel Dettling, Federal Inst. Technology, Switzerland.
Sandrine Dudoit, UC Berkeley, USA.
Byron Ellis, Harvard Department of Statistics, USA.
Laurent Gautier, Technial University of Denmark, Denmark.
Robert Gentleman, Harvard Medical School, USA.
Jeff Gentry, Dana-Farber Cancer Institute, USA.
Kurt Hornik, Technische Universitat Wien, Austria.
Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Germany.
Rafael Irizarry, Department of Biostatistics, Johns Hopkins University, USA.
Friedrich Leisch, Technische Universitat Wien, Austria.
Cheng Li, Harvard Medical School, USA.
Martin Maechler, Federal Inst. Technology, Switzerland.
A.J. Rossini, Biostatistics, Univ. of Washington and Fred Hutchinson Cancer Research Center, USA.
Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany.
Luke Tierney, University of Minnesota, USA.
Jean Yee Hwa Yang, UC Berkeley, USA.
Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA.
--
A.J. Rossini Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics rossini at u.washington.edu
FHCRC/SCHARP/HIV Vaccine Trials Net rossini at scharp.org
-------------- http://software.biostat.washington.edu/ ----------------
FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email
UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX
(my friday location is usually completely unpredictable.)
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
BioConductor 1.0
|
A.J. Rossini
| 32 |
|
From pd.mes at cbs.dk Mon May 18 09:30:11 2015
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 18 May 2015 09:30:11 +0200
Subject: Release of R 3.2.1 scheduled for June 18
Message-ID: <[email protected]>
We intend to have a patch release on June 18, nickname will be "World-Famous Astronaut". The detailed schedule will be made available via developer.r-project.org as usual.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
Release of R 3.2.1 scheduled for June 18
|
Peter Dalgaard
| 200 |
|
From pd.mes at cbs.dk Fri Apr 21 16:19:04 2017
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 21 Apr 2017 14:19:04 +0000
Subject: R 3.4.0 is released
Message-ID: <[email protected]>
The build system rolled up R-3.4.0.tar.gz (codename "You Stupid Darkness") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.4.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = f12a9c3881197b20b08dd3d1f9d005e6
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 0c53e7275ad2057cdc60448f4a71f354
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = ea102623c183b5b8ad93306db6a4f6b6
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 71562183d75dd2080d86c42bbf733bb7
MD5 (R-latest.tar.gz) = 75083c23d507b9c16d5c6afbd7a827e7
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = f60d286bb7294cef00cb0eed4052a66f
MD5 (VERSION-INFO.dcf) = 7a8c309440689143c16e8586128523e8
MD5 (R-3/R-3.4.0.tar.gz) = 75083c23d507b9c16d5c6afbd7a827e7
6474d9791fff6a74936296bde3fcb569477f5958e4326189bd6e5ab878e0cd4f AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
33bd1a8295b3af3e2e8b77c870799e991ced02356df50469b2e688b3cc593ebc FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
1798e1bb08e63dca195970600b107e4d6d5a07135da5bec9bcbe16a9c0f408db NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
a10f84be31f897456a31d31690df2fdc3f21a197f28b4d04332cc85005dcd0d2 NEWS.2
288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91 R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
52f934a4e8581945cbc1ba234932749066b5744cbd3b1cb467ba6ef164975163 THANKS
2613962d473138a6ddbd10949fff9dfa61160ce6c64b7b2808172857bdd62527 VERSION-INFO.dcf
288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91 R-3/R-3.4.0.tar.gz
This is the relevant part of the NEWS file
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.
* factor() now uses order() to sort its levels, not sort.list().
This makes factor() support custom vector-like objects if methods
for the appropriate generics are defined. This change has the
side effect of making factor() succeed on empty or length-one
non-atomic vector(-like) types (e.g., list), where it failed
before.
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.)
* Add utils::strcapture(). Given a character vector and a regular
expression containing capture expressions, strcapture() will
extract the captured tokens into a tabular data structure,
typically a data.frame.
* str() and strOptions() get a new option drop.deparse.attr with
improved but _changed_ default behaviour for expressions. For
expression objects x, str(x) now may remove extraneous white
space and truncate long lines.
* str(<looooooooong_string>) is no longer very slow; inspired by
Mikko Korpela's proposal in PR#16527.
* str(x)'s default method is more "accurate" and hence somewhat
more generous in displaying character vectors; this will
occasionally change R outputs (and need changes to some
*.Rout(.save) files).
For a classed integer vector such as x <- xtabs(~ c(1,9,9,9)),
str(x) now shows both the class and "int", instead of only the
latter.
* isSymmetric(m) is much faster for large asymmetric matrices m
_via_ pre-tests and a new option tol1 (with which strict back
compatibility is possible but not the default).
* The result of eigen() now is of class "eigen" in the default case
when eigenvectors are computed.
* Zero-length date and date-time objects (of classes "POSIX[cl]?t")
now print() "recognizably".
* xy.coords() and xyz.coords() get a new setLab option.
* The method argument of sort.list(), order() and sort.int() gains
an "auto" option (the default) which should behave the same as
before when method was not supplied.
* stopifnot(E, ..) now reports differences when E is a call to
all.equal() and that is not true.
* boxplot(<formula>, *) gain optional arguments drop, sep, and
lex.order to pass to split.default() which itself gains an
argument lex.order to pass to interaction() for more flexibility.
* The plot() method for ppr() has enhanced default labels (xmin and
main).
* sample.int() gains an explicit useHash option (with a back
compatible default).
* identical() gains an ignore.srcref option which drops "srcref"
and similar attributes when true (as by default).
* diag(x, nrow = n) now preserves typeof(x), also for logical,
integer and raw x (and as previously for complex and numeric).
* smooth.spline() now allows direct specification of lambda, gets a
hatvalues() method and keeps tol in the result, and optionally
parts of the internal matrix computations.
* addNA() is faster now, e.g. when applied twice. (Part of
PR#16895.)
* New option rstandard(<lm>, type = "predicted") provides the
"PRESS"-related leave-one-out cross-validation errors for linear
models.
* After seven years of deprecation, duplicated factor levels now
produce a warning when printed and an error in levels<- instead
of a warning.
* Invalid factors, e.g., with duplicated levels (invalid but
constructable) now give a warning when printed, _via_ new
function .valid.factor().
* sessionInfo() has been updated for Apple's change in OS naming as
from '10.12' ('macOS Sierra' _vs_ 'OS X El Capitan').
Its toLatex() method now includes the running component.
* options(interrupt=) can be used to specify a default action for
user interrupts. For now, if this option is not set and the
error option is set, then an unhandled user interrupt invokes the
error option. (This may be dropped in the future as interrupt
conditions are not error conditions.)
* In most cases user interrupt handlers will be called with a
"resume" restart available. Handlers can invoke this restart to
resume computation. At the browser prompt the r command will
invoke a "resume" restart if one is available. Some read
operations cannot be resumed properly when interrupted and do not
provide a "resume" restart.
* Radix sort is now chosen by method = "auto" for sort.int() for
double vectors (and hence used for sort() for unclassed double
vectors), excluding 'long' vectors.
sort.int(method = "radix") no longer rounds double vectors.
* The default and data.frame methods for stack() preserve the names
of empty elements in the levels of the ind column of the return
value. Set the new drop argument to TRUE for the previous
behavior.
* Speedup in simplify2array() and hence sapply() and mapply() (for
the case of names and common length > 1), thanks to Suharto
Anggono's PR#17118.
* table(x, exclude = NULL) now sets useNA = "ifany" (instead of
"always"). Together with the bug fixes for this case, this
recovers more consistent behaviour compatible to older versions
of R. As a consequence, summary() for a logical vector no longer
reports (zero) counts for NA when there are no NAs.
* dump.frames() gets a new option include.GlobalEnv which allows to
also dump the global environment, thanks to Andreas Kersting's
proposal in PR#17116.
* system.time() now uses message() instead of cat() when terminated
early, such that suppressMessages() has an effect; suggested by
Ben Bolker.
* citation() supports inst/CITATION files from package source
trees, with lib.loc pointing to the directory containing the
package.
* try() gains a new argument outFile with a default that can be
modified _via_ options(try.outFile = .), useful notably for
Sweave.
* The unexported low-level functions in package parallel for
passing serialized R objects to and from forked children now
support long vectors on 64-bit platforms. This removes some
limits on higher-level functions such as mclapply() (but
returning gigabyte results from forked processes _via_
serialization should be avoided if at all possible).
* Connections now print() without error even if invalid, e.g. after
having been destroyed.
* apropos() and find(simple.words = FALSE) no longer match object
names starting with . which are known to be internal objects
(such as .__S3MethodsTable__.).
* Convenience function hasName() has been added; it is intended to
replace the common idiom !is.null(x$name) without the usually
unintended partial name matching.
* strcapture() no longer fixes column names nor coerces strings to
factors (suggested by Bill Dunlap).
* strcapture() returns NA for non-matching values in x (suggested
by Bill Dunlap).
* source() gets new optional arguments, notably exprs; this is made
use of in the new utility function withAutoprint().
* sys.source() gets a new toplevel.env argument. This argument is
useful for frameworks running package tests; contributed by Tomas
Kalibera.
* Sys.setFileTime() and file.copy(copy.date = TRUE) will set
timestamps with fractions of seconds on platforms/filesystems
which support this.
* (Windows only.) file.info() now returns file timestamps including
fractions of seconds; it has done so on other platforms since R
2.14.0. (NB: some filesystems do not record modification and
access timestamps to sub-second resolution.)
* The license check enabled by options(checkPackageLicense = TRUE)
is now done when the package's namespace is first loaded.
* ppr() and supsmu() get an optional trace argument, and ppr(..,
sm.method = ..spline) is no longer limited to sample size n <=
2500.
* The POSIXct method for print() gets optional tz and usetz
arguments, thanks to a report from Jennifer S. Lyon.
* New function check_packages_in_dir_details() in package tools for
analyzing package-check log files to obtain check details.
* Package tools now exports function CRAN_package_db() for
obtaining information about current packages in the CRAN package
repository, and several functions for obtaining the check status
of these packages.
* The (default) Stangle driver Rtangle allows annotate to be a
function and gets a new drop.evalFALSE option.
* The default method for quantile(x, prob) should now be monotone
in prob, even in border cases, see PR#16672.
* bug.report() now tries to extract an email address from a
BugReports field, and if there is none, from a Contacts field.
* The format() and print() methods for object.size() results get
new options standard and digits; notably, standard = "IEC" and
standard = "SI" allow more standard (but less common)
abbreviations than the default ones, e.g. for kilobytes. (From
contributions by Henrik Bengtsson.)
* If a reference class has a validity method, validObject will be
called automatically from the default initialization method for
reference classes.
* tapply() gets new option default = NA allowing to change the
previously hardcoded value.
* read.dcf() now consistently interprets any 'whitespace' to be
stripped to include newlines.
* The maximum number of DLLs that can be loaded into R e.g. _via_
dyn.load() can now be increased by setting the environment
variable R_MAX_NUM_DLLS before starting R.
* Assigning to an element of a vector beyond the current length now
over-allocates by a small fraction. The new vector is marked
internally as growable, and the true length of the new vector is
stored in the truelength field. This makes building up a vector
result by assigning to the next element beyond the current length
more efficient, though pre-allocating is still preferred. The
implementation is subject to change and not intended to be used
in packages at this time.
* Loading the parallel package namespace no longer sets or changes
the .Random.seed, even if R_PARALLEL_PORT is unset.
NB: This can break reproducibility of output, and did for a CRAN
package.
* Methods "wget" and "curl" for download.file() now give an R error
rather than a non-zero return value when the external command has
a non-zero status.
* Encoding name "utf8" is mapped to "UTF-8". Many implementations
of iconv accept "utf8", but not GNU libiconv (including the late
2016 version 1.15).
* sessionInfo() shows the full paths to the library or executable
files providing the BLAS/LAPACK implementations currently in use
(not available on Windows).
* The binning algorithm used by bandwidth selectors bw.ucv(),
bw.bcv() and bw.SJ() switches to a version linear in the input
size n for n > nb/2. (The calculations are the same, but for
larger n/nb it is worth doing the binning in advance.)
* There is a new option PCRE_study which controls when grep(perl =
TRUE) and friends 'study' the compiled pattern. Previously this
was done for 11 or more input strings: it now defaults to 10 or
more (but most examples need many more for the difference from
studying to be noticeable).
* grep(perl = TRUE) and friends can now make use of PCRE's
Just-In-Time mechanism, for PCRE >= 8.20 on platforms where JIT
is supported. It is used by default whenever the pattern is
studied (see the previous item). (Based on a patch from Mikko
Korpela.)
This is controlled by a new option PCRE_use_JIT.
Note that in general this makes little difference to the speed,
and may take a little longer: its benefits are most evident on
strings of thousands of characters. As a side effect it reduces
the chances of C stack overflow in the PCRE library on very long
strings (millions of characters, but see next item).
Warning: segfaults were seen using PCRE with JIT enabled on
64-bit Sparc builds.
* There is a new option PCRE_limit_recursion for grep(perl = TRUE)
and friends to set a recursion limit taking into account R's
estimate of the remaining C stack space (or 10000 if that is not
available). This reduces the chance of C stack overflow, but
because it is conservative may report a non-match (with a
warning) in examples that matched before. By default it is
enabled if any input string has 1000 or more bytes. (PR#16757)
* getGraphicsEvent() now works on X11(type = "cairo") devices.
Thanks to Frederick Eaton (for reviving an earlier patch).
* There is a new argument onIdle for getGraphicsEvent(), which
allows an R function to be run whenever there are no pending
graphics events. This is currently only supported on X11
devices. Thanks to Frederick Eaton.
* The deriv() and similar functions now can compute derivatives of
log1p(), sinpi() and similar one-argument functions, thanks to a
contribution by Jerry Lewis.
* median() gains a formal ... argument, so methods with extra
arguments can be provided.
* strwrap() reduces indent if it is more than half width rather
than giving an error. (Suggested by Bill Dunlap.)
* When the condition code in if(.) or while(.) is not of length
one, an error instead of a warning may be triggered by setting an
environment variable, see the help page.
* Formatting and printing of bibliography entries (bibentry) is
more flexible and better documented. Apart from setting
options(citation.bibtex.max = 99) you can also use
print(<citation>, bibtex=TRUE) (or format(..)) to get the BibTeX
entries in the case of more than one entry. This also affects
citation(). Contributions to enable style = "html+bibtex" are
welcome.
C-LEVEL FACILITIES:
* Entry points R_MakeExternalPtrFn and R_ExternalPtrFn are now
declared in header Rinternals.h to facilitate creating and
retrieving an R external pointer from a C function pointer
without ISO C warnings about the conversion of function pointers.
* There was an exception for the native Solaris C++ compiler to the
dropping (in R 3.3.0) of legacy C++ headers from headers such as
R.h and Rmath.h - this has now been removed. That compiler has
strict C++98 compliance hence does not include extensions in its
(non-legacy) C++ headers: some packages will need to request
C++11 or replace non-C++98 calls such as lgamma: see SS1.6.4 of
'Writing R Extensions'.
Because it is needed by about 70 CRAN packages, headers R.h and
Rmath.h still declare
use namespace std;
when included on Solaris.
* When included from C++, the R headers now use forms such as
std::FILE directly rather than including the line
using std::FILE;
C++ code including these headers might be relying on the latter.
* Headers R_ext/BLAS.h and R_ext/Lapack.h have many improved
declarations including const for double-precision complex
routines. _Inter alia_ this avoids warnings when passing 'string
literal' arguments from C++11 code.
* Headers for Unix-only facilities R_ext/GetX11Image.h,
R_ext/QuartzDevice.h and R_ext/eventloop.h are no longer
installed on Windows.
* No-longer-installed headers GraphicsBase.h, RGraphics.h,
Rmodules/RX11.h and Rmodules/Rlapack.h which had a LGPL license
no longer do so.
* HAVE_UINTPTR_T is now defined where appropriate by Rconfig.h so
that it can be included before Rinterface.h when CSTACK_DEFNS is
defined and a C compiler (not C++) is in use. Rinterface.h now
includes C header stdint.h or C++11 header cstdint where needed.
* Package tools has a new function
package_native_routine_registration_skeleton() to assist adding
native-symbol registration to a package. See its help and SS5.4.1
of 'Writing R Extensions' for how to use it. (At the time it was
added it successfully automated adding registration to over 90%
of CRAN packages which lacked it. Many of the failures were
newly-detected bugs in the packages, e.g. 50 packages called
entry points with varying numbers of arguments and 65 packages
called entry points not in the package.)
INSTALLATION on a UNIX-ALIKE:
* readline headers (and not just the library) are required unless
configuring with --with-readline=no.
* configure now adds a compiler switch for C++11 code, even if the
compiler supports C++11 by default. (This ensures that g++ 6.x
uses C++11 mode and not its default mode of C++14 with 'GNU
extensions'.)
The tests for C++11 compliance are now much more comprehensive.
For gcc < 4.8, the tests from R 3.3.0 are used in order to
maintain the same behaviour on Linux distributions with long-term
support.
* An alternative compiler for C++11 is now specified with CXX11,
not CXX1X. Likewise C++11 flags are specified with CXX11FLAGS and
the standard (e.g., -std=gnu++11 is specified with CXX11STD.
* configure now tests for a C++14-compliant compiler by testing
some basic features. This by default tries flags for the
compiler specified by CXX11, but an alternative compiler, options
and standard can be specified by variables CXX14, CXX14FLAGS and
CXX14STD (e.g., -std=gnu++14).
* There is a new macro CXXSTD to help specify the standard for C++
code, e.g. -std=c++98. This makes it easier to work with
compilers which default to a later standard: for example, with
CXX=g++6 CXXSTD=-std=c++98 configure will select commands for g++
6.x which conform to C++11 and C++14 where specified but
otherwise use C++98.
* Support for the defunct IRIX and OSF/1 OSes and Alpha CPU has
been removed.
* configure checks that the compiler specified by $CXX $CXXFLAGS is
able to compile C++ code.
* configure checks for the required header sys/select.h (or
sys/time.h on legacy systems) and system call select and aborts
if they are not found.
* If available, the POSIX 2008 system call utimensat will be used
by Sys.setFileTime() and file.copy(copy.date = TRUE). This may
result in slightly more accurate file times. (It is available on
Linux and FreeBSD but not macOS.)
* The minimum version requirement for libcurl has been reduced to
7.22.0, although at least 7.28.0 is preferred and earlier
versions are little tested. (This is to support Debian 7
'Wheezy' LTS and Ubuntu 'Precise' 12.04 LTS, although the latter
is close to end-of-life.)
* configure tests for a C++17-compliant compiler. The tests are
experimental and subject to change in the future.
INCLUDED SOFTWARE:
* (Windows only) Tcl/Tk version 8.6.4 is now included in the binary
builds. The tcltk*.chm help file is no longer included; please
consult the online help at <URL: http://www.tcl.tk/man/> instead.
* The version of LAPACK included in the sources has been updated to
3.7.0: no new routines have been added to R.
PACKAGE INSTALLATION:
* There is support for compiling C++14 or C++17 code in packages on
suitable platforms: see 'Writing R Extensions' for how to request
this.
* The order of flags when LinkingTo other packages has been changed
so their include directories come earlier, before those specified
in CPPFLAGS. This will only have an effect if non-system include
directories are included with -I flags in CPPFLAGS (and so not
the default -I/usr/local/include which is treated as a system
include directory on most platforms).
* Packages which register native routines for .C or .Fortran need
to be re-installed for this version (unless installed with
R-devel SVN revision r72375 or later).
* Make variables with names containing CXX1X are deprecated in
favour of those using CXX11, but for the time being are still
made available _via_ file etc/Makeconf. Packages using them
should be converted to the new forms and made dependent on R (>=
3.4.0).
UTILITIES:
* Running R CMD check --as-cran with _R_CHECK_CRAN_INCOMING_REMOTE_
false now skips tests that require remote access. The remaining
(local) tests typically run quickly compared to the remote tests.
* R CMD build will now give priority to vignettes produced from
files in the vignettes directory over those in the inst/doc
directory, with a warning that the latter are being ignored.
* R CMD config gains a --all option for printing names and values
of all basic configure variables.
It now knows about all the variables used for the C++98, C++11
and C++14 standards.
* R CMD check now checks that output files in inst/doc are newer
than the source files in vignettes.
* For consistency with other package subdirectories, files named
*.r in the tests directory are now recognized as tests by R CMD
check. (Wish of PR#17143.)
* R CMD build and R CMD check now use the _union_ of R_LIBS and
.libPaths(). They may not be equivalent, e.g., when the latter
is determined by R_PROFILE.
* R CMD build now preserves dates when it copies files in preparing
the tarball. (Previously on Windows it changed the dates on all
files; on Unix, it changed some dates when installing vignettes.)
* The new option R CMD check --no-stop-on-test-error allows running
the remaining tests (under tests/) even if one gave an error.
* Check customization _via_ environment variables to detect side
effects of .Call() and .External() calls which alter their
arguments is described in SS8 of the 'R Internals' manual.
* R CMD check now checks any BugReports field to be non-empty and a
suitable single URL.
* R CMD check --as-cran now NOTEs if the package does not register
its native routines or does not declare its intentions on
(native) symbol search. (This will become a WARNING in due
course.)
DEPRECATED AND DEFUNCT:
* (Windows only) Function setInternet2() is defunct.
* Installation support for readline emulations based on editline
(aka libedit) is deprecated.
* Use of the C/C++ macro NO_C_HEADERS is defunct and silently
ignored.
* unix.time(), a traditional synonym for system.time(), has been
deprecated.
* structure(NULL, ..) is now deprecated as you cannot set
attributes on NULL.
* Header Rconfig.h no longer defines SUPPORT_OPENMP; instead use
_OPENMP (as documented for a long time).
* (C-level Native routine registration.) The deprecated styles
member of the R_CMethodDef and R_FortranMethodDef structures has
been removed. Packages using these will need to be re-installed
for R 3.4.0.
* The deprecated support for PCRE versions older than 8.20 will be
removed in R 3.4.1. (Versions 8.20-8.31 will still be accepted
but remain deprecated.)
BUG FIXES:
* Getting or setting body() or formals() on non-functions for now
signals a warning and may become an error for setting.
* match(x, t), duplicated(x) and unique(x) work as documented for
complex numbers with NAs or NaNs, where all those containing NA
do match, whereas in the case of NaN's both real and imaginary
parts must match, compatibly with how print() and format() work
for complex numbers.
* deparse(<complex>, options = "digits17") prints more nicely now,
mostly thanks to a suggestion by Richie Cotton.
* Rotated symbols in plotmath expressions are now positioned
correctly on x11(type = "Xlib"). (PR#16948)
* as<-() avoids an infinite loop when a virtual class is interposed
between a subclass and an actual superclass.
* Fix level propagation in unlist() when the list contains
zero-length lists or factors.
* Fix S3 dispatch on S4 objects when the methods package is not
attached.
* Internal S4 dispatch sets .Generic in the method frame for
consistency with standardGeneric(). (PR#16929)
* Fix order(x, decreasing = TRUE) when x is an integer vector
containing MAX_INT. Ported from a fix Matt Dowle made to
data.table.
* Fix caching by callNextMethod(), resolves PR#16973 and PR#16974.
* grouping() puts NAs last, to be consistent with the default
behavior of order().
* Point mass limit cases: qpois(-2, 0) now gives NaN with a warning
and qgeom(1, 1) is 0. (PR#16972)
* table() no longer drops an "NaN" factor level, and better obeys
exclude = <chr>, thanks to Suharto Anggono's patch for PR#16936.
Also, in the case of exclude = NULL and NAs, these are tabulated
correctly (again).
Further, table(1:2, exclude = 1, useNA = "ifany") no longer
erroneously reports <NA> counts.
Additionally, all cases of empty exclude are equivalent, and
useNA is not overwritten when specified (as it was by exclude =
NULL).
* wilcox.test(x, conf.int=TRUE) no longer errors out in cases where
the confidence interval is not available, such as for x = 0:2.
* droplevels(f) now keeps <NA> levels when present.
* In integer arithmetic, NULL is now treated as integer(0) whereas
it was previously treated as double(0).
* The radix sort considers NA_real_ and NaN to be equivalent in
rank (like the other sort algorithms).
* When index.return=TRUE is passed to sort.int(), the radix sort
treats NAs like sort.list() does (like the other sort
algorithms).
* When in tabulate(bin, nbin) length(bin) is larger than the
maximal integer, the result is now of type double and hence no
longer silently overflows to wrong values. (PR#17140)
* as.character.factor() respects S4 inheritance when checking the
type of its argument. (PR#17141)
* The factor method for print() no longer sets the class of the
factor to NULL, which would violate a basic constraint of an S4
object.
* formatC(x, flag = f) allows two new flags, and signals an error
for invalid flags also in the case of character formatting.
* Reading from file("stdin") now also closes the connection and
hence no longer leaks memory when reading from a full pipe,
thanks to G'abor Cs'ardi, see thread starting at <URL:
https://stat.ethz.ch/pipermail/r-devel/2016-November/073360.html>.
* Failure to create file in tempdir() for compressed pdf() graphics
device no longer errors (then later segfaults). There is now a
warning instead of error and compression is turned off for the
device. Thanks to Alec Wysoker (PR#17191).
* Asking for methods() on "|" returns only S3 methods. See <URL:
https://stat.ethz.ch/pipermail/r-devel/2016-December/073476.html>.
* dev.capture() using Quartz Cocoa device (macOS) returned invalid
components if the back-end chose to use ARGB instead of RGBA
image format. (Reported by Noam Ross.)
* seq("2", "5") now works too, equivalently to "2":"5" and
seq.int().
* seq.int(to = 1, by = 1) is now correct, other cases are integer
(instead of double) when seq() is integer too, and the
"non-finite" error messages are consistent between seq.default()
and seq.int(), no longer mentioning NaN etc.
* rep(x, times) and rep.int(x, times) now work when times is larger
than the largest value representable in an integer vector.
(PR#16932)
* download.file(method = "libcurl") does not check for URL
existence before attempting downloads; this is more robust to
servers that do not support HEAD or range-based retrieval, but
may create empty or incomplete files for aborted download
requests.
* Bandwidth selectors bw.ucv(), bw.bcv() and bw.SJ() now avoid
integer overflow for large sample sizes.
* str() no longer shows "list output truncated", in cases that list
was not shown at all. Thanks to Neal Fultz (PR#17219)
* Fix for cairo_pdf() (and svg() and cairo_ps()) when replaying a
saved display list that contains a mix of grid and graphics
output. (Report by Yihui Xie.)
* The str() and as.hclust() methods for "dendrogram" now also work
for deeply nested dendrograms thanks to non-recursive
implementations by Bradley Broom.
* sample() now uses two uniforms for added precision when the
uniform generator is Knuth-TAOCP, Knuth-TAOCP-2002, or a
user-defined generator and the population size is 2^25 or
greater.
* If a vignette in the vignettes directory is listed in
.Rbuildignore, R CMD build would not include it in the tarball,
but would include it in the vignette database, leading to a check
warning. (PR#17246)
* tools::latexToUtf8() infinite looped on certain inputs.
(PR#17138)
* terms.formula() ignored argument names when determining whether
two terms were identical. (PR#17235)
* callNextMethod() was broken when called from a method that
augments the formal arguments of a primitive generic.
* Coercion of an S4 object to a vector during sub-assignment into a
vector failed to dispatch through the as.vector() generic (often
leading to a segfault).
* Fix problems in command completion: Crash (PR#17222) and junk
display in Windows, handling special characters in filenames on
all systems.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.4.0 is released
|
Peter Dalgaard
| 134 |
|
From edd at debian.org Tue Apr 30 03:42:57 2002
From: edd at debian.org (Dirk Eddelbuettel)
Date: Mon, 29 Apr 2002 20:42:57 -0500
Subject: Debian packages of R 1.5.0 available
Message-ID: <[email protected]>
Debian packages for r-base_1.5.0 and r-recommended_1.5.0 have been uploaded
to main Debian archive and should hit the mirrors tomorrow. These packages
were built on i386, packages for the other architectures supported by Debian
should become available in the next few days.
Regards, Dirk
--
Good judgement comes from experience; experience comes from bad judgement.
-- Fred Brooks
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Debian packages of R 1.5.0 available
|
Dirk Eddelbuettel
| 27 |
|
From P.Dalgaard at biostat.ku.dk Fri Oct 24 13:24:01 2008
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Fri, 24 Oct 2008 13:24:01 +0200
Subject: DSC 2009 First announcement
Message-ID: <[email protected]>
The sixth international workshop on 'Distributed Statistical Computing'
(DSC 2009) will take place at the the University of Copenhagen, Denmark,
13th-14th of July 2009. This conference follows on from the successful
DSC 1999, 2001, and 2003 conferences at the Vienna University of
Technology, DSC 2005 at the University of Washington in Seattle, and DSC
2007 at the University of Auckland. The workshop will focus on, but is
not limited to, open source statistical computing and aims to provide a
platform for exchanging ideas about developments in statistical
computing (rather than 'only' the usage of statistical software for
applications).
It is expected that a large proportion of participants will bring a
presentation. We particularly welcome contributions advancing
statistical computing as an independent topic.
Home page:
http://www.r-project.org/dsc-2009
Organizing committee:
Peter Dalgaard, Claus Ekstr?m, Klaus K. Holst, S?ren H?jsgaard
<dsc2009 at biostat.ku.dk>
Programme committee:
Roger Bivand, G?ran Brostr?m, Jari Oksanen, Balasubramanian Narasimhan
(Naras), Peter Dalgaard
Important dates:
March 15: Submission deadline
April 15: Notification of accept/reject
May 1: Early registration ends
Fee structure (EUR, Academic/Non-Academic/Student)
Early: 170/270/90
Full: 200/300/100
On the Day: 220/330/110
("Students" not including Ph.D. students.)
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
DSC 2009 First announcement
|
Peter Dalgaard
| 607 |
|
From deleeuw at stat.ucla.edu Sun Mar 25 01:02:39 2001
From: deleeuw at stat.ucla.edu (Jan de Leeuw)
Date: Sat, 24 Mar 2001 16:02:39 -0800
Subject: R-1.2.2 for MacOS X (Darwin/X11)
Message-ID: <[email protected]>
A tarball with the 03/23/01 patch version of R-1.2.2 (with X11 and
tcl/tk support)
is at
http://www.stat.ucla.edu/~deleeuw/R/R-1.2.2.MacOSX.tar.gz
This is not a Classic or Carbon or Cocoa application, you need to
run it from the command line and you need to have an X11 server
running. It only uses the classical Unix part of Mac OS X, i.e. it
is similar in functionality to the Linux and OSF ports.
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
US mail: 8142 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
http://www.stat.ucla.edu/~deleeuw and http://home1.gte.net/datamine/
========================================================
No matter where you go, there you are. --- Buckaroo Banzai
http://www.stat.ucla.edu/sounds/nomatter.au
========================================================
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
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|
R-1.2.2 for MacOS X (Darwin/X11)
|
Jan de Leeuw
| 230 |
|
From p.dalgaard at biostat.ku.dk Fri Jul 2 16:25:08 1999
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 02 Jul 1999 16:25:08 +0200
Subject: R-0.64.2 is released (well, mostly)
Message-ID: <[email protected]>
I've rolled up R-0.64.2.tgz a moment ago.
However, due to a configuration error with the new machine at
Auckland, it is not up for FTP from there just yet. In any case, you
shouldn't get it from Auckland, but wait for it to be mirrored at a
CRAN site near you within a day or two.
For those who are too curious to wait, I've put a copy in
ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.64.2.tgz
There's also a version split in two for floppies and a patch file if
you prefer that.
For the R Core Team,
Peter D.
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 0.64.2
NEW FEATURES
o new target for R installation testing : make strict-tests.
o symnum(x) now nicely codes logical x.
o convolve() has a new type = c("circular", "open", "filter")
argument allowing more than the only circular convolution.
o par(xpd) now has three settings: FALSE (clip to plot region),
TRUE (clip to figure region), or NA (clip to device region).
o zapsmall(x) works for complex x.
o new global variable R.version.string (for plots & reports).
Deprecated version & Version for new R.version & R.Version.
o R CMD Rd2dvi has builtin "Usage" help and works for multiple files.
Useful for automatic reference manual of a package.
(doc/manual/lib2tex is more efficient for installed packages, however).
BUG FIXES
o power() is now fully implemented and documented.
o A couple of problems with group generic operations.
o A bug which meant that it was not possible to add elements
to zero length lists in the obvious way has been fixed.
x <- list(); x[[1]] <- 10
x <- list(); x[["a"]] <- 11
both now work.
o save.image() ignored dot-names. (esp. .First())
o lab= argument to plot() misinterpreted by axis() via ... passing
o NULL labels in text() caused segfault
o matrix(f,...) with f a factor now coerces to character
o documentation errors for substitute and is.vector, minor fixups for
trig and nlm
o Background colours are set properly on X11 devices with
colortype="pseudo": sometimes they were not allocated separately.
o C() works (again?) for a single argument.
o is.na() didn't work properly for "list" arguments.
o symnum() sometimes failed with arrays of rank >= 3.
o in some cases one could get nonblack color instead of
black on 2nd x11() window.
o influence.measures(.) $ is.influential was wrong on the
cooks.distance.
o printing of complex NaN/Inf was wrong as well.
o printing of complex named vectors had a wrong initial space.
o allow trailing space in character->numeric coercion
o library() gave wrong "masked" warnings in some cases.
o par(xpd) semantics were not compatible with S.
o rect() output was not clipped in PostScript.
o par(pin=c(width, height)) was behaving as par(pin=c(width, width)).
o Non-blank separated data files didn't have their 1st field
handled properly.
o "aux" directory moved to "tools" to avoid difficulties on
Windows.
o structure() clobbered factors with missing levels.
o pmatch() misbehaved on duplicate matches.
o R CMD Rd2dvi <file.Rd> works again.
o logical binops tried to set time series parameters before dimensions.
o upped the BUFSIZE in model.c (NOT proper long-term solution).
o dput(), dump() and deparse() now always use DBL_DIG (=15) digits
for numeric formatting.
o chull() now works for vertical borders, such as in chull(c(1,1,2),3:1).
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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|
R-0.64.2 is released (well, mostly)
|
Peter Dalgaard BSA
| 489 |
|
From p.dalgaard at biostat.ku.dk Mon Apr 12 14:05:25 2004
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 12 Apr 2004 14:05:25 +0200
Subject: R 1.9.0 is release
Message-ID: <[email protected]>
I've rolled up R-1.9.0.tgz a short while ago. This is a new version
with a number of new features, most notably a substantial
reorganization of the standard packages, a major update of the grid
package, and the fact that underscore can now be used as a regular
character in variable names. See below for further changes.
Because of the disturbances at the machine that hosted the CVS
archives, you will now have to wait for the file to show up on the
CRAN master site. You can then get it from
http://cran.r-project.org/src/base/R-1.9.0.tgz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
There is also a version split for floppies.
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
79ae9d20a7bed94d7c92504c8c130310 R-1.9.0.tgz
de40f2e366d3ed9e2b3e8813fb8bba6c R-1.9.0.tgz-split.aa
a963d3ac009ff6c5f321391e26cb0892 R-1.9.0.tgz-split.ab
0e8f55216051057dfafdabc5f578e68e R-1.9.0.tgz-split.ac
7add0d9b6dbd8cdbc36608b7166b910b R-1.9.0.tgz-split.ad
667222d63ce7e19bf869ea20439d0867 R-1.9.0.tgz-split.ae
42dcd15c23b07decb43a65f937942489 R-1.9.0.tgz-split.af
136279c8d59def0a5221e20ba763c997 R-1.9.0.tgz-split.ag
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 1.9.0
USER-VISIBLE CHANGES
o Underscore '_' is now allowed in syntactically valid names, and
make.names() no longer changes underscores. Very old code
that makes use of underscore for assignment may now give
confusing error messages.
o Package 'base' has been split into packages 'base', 'graphics',
'stats' and 'utils'. All four are loaded in a default
installation, but the separation allows a 'lean and mean'
version of R to be used for tasks such as building indices.
Packages ctest, eda, modreg, mva, nls, stepfun and ts have been
merged into stats, and lqs has been returned to MASS. In all
cases a stub has been left that will issue a warning and ensure
that the appropriate new home is loaded. All the time series
datasets have been moved to package stats. Sweave has been
moved to utils.
Package mle has been moved to stats4 which will become the
central place for statistical S4 classes and methods
distributed with base R. Package mle remains as a stub.
Users may notice that code in .Rprofile is run with only the
new base loaded and so functions may now not be found. For
example, ps.options(horizontal = TRUE) should be preceded by
library(graphics) or called as graphics::ps.options or,
better, set as a hook -- see ?setHook.
o There has been a concerted effort to speed up the startup of
an R session: it now takes about 2/3rds of the time of 1.8.1.
o A warning is issued at startup in a UTF-8 locale, as currently R
only supports single-byte encodings.
NEW FEATURES
o $, $<-, [[, [[<- can be applied to environments. Only character
arguments are allowed and no partial matching is done. The
semantics are basically that of get/assign to the environment with
inherits=FALSE.
o There are now print() and [ methods for "acf" objects.
o aov() will now handle singular Error() models, with a warning.
o arima() allows models with no free parameters to be fitted (to
find log-likelihood and AIC values, thanks to Rob Hyndman).
o array() and matrix() now allow 0-length `data' arguments for
compatibility with S.
o as.data.frame() now has a method for arrays.
o as.matrix.data.frame() now coerces an all-logical data frame
to a logical matrix.
o New function assignInNamespace() parallelling fixInNamespace.
o There is a new function contourLines() to produce contour
lines (but not draw anything). This makes the CRAN package
clines (with its clines() function) redundant.
o D(), deriv(), etc now also differentiate asin(), acos(), atan(),
(thanks to a contribution of Kasper Kristensen).
o The `package' argument to data() is no longer allowed to be a
(unquoted) name and so can be a variable name or a quoted
character string.
o There is a new class "Date" to represent dates (without times)
plus many utility functions similar to those for date-times.
See ?Date.
o Deparsing (including using dump() and dput()) an integer
vector now wraps it in as.integer() so it will be source()d
correctly. (Related to PR#4361.)
o .Deprecated() has a new argument `package' which is used in
the warning message for non-base packages.
o The print() method for "difftime" objects now handles arrays.
o dir.create() is now an internal function (rather than a call to
mkdir) on Unix as well as on Windows. There is now an option
to suppress warnings from mkdir, which may or may not have
been wanted.
o dist() has a new method to calculate Minkowski distances.
o expand.grid() returns appropriate array dimensions and dimnames
in the attribute "out.attrs", and this is used by the
predict() method for loess to return a suitable array.
o factanal(), loess() and princomp() now explicitly check for
numerical inputs; they might have silently coded factor
variables in formulae.
o New functions factorial(x) defined as gamma(x+1) and for
S-PLUS compatibility, lfactorial(x) defined as lgamma(x+1).
o findInterval(x, v) now allows +/-Inf values, and NAs in x.
o formula.default() now looks for a "terms" component before a
'formula' argument in the saved call: the component will have
`.' expanded and probably will have the original environment
set as its environment. And what it does is now documented.
o glm() arguments `etastart' and `mustart' are now evaluated via
the model frame in the same way as `subset' and `weights'.
o Functions grep(), regexpr(), sub() and gsub() now coerce their
arguments to character, rather than give an error.
The perl=TRUE argument now uses character tables prepared for
the locale currently in use each time it is used, rather than
those of the C locale.
o New functions head() and tail() in package `utils'.
(Based on a contribution by Patrick Burns.)
o legend() has a new argument 'text.col'.
o methods(class=) now checks for a matching generic, and so no
longer returns methods for non-visible generics (and
eliminates various mismatches).
o A new function mget() will retrieve multiple values from an
environment.
o model.frame() methods, for example those for "lm" and "glm",
pass relevant parts of ... onto the default method. (This has
long been documented but not done.) The default method is now
able to cope with model classes such as "lqs" and "ppr".
o nls() and ppr() have a `model' argument to allow the model frame
to be returned as part of the fitted object.
o "POSIXct" objects can now have a "tzone" attribute that
determines how they will be converted and printed. This means
that date-time objects which have a timezone specified will
generally be regarded as in their original time zone.
o postscript() device output has been modified to work around
rounding errors in low-precision calculations in gs >= 8.11.
(PR#5285, which is not a bug in R.)
It is now documented how to use other Computer Modern fonts,
for example italic rather than slanted.
o ppr() now fully supports categorical explanatory variables,
ppr() is now interruptible at suitable places in the
underlying FORTRAN code.
o princomp() now warns if both `x' and `covmat' are supplied,
and returns scores only if the centring used is known.
o psigamma(x, deriv=0), a new function generalizes, digamma() etc.
All these (psigamma, digamma, trigamma,...) now also work for x < 0.
o pchisq(*, ncp > 0) and hence qchisq() now work with much higher
values of ncp; it has become much more accurate in the left tail.
o read.table() now allows embedded newlines in quoted fields. (PR#4555)
o rep.default(0-length-vector, length.out=n) now gives a vector
of length n and not length 0, for compatibility with S.
If both `each' and `length.out' have been specified, it now
recycles rather than fills with NAs for S compatibility.
If both `times' and `length.out' have been specified, `times'
is now ignored for S compatibility. (Previously padding with
NAs was used.)
The "POSIXct" and "POSIXlt" methods for rep() now pass ... on
to the default method (as expected by PR#5818).
o rgb2hsv() is new, an R interface the C API function with the same name.
o User hooks can be set for onLoad, library, detach and
onUnload of packages/namespaces: see ?setHook.
o save() default arguments can now be set using option
"save.defaults", which is also used by save.image() if option
"save.image.defaults" is not present.
o New function shQuote() to quote strings to be passed to OS shells.
o sink() now has a split= argument to direct output to both the
sink and the current output connection.
o split.screen() now works for multiple devices at once.
o On some OSes (including Windows and those using glibc)
strptime() did not validate dates correctly, so we have added
extra code to do so. However, this cannot correct scanning
errors in the OS's strptime (although we have been able to
work around these on Windows). Some examples are now tested for
during configuration.
o strsplit() now has `fixed' and `perl' arguments and
split="" is optimized.
o subset() now allows a `drop' argument to remove unused factor
levels. The default is still to keep them.
o termplot() has an option to smooth the partial residuals.
o varimax() and promax() add class "loadings" to their loadings
component.
o Model fits now add a "dataClasses" attribute to the terms, which
can be used to check that the variables supplied for
prediction are of the same type as those used for fitting.
(It is currently used by predict() methods for classes "lm",
"mlm", "glm" and "ppr", as well as methods in packages MASS,
rpart and tree.)
o New command-line argument --max-ppsize allows the size of the
pointer protection stack to be set higher than the previous
limit of 10000.
o The fonts on an X11() device (also jpeg() and png() on Unix)
can be specified by a new argument `fonts' defaulting to the
value of a new option "X11fonts".
o New functions in the tools package: pkgDepends, getDepList and
installFoundDepends. These provide functionality for assessing
dependencies and the availability of them (either locally or
from on-line repositories).
o The parsed contents of a NAMESPACE file are now stored at
installation and if available used to speed loading the
package, so packages with namespaces should be reinstalled.
o Argument `asp' although not a graphics parameter is accepted
in the ... of graphics functions without a warning. It now
works as expected in contour().
o Package stats4 exports S4 generics for AIC() and BIC().
o The Mac OS X version now produces an R framework for easier linking
of R into other programs. As a result, R.app is now relocatable.
o Added experimental support for conditionals in NAMESPACE files.
o Added as.list.environment to coerce environments to lists
(efficiently).
o New function addmargins() in the stats package to add marginal
summaries to tables, e.g. row and column totals. (Based on a
contribution by Bendix Carstensen.)
o dendrogam edge and node labels can now be expressions (to be
plotted via stats:::plotNode called from plot.dendrogram).
The diamond frames around edge labels are more nicely scaled
horizontally.
o Methods defined in the methods package can now include
default expressions for arguments. If these arguments are
missing in the call, the defaults in the selected method will
override a default in the generic. See ?setMethod.
o Changes to package 'grid':
- Renamed push/pop.viewport() to push/popViewport().
- Added upViewport(), downViewport(), and seekViewport() to
allow creation and navigation of viewport tree
(rather than just viewport stack).
- Added id and id.lengths arguments to grid.polygon() to allow
multiple polygons within single grid.polygon() call.
- Added vpList(), vpStack(), vpTree(), and current.vpTree()
to allow creation of viewport "bundles" that may be pushed
at once (lists are pushed in parallel, stacks in series).
current.vpTree() returns the current viewport tree.
- Added vpPath() to allow specification of viewport path
in downViewport() and seekViewport().
See ?viewports for an example of its use.
NOTE: it is also possible to specify a path directly,
e.g., something like "vp1::vp2", but this is only
advised for interactive use (in case I decide to change the
separator :: in later versions).
- Added "just" argument to grid.layout() to allow justification
of layout relative to parent viewport *IF* the layout is not
the same size as the viewport. There's an example in
help(grid.layout).
- Allowed the "vp" slot in a grob to be a viewport name or a
vpPath. The interpretation of these new alternatives is to
call downViewport() with the name or vpPath before drawing the
grob and upViewport() the appropriate amount after drawing the
grob. Here's an example of the possible usage:
pushViewport(viewport(w=.5, h=.5, name="A"))
grid.rect()
pushViewport(viewport(w=.5, h=.5, name="B"))
grid.rect(gp=gpar(col="grey"))
upViewport(2)
grid.rect(vp="A", gp=gpar(fill="red"))
grid.rect(vp=vpPath("A", "B"), gp=gpar(fill="blue"))
- Added engine.display.list() function. This allows the user to
tell grid NOT to use the graphics engine display list and to handle
ALL redraws using its own display list (including redraws after
device resizes and copies).
This provides a way to avoid some of the problems with resizing
a device when you have used grid.convert(), or the gridBase package,
or even base functions such as legend().
There is a document discussing the use of display lists in grid
on the grid web site
(http://www.stat.auckland.ac.nz/~paul/grid/grid.html)
- Changed the implementation of grob objects. They are no longer
implemented as external references. They are now regular R objects
which copy-by-value. This means that they can be saved/loaded
like normal R objects. In order to retain some existing grob
behaviour, the following changes were necessary:
+ grobs all now have a "name" slot. The grob name is used to
uniquely identify a "drawn" grob (i.e., a grob on the display
list).
+ grid.edit() and grid.pack() now take a grob name as the first
argument instead of a grob. (Actually, they take a gPath -
see below)
+ the "grobwidth" and "grobheight" units take either a grob
OR a grob name (actually a gPath - see below). Only in the
latter case will the unit be updated if the grob "pointed to"
is modified.
In addition, the following features are now possible with grobs:
+ grobs now save()/load() like any normal R object.
+ many grid.*() functions now have a *Grob() counterpart. The
grid.*() version is used for its side-effect of drawing
something or modifying something which has been drawn; the
*Grob() version is used for its return value, which is a grob.
This makes it more convenient to just work with grob
objects without producing any graphical output
(by using the *Grob() functions).
+ there is a gTree object (derived from grob), which is a grob
that can have children. A gTree also has a "childrenvp" slot
which is a viewport which is pushed and then "up"ed before the
children are drawn; this allows the children of a gTree to
place themselves somewhere in the viewports specified in the
childrenvp by having a vpPath in their vp slot.
+ there is a gPath object, which is essentially a concatenation
of grob names. This is used to specify the child of
(a child of ...) a gTree.
+ there is a new API for creating/accessing/modifying grob objects:
grid.add(), grid.remove(), grid.edit(), grid.get() (and their
*Grob() counterparts can be used to add, remove, edit, or extract
a grob or the child of a gTree. NOTE: the new grid.edit() API
is incompatible with the previous version.
- Added stringWidth(), stringHeight(), grobWidth(), and grobHeight()
convenience functions (they produce "strwidth", "strheight",
"grobwidth", and "grobheight" unit objects, respectively).
- Allowed viewports to turn off clipping altogether.
Possible settings for viewport clip arg are now:
"on" = clip to the viewport (was TRUE)
"inherit" = clip to whatever parent says (was FALSE)
"off" = turn off clipping
Still accept logical values (and NA maps to "off")
UTILITIES
o R CMD check now runs the (Rd) examples with default RNGkind
(uniform & normal) and set.seed(1).
example(*, setRNG = TRUE) does the same.
o undoc() in package `tools' has a new default of `use.values =
NULL' which produces a warning whenever the default values of
function arguments differ between documentation and code.
Note that this affects "R CMD check" as well.
o Testing examples via massage-examples.pl (as used by R CMD
check) now restores the search path after every help file.
o checkS3methods() in package 'tools' now also looks for generics
in the loaded namespaces/packages listed in the Depends fields
of the package's DESCRIPTION file when testing an installed
package.
o The DESCRIPTION file of packages may contain a 'Suggests:'
field for packages that are only used in examples or
vignettes.
o Added an option to package.dependencies() to handle the
'Suggests' levels of dependencies.
o Vignette dependencies can now be checked and obtained via
vignetteDepends.
o Option 'repositories' to list URLs for package repositories
added.
o package.description() has been replaced by packageDescription().
o R CMD INSTALL/build now skip Subversion's .svn directories as
well as CVS directories.
C-LEVEL FACILITIES
o arraySubscript and vectorSubscript take a new argument which
is a function pointer that provides access to character
strings (such as the names vector) rather than assuming these
are passed in.
o R_CheckUserInterrupt is now described in `Writing R Extensions'
and there is a new equivalent subroutine rchkusr for calling
from FORTRAN code.
o hsv2rgb and rgb2hsv are newly in the C API.
o Salloc and Srealloc are provided in S.h as wrappers for S_alloc
and S_realloc, since current S versions use these forms.
o The type used for vector lengths is now R_len_t rather than
int, to allow for a future change.
o The internal header nmath/dpq.h has slightly improved macros
R_DT_val() and R_DT_Cval(), a new R_D_LExp() and improved
R_DT_log() and R_DT_Clog(); this improves accuracy in several
[dpq]-functions {for "extreme" arguments}.
DEPRECATED & DEFUNCT
o print.coefmat() is defunct, replaced by printCoefmat().
o codes() and codes<-() are defunct.
o anovalist.lm (replaced in 1.2.0) is now defunct.
o glm.fit.null(), lm.fit.null() and lm.wfit.null() are defunct.
o print.atomic() is defunct.
o The command-line arguments --nsize and --vsize are no longer
recognized as synonyms for --min-nsize and --min-vsize (which
replaced them in 1.2.0).
o Unnecessary methods coef.{g}lm and fitted.{g}lm have been
removed: they were each identical to the default method.
o La.eigen() is deprecated now eigen() uses LAPACK by default.
o tetragamma() and pentagamma() are deprecated, since they are
equivalent to psigamma(, deriv=2) and psigamma(, deriv=3).
o LTRUE/LFALSE in Rmath.h have been removed: they were
deprecated in 1.2.0.
o package.contents() has been deprecated.
INSTALLATION CHANGES
o The defaults for configure are now --without-zlib
--without-bzlib --without-pcre.
The included PCRE sources have been updated to version 4.5 and
PCRE >= 4.0 is now required if --with-pcre is used.
The included zlib sources have been updated to 1.2.1, and this
is now required if --with-zlib is used.
o configure no longer lists bzip2 and PCRE as `additional
capabilities' as all builds of R have had them since 1.7.0.
o --with-blas=goto to use K. Goto's optimized BLAS will now work.
BUG FIXES
o When lm.{w}fit() disregarded arguments in ... they reported
the values and not the names.
o lm(singular.ok = FALSE) was looking for 0 rank, not rank < p.
o The substitution code for strptime in the sources no longer
follows glibc in silently `correcting' invalid inputs.
o The cor() function did not remove missing values in the
non-Pearson case.
o [l]choose() use a more accurate formula which also slightly
improves p- and qhyper(); choose(n, k) now returns 0 instead
of NaN for k < 0 or > n.
o find(simple.words=TRUE) (the default) was still using regular
expressions for e.g. "+" and "*". Also, it checked the mode
only of the first object matching a regular expression found
in a package.
o Memory leaks in [dpq]wilcox and [dqr]signrank have been plugged.
These only occurred when multiple values of m or n > 50 were
used in a single call. (PR#5314, plus another potential leak.)
o Non-finite input values to eigen(), La.eigen(), svd() and
La.svd() are now errors: they often caused infinite
looping. (PR#5406, PR#4366, PR#3723: the fix for 3723/4366
returned a vector of NAs, not a matrix, for the eigenvectors.)
o stepfun(x,y) now gives an error when `x' has length 0 instead
of an invalid result (that could lead to a segmentation
fault).
o buildVignettes() uses file.remove() instead of unlink() to
remove temporary files.
o methods(class = "lqs") does not produce extraneous entries anymore.
o Directly calling a method that uses NextMethod() no longer
produces the erroneous error message 'function is not a
closure'.
o chisq.test(x, simulate.p.value = TRUE) could hang in an infinite
loop or segfault, as r2dtable() did, when the entries in x where
large. (PR#5701)
o fisher.test(x) could give a P-value of 'Inf' in similar cases which
now result in an error (PR#4688). It silently truncated
non-integer 'x' instead of rounding.
o cutree(a, h=h) silently gave wrong results when 'a' was an
agnes object; now gives an error and reminds of as.hclust().
o postscript() could crash if given a font value outside the
valid range 1...5.
o qchisq(1-e, .., ncp=.) did not terminate for small e.
(PR#6421 (PR#875))
o contrasts() turns a logical variable into a factor. This now
always has levels c("FALSE", "TRUE") even if only one (or
none) of these occur in the variable.
o model.frame()'s lm and glm methods had 'data' and 'na.action'
arguments which they ignored and have been removed.
o The defaults data=list() in lm() and glm() could never be
used and have been removed. glm had na.action=na.fail, again
never used.
o tools:::.getInternalS3generics() was omitting all the members
of the S3 group generics, which also accept methods for members.
o Some BLASes were returning NA %*% 0 as 0 and some as NA. Now
slower but more careful code is used if NAs are present. (PR#4582)
o package.skeleton() no longer generates invalid filenames for
code and help files. Also, care is taken not to generate
filenames that differ only by case.
o pairs() now respects axis graphical parameters such as
cex.main, font.main and las.
o Saving images of packages with namespaces (such as mle) was
not compressing the image.
o When formula.default() returned a terms object, it returned a
result of class c("terms", "formula") with different
subsetting rules from an object of class "formula".
o The standalone Rmath library did not build correctly on systems
with inaccurate log1p.
o Specifying asp is now respected in calls like plot(1, 10, asp=1)
with zero range on both axes.
o outer() called rep() with an argument the generic does not
have, and discarded the class of the answer.
o object.size() now returns a real (not integer) answer and so
can cope with objects occupying more than 2Gb.
o Lookups base:: and ::: were not confining their search to the
named package/namespace.
o qbinom() was returning NaN for prob = 0 or 1 or size = 0 even
though the result is well-defined. (In part, PR#5900.)
o par(mgp)[2] was being interpreted as relative to par(mgp)[3].
(PR#6045)
o Versioned install was broken both with and without namespaces:
no R code was loaded.
o methods(), getS3method() and the registration of S3 methods in
namespaces were broken if the S3 generic was converted into an
S4 generic by setting an S4 method.
o Title and copyright holder of the reference manual are now in
sync with the citation() command.
o The validation code for POSIXlt dates and hence
seq(, by="DSTdays") now works for large mday values (not
just those in -1000...1000). (PR#6212)
o The print() method for data frames now copes with data frames
containing arrays (other than matrices).
o texi2dvi() and buildVignettes() use clean=FALSE as default
because the option is not supported on some Solaris
machines. For buildVignettes() this makes no difference as it
uses an internal cleanup mechanism.
o The biplot() method for "prcomp" was not registered nor exported.
(PR#6425)
o Latex conversion of .Rd files was missing newline before
\end{Section} etc which occasionally gave problems, as fixed for
some other \end{Foo} in 1.8.1. (PR#5645)
o Work around a glibc bug to make the %Z format usable in strftime().
o The glm method for rstandard() was wrongly scaled for cases where
summary(model)$dispersion != 1.
o Calling princomp() with a covariance matrix (rather than a
list) failed to predict scores rather than predict NA as
intended. (PR#6452)
o termplot() is more tolerant of variables not in the data= argument.
(PR#6327)
o isoreg() could segfault on monotone input sequences. (PR#6494)
o Rdconv detected \link{\url{}} only very slowly. (PR#6496)
o aov() with Error() term and no intercept incorrectly assigned
terms to strata. (PR#6510)
o ftable() incorrectly handled arguments named "x". (PR#6541)
o vector(), matrix(), array() and their internal equivalents
report correctly that the number of elements specified was too
large (rather than reporting it as negative).
o Minor copy-paste error in example(names). (PR#6594)
o length<-() now works correctly on factors (and is now generic
with a method for factors).
o x <- 2^32; x:(x+3) no longer generates an error (but gives a
result of type "double").
o pgamma(30, 100, lower=FALSE, log=TRUE) is not quite 0, now.
pgamma(x, alph) now only uses a normal approximation for
alph > 1e5 instead of alph > 1000. This also improves the accuracy
of ppois().
o qgamma() now does one or more final Newton steps, increasing
accuracy from around 2e-8 to 3e-16 in some cases. (PR#2214).
It allows values p close to 1 not returning Inf, with accuracy for
'lower=FALSE', and values close to 0 not returning 0 for
'log=TRUE'. These also apply to qchisq(), e.g.,
qchisq(1e-13, 4, lower=FALSE) is now finite and
qchisq(1e-101, 1) is positive.
o gamma(-n) now gives NaN for all negative integers -n.
o The Unix version of browseURL() now protects the URL from the
shell, for example allowing & and $ to occur in the URL.
It was incorrectly attempting to use -remote "openURL()" for
unknown browsers.
o extractAIC.coxph() works around an inconsistency in the
$loglik output from coxph. (PR#6646)
o stem() was running into integer overflows with nearly-constant
inputs, and scaling badly for constant ones. (Partly PR#6645)
o system() under Unix was losing the 8095th char if the output
was split. (PR#6624)
o plot.lm() gave incorrect results if there were zero weights.
(PR#6640)
o Binary operators warned for inconsistent lengths on vector op
vector operations, but not on vector op matrix ones. (PR#6633
and more.)
Comparison operators did not warn about inconsistent lengths
for real vectors, but did for integer, logical and character
vectors.
o spec.pgram(x, ..., pad, fast, ...) computed the periodogram with
a bias (downward) whenever 'pad > 0' (non-default) or 'fast = TRUE'
(default) and nextn(n) > n where n = length(x); similarly for
'df' (approximate degrees of freedom for chisq).
o dgamma(0, a) now gives Inf for a < 1 (instead of NaN), and
so does dchisq(0, 2*a, ncp).
o pcauchy() is now correct in the extreme tails.
o file.copy() did not check that any existing `from' file had
been truncated before appending the new contents.
o The QC files now check that their file operations succeeded.
o replicate() worked by making the supplied expression the
body of an anonymous function(x), leading to a variable
capture issue. Now, function(...) is used instead.
o chisq.test(simulate.p.value = TRUE) was returning slightly
incorrect p values, notably p = 0 when the data gave the most
extreme value.
o terms.formula(simplify = TRUE) was losing offset terms.
Multiple offset terms were not being removed correctly if two
of them appeared first or last in the formula. (PR#6656)
o Rd conversion to latex did not add a new line before
\end{Section} in more cases than were corrected in 1.8.1.
o split.default() dropped NA levels in its internal code but
returned them as NA in all components in the interpreted code
for factors. (PR#6672)
o points.formula() had problems if there was a subset argument
and no data argument. (PR#6652)
o as.dist() does a bit more checking of its first argument and now
warns when applied to non-square matrices.
o mle() gives a more understandable error message when its 'start'
argument is not ok.
o All uses of dir.create() check the return value.
download.packages() checks that destdir exists and is a directory.
o Methods dispatch corrects an error that failed to find
methods for classes that extend sealed classes (class unions
that contain basic classes, e.g.).
o Sweave no longer wraps the output of code chunks with
echo=false and results=tex in Schunk environments.
o termplot() handles models with missing data better, especially
with na.action=na.exclude.
o 1:2 * 1e-100 now prints with correct number of spaces.
o Negative subscripts that were out of range or NA were not handled
correctly. Mixing negative and NA subscripts is now caught as
an error: it was not caught on some platforms and segfaulted
on others.
o gzfile() connections had trouble at EOF when used on uncompressed
file.
o The Unix version of dataentry segfaulted if the `Copy' button
was used. (PR#6605)
o unlist on lists containing expressions now works (PR#5628)
o D(), deriv() and deriv3() now also can deal with gamma and lgamma.
o The X11 module can now be built against XFree86 4.4.0 headers (still
with some warnings).
o seq.POSIXt(from, to, by="DSTdays") was shorter than expected
for rare times in the UK time zone. (PR#4558)
o c/rbind() did not support vectors/matrices of mode "list". (PR#6702)
o summary() methods for POSIX[cl]t and Date classes coerced the
number of NAs to a date on printing.
o KalmanSmooth would sometimes return NA values with NA inputs.
(PR#6738)
o fligner.test() worked correctly only if data were already sorted
by group levels. (PR#6739)
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 1.9.0 is release
|
Peter Dalgaard
| 378 |
|
From ripley at stats.ox.ac.uk Fri Dec 21 07:13:10 2001
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 21 Dec 2001 06:13:10 +0000 (GMT)
Subject: R 1.4.0 on Windows
Message-ID: <[email protected]>
(1) We've been unable to contact the maintainer to find out when the
official release of R 1.4.0 on Windows might be available. As the
holidays shutdown is looming, last night I built a binary distribution
from the released sources and put the SetupR.exe and miniR* versions at
http://www.stats.ox.ac.uk/pub/RWin/
(This has the post-release mgcv_0.6-2.)
This is not the official release, so problem reports to me only, please.
(I'd be interested to hear, but am unlikely to be able to change anything
until 2002.)
(2) The bin/windows/contrib section on CRAN has been updated to include
the 1.4.0 versions of packages. (On TUWien now, mirrored elsewhere soon.)
This means that update.packages() will pick up the latest versions. Some
of these may not work with rw1031 (VR and grid for sure, maybe others).
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UK Fax: +44 1865 272595
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R 1.4.0 on Windows
|
Prof Brian Ripley
| 288 |
|
From P.Dalgaard at biostat.ku.dk Thu Jun 28 13:43:56 2007
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Thu, 28 Jun 2007 13:43:56 +0200
Subject: R 2.5.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.5.1.tar.gz a short while ago. This is a maintenance
release and fixes a number of mostly minor bugs and platform issues. See
the full list of changes below.
You can get it (in a short while) from
http://cran.r-project.org/src/base/R-2/R-2.5.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
a8efde35b940278de19730d326f58449 AUTHORS
eb723b61539feef013de476e68b5c50a COPYING
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
24ad9647e525609bce11f6f6ff9eac2d FAQ
70447ae7f2c35233d3065b004aa4f331 INSTALL
f04bdfaf8b021d046b8040c8d21dad41 NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
162f6d5a1bd7c60fd652145e050f3f3c R-2.5.1.tar.gz
162f6d5a1bd7c60fd652145e050f3f3c R-latest.tar.gz
433182754c05c2cf7a04ad0da474a1d0 README
020479f381d5f9038dcb18708997f5da RESOURCES
4eaf8a3e428694523edc16feb0140206 THANKS
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 2.5.1
NEW FEATURES
o density(1:20, bw = "SJ") now works as bw.SJ() now tries a larger
search interval than the default (lower, upper) if it does not
find a solution within the latter.
o The output of library() (no arguments) is now sorted by library
trees in the order of .libPaths() and not alphabetically.
o R_LIBS_USER and R_LIBS_SITE feature possible expansion of
specifiers for R version specific information as part of the
startup process.
o C-level warning calls now print a more informative context,
as C-level errors have for a while.
o There is a new option "rl_word_breaks" to control the way the
input line is tokenized in the readline-based terminal
interface for object- and file-name completion.
This allows it to be tuned for people who use their space bar
vs those who do not. The default now allows filename-completion
with +-* in the filenames.
o If the srcfile argument to parse() is not NULL, it will be added
to the result as a "srcfile" attribute.
o It is no longer possible to interrupt lazy-loading (which was
only at all likely when lazy-loading environments), which
would leave the object being loaded in an unusable state.
This is a temporary measure: error-recovery when evaluating
promises will be tackled more comprehensively in 2.6.0.
INSTALLATION
o 'make check' will work with --without-iconv, to accommodate
building on AIX where the system iconv conflicts with
libiconv and is not compatible with R's requirements.
o There is support for 'DESTDIR': see the R-admin manual.
o The texinfo manuals are now converted to HTML with a style
sheet: in recent versions of makeinfo the markup such as @file
was being lost in the HTML rendering.
o The use of inlining has been tweaked to avoid warnings from
gcc >= 4.2.0 when compiling in C99 mode (which is the default
from configure).
BUG FIXES
o as.dendrogram() failed on objects of class "dendrogram".
o plot(type ="s") (or "S") with many (hundreds of thousands)
of points could overflow the stack. (PR#9629)
o Coercing an S4 classed object to "matrix" (or other basic class)
failed to unset the S4 bit.
o The 'useS4' argument of print.default() had been broken by an
unrelated change prior to 2.4.1. This allowed print() and
show() to bounce badly constructed S4 objects between
themselves indefinitely.
o Prediction of the seasonal component in HoltWinters() was one
step out at one point in the calculations.
decompose() incorrectly computed the 'random' component for a
multiplicative fit.
o Wildcards work again in unlink() on Unix-alikes (they did not
in 2.5.0).
o When qr() used pivoting, the coefficient names in qr.coef() were
not pivoted to match. (PR#9623)
o UseMethod() could crash R if the first argument was not a
character string.
o R and Rscript on Unix-alikes were not accepting spaces in -e
arguments (even if quoted).
o Hexadecimal integer constants (e.g. 0x10L) were not being parsed
correctly on platforms where the C function atof did not
accept hexadecimal prefixes (as required by C99, but not
implemented in MinGW as used by R on Windows). (PR#9648)
o libRlapack.dylib on Mac OS X had no version information and
sometimes an invalid identification name.
o Rd conversion of \usage treated '\\' as a single backslash in
all but latex: it now acts consistently with the other
verbatim-like environments (it was never 'verbatim' despite
the documentation).
\code{\.} is now rendered as '\.' in all formats, as
documented (it was not the case for latex conversion).
codoc() (and checkDocStyle() and checkDocUsage()) now apply
the same transformations to \usage as Rd conversion does,
so {, % and \\ in strings in usages will now be related
correctly to the help files.
o rbind() failed if the only data frame had 0 rows. (PR#9657)
o <a data.frame>[i, j] could sometimes select the wrong column
when j is numeric if there are duplicate column names.
o sample(x, size, replace=TRUE, prob) had a memory leak if
10000 < size <= 100000.
o x <- cbind(1:2); rownames(x) <- factor(c("A",NA)) now longer
segfaults.
o R CMD BATCH no longer assumes Sys.unsetenv() is supported (it
is not on older Solaris systems).
o median() returned a logical result when it was 'NA': it now
returns an NA of appropriate type (e.g. integer or double).
o grep(fixed = TRUE, perl = TRUE) ignored 'fixed', although it
was documented to ignore 'perl'
Same for [g]regexpr and [g]sub.
o getNamespaceExports("base") works again.
o runmed(c(), 1) no longer segfaults.
o qr.coef(QR, b) failed for an LAPACK-produced QR if b was
integer or for an over-determined system.
qr.solve() for an under-determined system produces a
solution with 0 and not NA for columns which are unused.
o segments() was not handling full transparency correctly in PDF.
(PR#9694)
Nor was arrows().
o callGeneric() inside a method with extra arguments {and hence
currently defined via .local()} now works.
o [g]sub(fixed=TRUE, useBytes=FALSE) could substitute in the
wrong place in an MBCS locale.
gregexpr() could give incorrect answers in MBCS locales for
perl = TRUE or fixed = TRUE (unless useBytes = TRUE).
o The legacy quartz() device no longer crashes in locator()
if the user attempts to close the window.
o "CGGStackRestore: gstack underflow" warning is no longer shown
in legacy quartz() device.
o formatC() now limits 'digits' to 50 to avoid problems in
C-level sprintf in some OSes.
o seq.int(x, y, by=z) gave 'x' (and not an error) if
0 > (y-x)/z > -1.
o promptClass() now lists methods, including those for generics in
other attached packages.
o Connection-related functions such as readBin() no longer crash
when supplied with a non-connection object.
o as.character.srcref() didn't handle bad srcref objects cleanly.
o predict.nls() no longer requires 'newdata' to contain exactly
the variable names needed to fit the model: variables used on
the LHS only are no longer required and further variables are
allowed.
o plot.hclust() had a 'out by one' error, and ignored the last
object when computing the window region (and could overrun
arrays).
o deriv() was creating results with double (and not integer) dims.
o The unserialize code (e.g. as called by load()) looked for a
function findPackageEnv() to set a saved package environment.
This was missing, but is now supplied.
o [cr]bind could segfault when creating a list matrix result.
(Reported by Martin Morgan.)
o besselI(x, nu, exp=TRUE) and besselY(x, nu) could give wrong
answers for nu < 0. (Reported by Hiroyuki Kawakatsu.)
o [g]sub could confuse a trailing byte '\' for a backreference
in MBCSs where '\' can occur as a trailing byte (not UTF-8 nor
EUC-JP, but SJIS and the CJK character sets used on Windows).
(PR#9751)
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.5.1 is released
|
Peter Dalgaard
| 418 |
|
From p.dalgaard at biostat.ku.dk Mon Jun 20 12:18:39 2005
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 20 Jun 2005 12:18:39 +0200
Subject: R 2.1.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.1.1.tar.gz a short while ago. This is a maintenance
release containing mainly bugfixes.
See the full list of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.1.1.tar.gz
(give it some time to arrive there) or wait for it to be mirrored at a
CRAN site nearer to you. If you're *really* impatient,
www.biostat.ku.dk/~pd/R-release should work too. Binaries for various
platforms will appear in due course.
There is also a version split for floppies.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
94d55d512a9ba36caa9b7df079bae19f COPYING
d8045f3b8f929c1cb29a1e3fd737b499 COPYING.LIB
70447ae7f2c35233d3065b004aa4f331 INSTALL
1504edf0958138c034375749c3a189ee NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
e755b0ba5851ec261000af6b5c510335 R-2.1.1.tar.gz
97ff97d7094ef8d4cb0615bc9c3c4fe0 R-2.1.1.tar.gz-split.aa
40bbb45da53c04fefcaa8370ca84df81 R-2.1.1.tar.gz-split.ab
1fe3281097b6bce8c5d1eef2d1105f6a R-2.1.1.tar.gz-split.ac
eaaa59c6f78b47ca45439f59f4bc99a2 R-2.1.1.tar.gz-split.ad
7b3f0fba58926784052632133b926311 R-2.1.1.tar.gz-split.ae
7bf0703625535bec3da0a5e66e6c1d28 R-2.1.1.tar.gz-split.af
d1da10e9d40f1266a5aa8d71e5def67e R-2.1.1.tar.gz-split.ag
e90ea3c12153908184a4cb5307ffde09 R-2.1.1.tar.gz-split.ah
03f19a0d058aba30c686400fc3f85d76 R-2.1.1.tar.gz-split.ai
e755b0ba5851ec261000af6b5c510335 R-latest.tar.gz
56a780cdec835c5c598f8dfc0738f7f3 README
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 2.1.1
NEW FEATURES
o bug.report() now reports the locale in use.
o upgrade.packageStatus() allows user input "c" to cancel the
upgrade, just as update.packages() does.
o glm() now accepts 1D arrays (e.g. tables) as a response,
dropping them to a vector whilst preserving names.
o df() with one infinite df now works (to match pf()).
o Added tclServiceMode() function to the tcltk package to allow
updating to be suspended.
o The Encoding: field of a DESCRIPTION file is now documented,
and used by packageDescription() and library(help=).
o There has been progress on translations: existing translations
have been revised and expanded, and French and Korean have
been added.
The Windows installer supports a wide range of languages for
installation.
BUG FIXES
o lm(qr=FALSE) now works.
o predict.glm() not longer loses names for "response" predictions.
(PR#7792)
o Typo in menu(graphics=TRUE) meant it failed on Unix if tcltk
was not available.
o When names.dist() was removed, the result of cmdscale() lost
its rownames. The example also lost the labels.
o R CMD check assumed 'tar' was GNU tar and so supported -z.
o read.table() was not handing escaped quotes inside quoted fields
in the first five lines of the file. (PR#7789)
It was also not handling correctly EOF in the first five lines
when reading from stdin(). (PR#7772)
o 'make uninstall' was incomplete.
o make.packages.html() called by help.start() was failing if
there were installed packages with help titles invalid in the
current locale.
o printCoefmat(signif.legend = FALSE) was non-functional. (PR#7802)
o Some as.date.frame() methods failed because the expression
deparsed into multiple lines. (PR#7808)
o setRepositories() had a typo. (PR#7810)
o Printing arrays/data frames with multibyte characters in the
column labels was sometimes misaligned or using excessive space.
(PR#7803)
o The Tcl/Tk console did not support multibyte characters.
o as.POSIXlt() could give infinite recursion if passed a corrupt
"POSIXct" object (generated by an incorrect call to c.POSIXct,
PR#7826).
o update.packages() was not passing 'type' correctly to
install.packages().
o Printing the result of an unbalanced model.tables() call
sometimes got confused if terms() had rearranged interaction
terms. (PR#7829)
o .Platform$pkgType was wrong on the CRAN MacOS X build, and
.install.macbinary() was missing.
o as.personList() as used by citation() got confused by names
containing "and". (PR#7797)
o Subscripting an array by a matrix containing zero or negative
values or the wrong number of columns was not handled
consistently. (PR#7824)
o select.list(multiple=TRUE) now detects and tries again for invalid
text input.
o add1.[g]lm could give strange results with interaction terms
when the model and the upper scope had different orders for
the main effects. (PR#7842)
o A bug had sneaked into the anova.mlmlist() code, affecting the
Greenhouse-Geisser epsilon. Code wrongly assumed a matrix to
be symmetric. (Thanks to Bela Bauer.)
o anova.mlmlist() and mauchley.test() are now more tolerant to rank
deficiency in the M and X matrices (also when they are implicitly
generated via model.matrix()).
o anova.mlm had a scoping issue (PR#7898)
o pf() with infinite df is allowed again. It is now more accurate
for extreme ratios of dfs, especially when there is a
non-centrality parameter.
o df() was inaccurate for large df (1e16 or greater).
o dt() was inaccurate for large df (1e9 or greater) with a
non-centrality parameter.
o runmed(*, algorithm="Turlach") seg.faulted in rare cases.
o strwrap() now makes a reasonable job of text that is invalid in the
current locale.
o Reading with encoding "UCS-2LE" will remove any Byte Order
Mark, as most implementations of iconv fail to handle BOMs
(which are present in 'Windows Unicode' files).
o unique() for a list was incorrectly reporting `unimplemented'.
o The parser's contextstack was not protected against overflow,
e.g. more than 50 unmatched '('. (PR#7859)
o source(file, chdir = TRUE) was not checking that 'file' was a
filepath (rather than a URL). For 2.1.0 only, it did not work
even if 'file' was a filepath.
o Hershey fonts were being sized based on pixels not points so came
out too small on devices where pixels were noticeably different
from points (e.g., win.printer() and high-resolution screens).
Fix means that default size of Hershey fonts may be slightly
different, for example, smaller by default on PostScript and PDF.
o The branch cuts in the complex versions of the inverse
trigonometric and hyperbolic functions were non-standard.
(PR#7871)
o truncate() on file() connections was limited to files < 2Gb. It
now works for larger files at least on 64-bit OSes and others
where ftruncate supports such files. (Related to PR#7879)
o proj.aovlist() did not work correctly on objects fitted from a
data frame with row names.
o The coding standards recommendations had
nuke-trailing-whitespace where newer versions of ESS need
ess-nuke-trailing-whitespace. (PR#7888)
o package.skeleton() missed the first newline in the DESCRIPTION file.
o pbirthday() reported p = 1 too often when coincident > 2.
o plot(1:3, exp(1:3), log = "y", ylim = c(30,1)) {reversed
log-scale axis} now works, based on Uwe Ligges' suggestions.
(PR#7894)
o install.packages() was aborting when a package in a bundle was
chosen from a menu. It failed if more than one package in a
bundle was chosen from the command line.
o qcauchy() suffered from underflow in the extreme tails. (PR#7902)
o Printing of raw matrices/arrays was not implemented. (PR#7912)
o getCallingDLL()'s default first argument did not correspond to
its description and has been changed. The mismatch caused
symbols in .C/.Call/.Fortran calls without a PACKAGE= argument
to be potentially looked up in the wrong namespace.
o Binary save() of raw vectors was not working correctly on
big-endian platforms. (PR#7812)
o as.Date.factor() now accepts a format argument.
o Workaround added for FreeBSD which does not have alloca.h _and_
does not allow alloca() to be declared.
o identify() now respects 'cex'. (PR#660)
Warnings from identify() are now printed immediately even on
consoles with delayed printing.
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.1.1 is released
|
Peter Dalgaard
| 391 |
|
From pd@me@ @end|ng |rom cb@@dk Thu Jun 23 09:55:57 2022
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Thu, 23 Jun 2022 07:55:57 +0000
Subject: [Rd] R 4.2.1 is released
Message-ID: <[email protected]>
The build system rolled up R-4.2.1.tar.gz (codename "One Push-Up") this morning.
The list below details the changes in this release.
You can get the source code from
https://cran.r-project.org/src/base/R-4/R-4.2.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = 320967884b547734d6279dedbc739dd4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = f593bc2137bcb005337630ca5611a26f
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 1004838de767cced995c375aae100afc
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = b38d94569700664205a76a7de836ba83
MD5 (NEWS.3) = e55ed2c8a547b827b46e08eb7137ba23
MD5 (R-latest.tar.gz) = d363458f20d011c9edf55c8c828af242
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = a79b9b338cab09bd665f6b62ac6f455b
MD5 (THANKS) = 45b6d2e88a6ecb5b24fa33a781351cd5
MD5 (VERSION-INFO.dcf) = 4a0d3c959d821eb56df62f39325c5506
MD5 (R-4/R-4.2.1.tar.gz) = d363458f20d011c9edf55c8c828af242
60a0d150e6fc1f424be76ad7b645d236b56e747692a4679f81ce6536c550e949 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
1b1f962382ff185e14b6b5b9b40dc87360399466c7d7ce928ae443261e3955c9 FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
8ee3b9f7ca0ac8366c8aa5be33d6bb13dbf7b084e119aa71d5b232590d166d6b NEWS
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4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
8b7d3856100220f4555d4d57140829f2e81c27eccec5b441f5dce616e9ec9061 RESOURCES
8319c5415de58ee10d4bc058d79c370fd8e6b2ad09e25d7a1e04b74ca5f380a6 THANKS
59604d5bbdd869681bef33e84ddec3a7c4a4dedab6e154f4cf40e4694ff69ece VERSION-INFO.dcf
4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f R-4/R-4.2.1.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 4.2.1:
NEW FEATURES:
* New function utils::findCRANmirror() to find out if a CRAN mirror
has been selected, otherwise fallback to the main site. This
behaves in the same way as tools::CRAN_package_db() and is
intended for packages wishing to access CRAN for purposes other
than installing packages.
The need for this was shown by a day when the main CRAN website
was offline and a dozen or so packages which had its URL
hardcoded failed their checks.
INSTALLATION on a UNIX-ALIKE:
* The libraries searched for by --with-blas (without a value) now
include BLIS (after OpenBLAS but before ATLAS). And on macOS,
the Accelerate framework (after ATLAS). (This is patterned after
the AX_BLAS macro from the Autoconf Archive.)
* The included LAPACK sources have been updated to 3.10.1.
UTILITIES:
* The (full path to) the command tidy to be used for HTML
validation can be set by environment variable R_TIDYCMD.
* Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
false value will override R CMD check --as-cran and turn off HTML
validation. This provides a way to circumvent a problematic
tidy.
The 2006 version that ships with macOS is always skipped.
C-LEVEL FACILITIES:
* The undocumented legacy declarations of Sint, Sfloat, SINT_MAX
and SINT_MIN in header R.h are deprecated.
BUG FIXES:
* fisher.test(d) no longer segfaults for "large" d; fixing PR#18336
by preventing/detecting an integer overflow reliably.
* tar(., files=*) now produces correctly the warning about invalid
uid or gid of files, fixing PR#18344, reported by Martin Morgan.
* tk_choose.files() with multi = FALSE misbehaved on paths
containing spaces (PR#18334) (regression introduced in R 4.0.0).
* sort(x, partial = ind, *) now works correctly notably for the
non-default na.last = FALSE or TRUE, fixing PR#18335 reported by
James Edwards.
* Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used
for checking .Rd cross-references in R CMD check (as documented)
and not for other uses looking for a CRAN mirror.
* The search for a CRAN mirror when checking packages now uses
getOption("repos") if that specifies a CRAN mirror, even when it
does not also specify all three Bioconductor repositories (as was
previously required).
* The HTML code generated by tools::Rd2HTML() has been improved to
pass tidy 5.8.0.
BUG FIXES on Windows:
* Writing to a clipboard connection works again, fixing a
regression in R 4.2.0 (PR#18332). Re-using a closed clipboard
connection longer issues a spurious warning about an ignored
encoding argument.
* C function getlocale no longer attempts to query an unsupported
category from the OS, even when requested at R level, which may
cause crashes when R 4.2.0 (which uses UCRT) is embedded
(reported by Kevin Ushey).
* Accent keys now work in GraphApp Unicode windows, which are used
by Rgui whenever running in a multibyte locale (so also in UTF-8,
hence fixing a regression in R 4.2.0 for users of systems where R
4.1 used a single-byte locale).
* Completion in Rgui now works also with non-ASCII characters.
* Rgui no longer truncates usage information with --help.
* Text injection from external applications via SendInput now works
in GraphApp Unicode windows, fixing a regression in R 4.2.0 for
Rgui users of systems where R 4.1 used a single-byte locale but R
4.2.0 uses UTF-8.
* Performance of txtProgressBar() in Rgui when running in a
multi-byte locale has been improved (fixing a performance
regression in R 4.2.0 for users of systems where R 4.1 used a
single-byte locale).
* The script editor in Rgui now works also on systems using UTF-8
as the native encoding. Users of the script editor have to
convert their scripts with non-ASCII characters to UTF-8 before
reading them in R 4.2.1 or newer (on recent Windows where UTF-8
is used). This fixes a regression in R 4.2.0, which prevented
some operations with scripts when they contained non-ASCII
characters.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[Rd] R 4.2.1 is released
|
Peter Dalgaard
| 592 |
|
From p.dalgaard at biostat.ku.dk Wed Oct 6 15:19:29 1999
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 06 Oct 1999 15:19:29 +0200
Subject: R-0.65.1 is released
Message-ID: <[email protected]>
I've rolled up R-0.65.1.tgz a moment ago.
As usual, you shouldn't get it from Auckland, but wait for it to be
mirrored at a CRAN site near you within a day or two.
For those who are too curious to wait, I'll put a copy in
ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.65.1.tgz
There's also a version split in two for floppies and a patch file if
you prefer that. (If you use the patch file, you will miss a logo.bmp
file in the gnuwin32 directory, but that is probably immaterial to
most of you).
For the R Core Team,
Peter D.
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 0.65.1
NEW FEATURES
o .C, .Fortran. .Call and .External now have an argument PACKAGE
to specify the shared library to be used for the symbol. See
?Foreign. Package writers are encouraged to use this.
o On startup (unless --no-environ), first .Renviron is looked for in
the current directory, and then in $HOME/ (= ~/ ).
o New options(error.halt = FALSE) (default is TRUE) allows
continuation after an error in batch processing.
o In graphics, lty has now 6 instead of 4 predefined line types.
o as.hclust.twins() in package mva to convert (and plot)
objects from agnes() and daisy() of package cluster.
o R INSTALL now can directly install pkg_version.tar.gz files
as obtained from CRAN. New function update.packages()
& friends for automatically downloading packages from CRAN and
install them on the fly (on Unix and Windows).
o New function commandArgs() to record the command-line used.
o New arguments `local' and `now' to dyn.load.
o diag(x) now keeps names when appropriate and barfs when x is an array.
o functions source.url, url.show, read.table.url, scan.url to read
from an http server instead of a file.
o grid() gets useful defaults: grid lines drawn at tick marks.
o set operations union(), intersect(), setdiff() and is.element().
o New function stars() for star plots and segment diagrams of
multivariate data.
o Version info now in the top-level file `VERSION'.
o barplot has a "plot = TRUE" argument and now returns locations of
all bars even when "beside = TRUE".
o hist has an "nclass" argument purely for S compatibility.
o Character strings can now, with most compilers, be passed
on and from Fortran. See ?Foreign for details.
o Functions as.single and single now have the effect with
.C and .Fortran of passing a numeric argument as float/REAL
rather than as double/DOUBLE PRECISION, by setting the
attribute "Csingle". See ?Foreign for details.
o Comparison of strings uses the current locale on systems where
this is available, and so is always consistent with the ordering
used by sort().
o sapply has a new argument USE.NAMES=TRUE and now returns a named
result when its input was a character.
o plot.stepfun has new arguments lty and lwd.
o x labels in boxplot now handled differently, so that math
expressions are allowed.
o postscript() argument `onefile' now does something, and there
is a new paper type `special' and new argument `pagecentre'.
See ?postscript for details.
o Experimental function dev2bitmap() to copy to a bitmap graphics format.
BUG FIXES
o centering in text() will be more accurate, particularly on devices
with full font metric information (postscript, x11, not windows).
o arguments after --no-readline in the Unix version were ignored.
o couldn't set attributes in hashed environments.
o [<-.data.frame mishandled dfr[1] <- 1 (forgotten drop=FALSE)
o sys.on.exit didn't work
o sys.parent didn't quite work either for n >= 2.
o par("mfg") was wrong, par(mfg=) switched to down columns. Now
par(mfrow/mfcol = c(nr, nc)) followed by par(mfg=c(i,j)) is
the preferred style.
o plot( <aov.object> ) failed after 2nd plot, PR#279
o Several patches for systems with long != int.
o approx failed if inputs contained NAs.
o weighted lm fits with 1 diml x failed if any weight was zero.
o lm.influence failed when there were undetermined coefficients, PR#280.
o problem with function()... inside saved functions because arg count
increased to accommodate stored source. (Incorrect number of
arguments to "lambda")
o improvements to generation of HTML help files: should work
better on viewers other than Netscape.
o stl in package ts could conflict with package leaps: the Fortran
symbols have been changed.
o help page for factor is improved and corrected.
o na.omit.ts and na.contiguous now preserve time-series attributes.
o more automatic testing ("make check") using options(error.halt=FALSE)
led to the elimination of dozens (!) of seg.fault possibilities.
o family quasi handles zero observations with var=mu^2 more correctly.
o dynamically-loaded libraries are searched last-loaded first, as
documented (under Unix it used to be first-loaded first).
o rowsum failed with a matrix and a single group (drop=FALSE needed).
o deriv(y ~ <expr>(x)) now works as well as deriv(~ <expr>(x)).
o qr over-estimated ranks in some degenerate cases.
qr did not work correctly if n < p and the first n cols were
rank-deficient.
o str() wouldn't work quite right for named characters; doesn't quote
symbols anymore.
o Colour conversion (rgb, gray, hsv) truncated doubles and so
gave machine-dependent results on the examples. It now rounds.
o cat() now admits again that it can't handle lists instead of
"random" segfaulting.
o More accurate rounding (including rounding to even) on platforms
without rint (e.g. Windows).
o qgeom() is now left-continuous with a tolerance, and so the
example on the help page will be platform-independent.
o pretty() has been changed to use tolerance around integers and
so will be more platform-independent. The exact output has
probably changed on all platforms for some input.
o image() & filled.contour() now work for 1x1 matrices
and with constant z values.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-0.65.1 is released
|
Peter Dalgaard BSA
| 498 |
|
From pd.mes at cbs.dk Fri Jun 30 11:44:29 2017
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 30 Jun 2017 09:44:29 +0000
Subject: R 3.4.1 is released
Message-ID: <[email protected]>
The build system rolled up R-3.4.1.tar.gz (codename "Single Candle") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.4.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = f12a9c3881197b20b08dd3d1f9d005e6
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 8c65d9a0af345a185d3770c9876f1d51
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 4cd5e22f3fffd3525a65acd7d3ed0e28
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 71562183d75dd2080d86c42bbf733bb7
MD5 (R-latest.tar.gz) = 3a79c01dc0527c62e80ffb1c489297ea
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = f60d286bb7294cef00cb0eed4052a66f
MD5 (VERSION-INFO.dcf) = cc04bf1371ce85ec7fb32143692ead4e
MD5 (R-3/R-3.4.1.tar.gz) = 3a79c01dc0527c62e80ffb1c489297ea
6474d9791fff6a74936296bde3fcb569477f5958e4326189bd6e5ab878e0cd4f AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
f0d18e22b9bdfe1dd91547d401b4ef5c8828b2c956a51dc54e7476196b48f87e FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
c732c6ec885f4085ba20ae837ac9bcf2ad0952e61fcf910953bdd8dd2c103d23 NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
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a10f84be31f897456a31d31690df2fdc3f21a197f28b4d04332cc85005dcd0d2 NEWS.2
shasum: R-2:
shasum: R-3: Is a directory
02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78 R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
52f934a4e8581945cbc1ba234932749066b5744cbd3b1cb467ba6ef164975163 THANKS
e53d0641f90183fee5b7bec130b77d398634211a111fee3ceefb1536275865be VERSION-INFO.dcf
02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78 R-3/R-3.4.1.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 3.4.1:
INSTALLATION on a UNIX-ALIKE:
* The deprecated support for PCRE versions older than 8.20 has been
removed.
BUG FIXES:
* getParseData() gave incorrect column information when code
contained multi-byte characters. (PR#17254)
* Asking for help using expressions like ?stats::cor() did not
work. (PR#17250)
* readRDS(url(....)) now works.
* R CMD Sweave again returns status = 0 on successful completion.
* Vignettes listed in .Rbuildignore were not being ignored
properly. (PR#17246)
* file.mtime() no longer returns NA on Windows when the file or
directory is being used by another process. This affected
installed.packages(), which is now protected against this.
* R CMD INSTALL Windows .zip file obeys --lock and --pkglock flags.
* (Windows only) The choose.files() function could return incorrect
results when called with multi = FALSE. (PR#17270)
* aggregate(<data.frame>, drop = FALSE) now also works in case of
near-equal numbers in by. (PR#16918)
* fourfoldplot() could encounter integer overflow when calculating
the odds ratio. (PR#17286)
* parse() no longer gives spurious warnings when extracting srcrefs
from a file not encoded in the current locale.
This was seen from R CMD check with inst/doc/*.R files, and check
has some additional protection for such files.
* print.noquote(x) now always returns its argument x (invisibly).
* Non-UTF-8 multibyte character sets were not handled properly in
source references. (PR#16732)
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.4.1 is released
|
Peter Dalgaard
| 138 |
|
From fharrell at virginia.edu Sun Sep 22 02:29:20 2002
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Sat, 21 Sep 2002 20:29:20 -0400
Subject: Updates to Hmisc and Design Libraries
Message-ID: <[email protected]>
The Hmisc and Design libraries have had major improvements. New versions for Linux/Unix/Windows may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/r
Thanks to Xiao Gang Fan for porting the libraries to Windows once again.
Change logs may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/common
Several bugs have been fixed in Design, and many bugs have been fixed in Hmisc and new features and functions have been added. Advanced table making functions related to summary.formula have been enhanced to automatically add results of statistical tests comparing columns in tables. Some new latex options have been added. The contents function has been enhanced and an html method written for it. For example, html(contents(mydataframe)) will produce an html document whose initial part is a table containing variable names, labels, units, storage mode, number of levels, and number of NAs. The number of levels is hyperlinked to a separate table containin the factor levels.
R help files for Hmisc have been significantly improved. But there are many aspects of Hmisc and Design help files that still do not pass R CMD CHECK, hence the non-appearance of Hmisc and Design on CRAN. It will take some time to make all the help files meet CRAN package specifications.
Thanks to those who have reported bugs and fixes.
--
Frank E Harrell Jr Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine http://hesweb1.med.virginia.edu/biostat
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Updates to Hmisc and Design Libraries
|
Frank E Harrell Jr
| 62 |
|
From p.dalgaard at biostat.ku.dk Wed Apr 7 17:25:26 1999
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 07 Apr 1999 17:25:26 +0200
Subject: R-0.64.0 is released
Message-ID: <[email protected]>
I've put up R-0.64.0.tgz up for FTP from Auckland a little while ago.
As usual, don't get it from there unless you are desperate, but wait
for it to be mirrored at a CRAN site near you within a day or two.
For those who *are* desperate, I've left a copy in
ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.64.0.tgz
(Be gentle, that's my desktop PC!)
There's also a version split in two for floppies if you prefer that.
We haven't been very active removing minor bugs this time, but there
are a couple of new features that we wanted to get out in the open.
For the R Core Team,
Peter D.
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 0.64.0
NEW FEATURES
o Files BUGS and FAQ are now included with distribution and
various "front matter" files have been cleaned up.
o readline has now an argument prompt = ""
o coplot() now labels levels when conditioning variable is factor
(John Maindonald).
o A new function filled.contour() has been added. It produces
a variant of contour plots where the area between contours
is filled with a solid colour. The function (currently)
uses the layout() function and so is restricted to a full
page display.
o The function terrain.colors() has been modified to remove a
visual discontinuity (at yellow). In addition, a function
cm.colors() which implements a Cleveland-style cyan-magenta
palette has been added.
o Primitive function .External() to call dynamically loaded
`internal'-style functions (code from Jean Meloche).
o Function page() to view an R object in a pager.
o Support for handling embedded '\n's in text strings
handed to low-level graphics functions has been added.
Some changes to the PostScript graphics driver were
needed to support this, so there may some minor change
in the appearance of plots produced in PostScript.
o The LaTeX documentation is now split into 2 parts: the (currently
almost non-existent) manual and a reference index.
Manual: new section on loading C++ code.
o [EXPERIMENTAL] Gnome support added. Use ./configure --with-gnome
to try it, but don't expect too much yet.
o HDF5 support improved. Still not perfect, though.
o The X11 graphics driver can now use a variety of strategies
for handing color. This means that it is now possible to
use black and white or grayscale graphics on color displays.
There are two strategies for handing color on pseudocolor
displays. The original "allocate-colors-until-they-run-out"
strategy has been supplemented by one which allocates a
color cube at startup and approximates requested colors
by those in the cube. On truecolor displays, there is no
limit on the number of colors which can be displayed and
you get exactly the color you request. (Note that
Directcolor and staticcolor displays are not supported yet).
o The "persp" function now allows shading of the rendered
surface using a simple lighting model.
o Many functions providing an interface to the operating system
have been made "platform independent". See the manual entries
for "file", "list.files" and "file.show" for details of the new
interface. The system.file() interface has been changed.
o There is a new function "eval.with.vis" which behaves exactly
like "eval", but which returns both the result of the evaluation
an a logical value indicating whether the value is ``visible''.
This has been used to replace some ad-hoc tests for whether
value should be printed or not in "source". As a consequence,
the "example" and "demo" functions no longer print invisible
values when the example script is run.
o Index files in data directories in packages should be `00Index'
not `index.doc'.
o Function interaction() to compute factor interactions.
o load() can load to specific environments.
o Sockets interface: make/read/write/close.socket()
o Function chull() for planar convex hulls
o pairs.formula() allows formula notations for scatter plot matrix.
o new dataset co2.
o documentation for datasets mtcars, plants, pressure, randu and sleep.
o the sunspots dataset is now monthly rather than annual.
BUG FIXES
o strsplit(), scan() and friends use a much larger char buffer
(still fixed size; this will change again)
o ts() allows a data-frame argument `data'.
o anova.lm handles singular models better, and deparses responses.
o dump() now uses digits=12 rather than the current setting.
o tabulate ignores entries beyond nbins rather than core dumps.
o ?.C documents what C/Fortran types R objects correspond to
in foreign function calls, which is not what everyone thought.
o changed long to int in several .C calls to follow the above rules.
o rbind(x1,x2) now does not lose dimnames when xi are
character or complex.
o readline() accidentally inherited menu()'s prompt.
o .C() and .Fortran() now correctly report that there might be
NaN/Infs, not just NAs, unless NAOK=TRUE.
o Resizing an inactive graphics window to an invalid size left
that window active and produced a spurious prompt and newline
in the console window. This no longer happens.
o poly() rescales x to increase accuracy
o apply() preserves names in yet another case [-> new example].
o phyper() now works for larger arguments than before.
o Missing values didn't work in log plot
o outer() doesn't produce all-empty dimnames any more
o quantile.default() works when `probs' has zero length
o example() now works again in all cases [AnIndex spaces].
o typos fixed in nlm() message, glm help
o pt() now works better for extreme `df' arguments and gives
at least an approximate answer for ncp > 37.6. __more to change__
o fixed some glitches with formatC() and its docs.
o several fixes in *.c code to make -Wall happy
o curve() [and plot.function()] now use proper `x' values with log="x";
`type = "."' now works with curve() and plot.function()
o zapped old windows files since they didn't build any more.
The sources for the later gnuwin32 version are expected to
appear here for 0.64.1. The #ifdef Win32's here are for that
version.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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Send "info", "help", or "[un]subscribe"
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|
R-0.64.0 is released
|
Peter Dalgaard BSA
| 471 |
|
From pd.mes at cbs.dk Wed Oct 5 19:43:42 2016
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Wed, 5 Oct 2016 17:43:42 +0000
Subject: R-3.3.2 on October 31
Message-ID: <[email protected]>
Just a quick heads-up, mostly for those who want to keep their packages up to date with respect to updates of R: We intend to have a patch release on October 31. Nickname and detailed schedule will be made available on developer.r-project.org in due course.
For the R Core Team
Peter Dalgaard
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R-3.3.2 on October 31
|
Peter Dalgaard
| 128 |
|
From pd@me@ @end|ng |rom cb@@dk Fri Apr 26 09:41:13 2019
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Fri, 26 Apr 2019 07:41:13 +0000
Subject: R 3.6.0 is released
Message-ID: <[email protected]>
The build system rolled up R-3.6.0.tar.gz (codename "Planting of a Tree") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 28a3942a7129877e9af1d5ea16202052
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 6d227865440cc1ece3d97bdf4a8ee41e
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 591dcf615162127f904e4e461f330ce9
MD5 (R-latest.tar.gz) = 65601eac6d353f7efb5b48c29097c2fb
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 08158353102084599797db8c9ccf8e2a
MD5 (VERSION-INFO.dcf) = 97d5e3df5e5ac56750695e4b49145fae
MD5 (R-3/R-3.6.0.tar.gz) = 65601eac6d353f7efb5b48c29097c2fb
2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
38219d9c6221ccfbf075ef03711b420a1aa8731f890c8f2337148b602a217c2d FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
184dfa18e3069782d1092b289a6fe6ef85feb951cd4d1566b225c746d29a5420 NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
ca04f78ffe54afa326fe3ed40e7e1411aca0000ed2fa5ead97ddf51c6aa5b7bc NEWS.2
36fcac3e452666158e62459c6fc810adc247c7109ed71c5b6c3ad5fc2bf57509 R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
2d2e85e85574c4430951f6b070c08cd5aff1602abfd1bb162bed6d89c436b11f THANKS
05bd1202b132c8e91a8887d923fcc525cfb3bf81c67847d15876b88bf0c68a71 VERSION-INFO.dcf
36fcac3e452666158e62459c6fc810adc247c7109ed71c5b6c3ad5fc2bf57509 R-3/R-3.6.0.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 3.6.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Serialization format version 3 becomes the default for
serialization and saving of the workspace (save(), serialize(),
saveRDS(), compiler::cmpfile()). Serialized data in format 3
cannot be read by versions of R prior to version 3.5.0.
Serialization format version 2 is still supported and can be
selected by version = 2 in the save/serialization functions. The
default can be changed back for the whole R session by setting
environment variables R_DEFAULT_SAVE_VERSION and
R_DEFAULT_SERIALIZE_VERSION to 2. For maximal
back-compatibility, files vignette.rds and partial.rdb generated
by R CMD build are in serialization format version 2, and resave
by default produces files in serialization format version 2
(unless the original is already in format version 3).
* The default method for generating from a discrete uniform
distribution (used in sample(), for instance) has been changed.
This addresses the fact, pointed out by Ottoboni and Stark, that
the previous method made sample() noticeably non-uniform on large
populations. See PR#17494 for a discussion. The previous method
can be requested using RNGkind() or RNGversion() if necessary for
reproduction of old results. Thanks to Duncan Murdoch for
contributing the patch and Gabe Becker for further assistance.
The output of RNGkind() has been changed to also return the
'kind' used by sample().
NEW FEATURES:
* Sys.setFileTime() has been vectorized so arguments path and time
of length greater than one are now supported.
* axis() gets new option gap.axis = NA for specifying a
multiplication factor for the minimal "gap" (distance) between
axis labels drawn. Its default is 1 for labels _parallel_ to the
axis, and 0.25 for perpendicular ones.
Perpendicular labels no longer overlap, fixing bug PR#17384.
* The default method of plot() gains new arguments xgap.axis = NA
and ygap.axis = NA to be passed to the x- and y- axis(..,
gap.axis=*) calls.
* removeSource() now works not only for functions but also for some
language objects.
* as.call(), rep.int(), rep_len() and nchar() dispatch internally.
* is(object, class2) looks for class2 in the calling namespace
after looking in the namespace of class(object).
* extendrange(.., f) with a length-2 f now extends separately to
the left and the right.
* lengths() dispatches internally to S4 methods.
* download.file() on Windows now uses URLdecode() to determine the
file extension, and uses binary transfer (mode = "wb") also for
file extension .rds.
The help page for download.file() now contains the same
information on all platforms.
* Setting C locale for collation _via_ environment variables LC_ALL
and LC_COLLATE and _via_ a call to Sys.setlocale() now takes
precedence over environment variable R_ICU_LOCALE.
* There is a new function, nullfile(), to give the file name of the
null system device (e.g., /dev/null) on the current platform.
* There are two new options, keep.parse.data and
keep.parse.data.pkgs, which control whether parse data are
included into sources when keep.source or keep.source.pkgs is
TRUE. By default, keep.parse.data.pkgs is now FALSE, which
changes previous behavior and significantly reduces space and
time overhead when sources are kept when installing packages.
* In rapply(x, ..), x can also be "list-like" and of length >=
2^{31}.
* trimws() gets new optional whitespace argument, allowing more
extensive definitions of "space", such as including Unicode
spaces (as wished in PR#17431).
* weighted.mean() no longer coerces the weights to a double/numeric
vector, since sum() now handles integer overflow. This makes
weighted.mean() more polymorphic and endomorphic, but be aware
that the results are no longer guaranteed to be a vector of type
double.
* When loading namespaces, S3 method registrations which overwrite
previous registrations are now noted by default (using
packageStartupMessage()).
* compiler::cmpfile() gains a version argument, for use when the
output file should be saved in serialization format 2.
* The axis labeling in the default method of pairs() may now be
toggled by new options horOdd and verOdd.
* (Not Windows nor macOS.) Package tcltk now supports an
environment variable R_DONT_USE_TK which if set disables Tk
initialization. This is intended for use to circumvent errors in
loading the package, e.g. with recent Linux running under an
address sanitizer.
* The numeric method of all.equal() gets optional arguments countEQ
and formatFUN. If countEQ is true, the mean error is more
sensible when many entries are *eq*ual.
* outer(x,y, FUN = "*") is more efficient using tcrossprod(u,v)
instead of u %*% t(v).
* vcov(<mlm>) is more efficient via new optional arguments in
summary.mlm().
* The default method of summary() gets an option to choose the
_kind_ of quantile()s to use; wish of PR#17438.
* Fitting multiple linear models _via_ lm() does work with _matrix_
offsets, as suggested in PR#17407.
* The new functions mem.maxVSize() and mem.maxMSize() allow the
maximal size of the vector heap and the maximal number of nodes
allowed in the current R process to be queried and set.
* news() gains support for NEWS.md files.
* An effort has been started to have our reference manuals, i.e.,
all help pages. show platform-independent information (rather
than Windows or Unix-alike specifics visible only on that
platform). Consequently, the Windows version of X11() / x11()
got identical formal arguments to the Unix one.
* sessionInfo()$running has been factored out in a new variable
osVersion.
* slice.index() now also works for multi-dimensional margins.
* untar() used with an external tar command assumes this supports
decompression including xz and automagically detecting the
compression type. This has been true of all mainstream
implementations since 2009 (for GNU tar, since version 1.22):
older implementations are still supported _via_ the new argument
support_old_tars whose default is controlled by environment
variable R_SUPPORT_OLD_TARS. (It looks like NetBSD and OpenBSD
have 'older' tar commands for this purpose.)
* The new function asplit() allow splitting an array or matrix by
its margins.
* New functions errorCondition() and warningCondition() provide a
convenient way to create structured error and warning objects.
.Deprecated() now signals a warning of class "deprecatedWarning",
and .Defunct() now signals an error of class "defunctError".
* Many 'package not found' errors are now signaled as errors of
class "packageNotFoundError".
* As an experimental feature, when loadNamespace() fails because
the requested package is not available the error is initially
signaled with a retry_loadNamespace restart available. This
allows a calling handler to try to install the package and
continue.
* S3method() directives in NAMESPACE can now also be used to
perform _delayed_ S3 method registration.
* Experimentally, setting environment variable
_R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the
variable is set to a 'true' value) when && or || encounter and
use arguments of length more than one.
* Added "lines" and "chars" coordinate systems to grconvertX() and
grconvertY().
* getOption() is more efficient notably for the rare case when
called with two arguments, from several contributors in PR#17394.
* In .col(dim) and .row(dim), dim now may also be an integer-valued
"double".
* sQuote() and dQuote() get an explicit q argument with obvious
default instead of using getOption("fancyQuotes") implicitly and
unconditionally.
* unzip() can list archives with comments and with spaces in file
names even using an external unzip command.
* Command line completion has a new setting rc.settings(dots =
FALSE) to remove ... from the list of possible function
arguments.
* library() no longer checks packages with compiled code match
R.version$platform. loadNamespace() never has, and increasingly
the 'canonical name' does not reflect the important
characteristics of compiled code.
* The primitive functions drop() and unclass() now avoid
duplicating their data for atomic vectors that are large enough,
by returning ALTREP wrapper objects with adjusted attributes.
R-level assignments to change attributes will also use wrapper
objects to avoid duplicating data for larger atomic vectors. R
functions like structure() and unname() will therefore not
duplicate data in these settings. Generic vectors as produced by
list() are not yet covered by this optimization but may be in due
course.
* In formals(), envir becomes an optional argument instead of being
hardwired.
* Instead of signalling an error for an invalid S4 object x, str(x)
now gives a warning and subsequently still shows most parts of x,
e.g., when slots are missing.
* gamma(x) and lgamma(x) no longer warn when correctly returning
Inf or underflowing to zero. This helps maximum likelihood and
similar computations.
* convertColor() is now vectorized, so a lot faster for converting
many colours at once. The new argument vectorized to
colorConverter() ensures that non-vectorized colour converters
still work. (Thanks to Brodie Gaslam.)
* download.file() and url() get new argument headers for custom
HTTP headers, e.g., allowing to perform basic http
authentication, thanks to a patch contributed by G'abor Cs'ardi.
* File-based connection functions file(), gzfile(), bzfile() and
xzfile() now signal an error when used on a directory.
* For approx(), splinefun() _etc_, a new setting ties =
c("ordered", <fun>) allows skipping the sorting and still treat
ties.
* format(x) gives a more user friendly error message in the case
where no method is defined. A minimal method is provided in
format.default(x) when isS4(x) is true.
* which(x) now also works when x is a long vector, thanks to
Suharto Anggono's PR#17201. *NB*: this may return a double
result, breaking the previous guarantee of an integer result.
* seq.default() is more careful to return an integer (as opposed to
double) result when its arguments are large and/or classed
objects; see comment #9 of Suharto Anggono's PR#17497.
* The plot() method for lm and glm fits, plot.lm(), gains a new
option iter.smooth with a default of 0 for binomial fits, no
longer down-weighting when smoothing the residuals.
* zip() passes its list of files _via_ standard input to the
external command when too long for the command line (on some
platforms).
* data() gains an overwrite argument.
* t.test() now also returns the standard error (in list component
stderr).
* model.matrix(*, contrasts.arg = CC) now warns about invalid
contrasts.args.
* Performance of substr() and substring() has been improved.
* stopifnot() has been simplified thanks to Suharto Anggono's
proposals to become considerably faster for cheap expressions.
* The default 'user agent' has been changed when accessing http://
and https:// sites using libcurl. (A site was found which caused
libcurl to infinite-loop with the previous default.)
* sessionInfo() now also contains RNGkind() and prints it when it
differs from the default; based on a proposal and patch by Gabe
Becker in PR#17535. Also, RNGversion(getRversion()) works
directly.
* library() and require() now allow more control over handling
search path conflicts when packages are attached. The policy is
controlled by the new conflicts.policy option.
* barplot() gets a formula method, thanks to a patch proposal by
Arni Magnusson in PR#17521.
* pmax() and pmin(x) now also work for long vectors, thanks to
Suharto Anggono's PR#17533.
* bxp() now warns when omitting duplicated arguments.
* New hcl.colors() function to provide wide range of HCL-based
colour palettes with much better perceptual properties than the
existing RGB/HSV-based palettes like rainbow().
Also a new hcl.pals() function to list available palette names
for hcl.colors().
Contributed by Achim Zeileis.
* The default colours for image() and filled.contour() are now
based on hcl.colors().
* The palette-generating functions rainbow(), gray.colors(), etc.
get a new rev argument to facilitate reversing the order of
colors.
* New str2lang() and str2expression() as streamlined versions of
parse(text=., keep.source=FALSE) allow to abstract typical call
constructions, e.g., in formula manipulations. (Somewhat
experimental)
* Add update_PACKAGES() for incrementally updating a package
repository index, instead of rebuilding the index from scratch.
Thanks to Gabe Becker in PR#17544 for the patch, based on part of
his switchr package.
INSTALLATION on a UNIX-ALIKE:
* The options selected for the C++ compiler default to the C++11
standard if supported, otherwise to the C++98 standard.
* Visibility macros such as C_VISIBILITY can now be user-set
(including to empty), e.g. in config.site.
* Macro FCLIBS, which has sometimes been needed on Solaris, has
been renamed to FCLIBS_XTRA.
* Macro F77 is always set to the value of FC, so the latter should
be set to user-select the Fortran compiler for both fixed-form
and free-form Fortran. In particular, gfortran is now the first
choice for F77, not f95.
Macros FFLAGS and FCFLAGS remain distinct to allow for a compiler
which needs a flag to select free- or fixed-form Fortran (most
use the source-file extension to choose: .f is fixed-form and
.f90 and .f95 are free-form).
If only one of them is set, its value is used for both.
* The special-casing of CFLAGS, CXXFLAGS and FFLAGS for Intel
compilers on Linux has been removed: we do not have recent
experience but the generic defaults now chosen are the same as
those previously special-cased for x86_64.
If necessary, override the defaults on the configure command line
or in file config.site.
* Long-untested configure support for HP-UX and very old versions
of Linux has been removed.
* configure --with-blas (without specifying a value) includes
OpenBLAS in its search (before ATLAS and a generic BLAS). This
follows recent versions of the ax_blas autoconf macro.
* The configure macro MAKEINFO has been updated to TEXI2ANY.
* Support for make install-strip has been enhanced.
PACKAGE INSTALLATION:
* Source package installation is by default 'staged': the package
is installed into a temporary location under the final library
directory and moved into place once the installation is complete.
The benefit is that partially-installed packages are hidden from
other R sessions.
The overall default is set by environment variable
R_INSTALL_STAGED. R CMD INSTALL has new options --staged-install
and --no-staged-install, and packages can use the StagedInstall
field in their DESCRIPTION file to opt out. (That opt-out is a
temporary measure which may be withdrawn in future.)
Staged installation requires either --pkglock or --lock, one of
which is used by default.
* The interpretation of source code with extension .f is changing.
Previously this denoted FORTRAN 77 code, but current compilers no
longer have a FORTRAN 77 mode and interpret it as 'fixed-form'
Fortran 90 (or later where supported) code. Extensions .f90 and
.f95 continue to indicate 'free-form' Fortran code.
Legal FORTRAN 77 code is also legal fixed-form Fortran 9x;
however this change legitimizes the use of later features, in
particular to replace features marked 'obsolescent' in Fortran 90
and 'deleted' in Fortran 2018 which gfortran 8.x and later warn
about.
* Packages containing files in the src directory with extensions
.f90 or .f95 are now linked using the C or C++ compiler rather
than the Fortran 9x compiler. This is consistent with fixed-form
Fortran code and allows mixing of C++ and free-form Fortran on
most platforms.
Consequentially, a package which includes free-form Fortran 9x
code which uses OpenMP should include SHLIB_OPENMP_CFLAGS (or the
CXXFLAGS version if they also include C++ code) in PKG_LIBS
rather than SHLIB_OPENMP_FCFLAGS - fortunately on almost all
current platforms they are the same flag.
* Macro PKG_FFLAGS will be used for the compilation of both
fixed-form and free-form Fortran code unless PKG_FCFLAGS is also
set (in src/Makevars or src/Makevars.win).
* The make macro F_VISIBILITY is now preferred for both fixed-form
and free-form Fortran, for use in src/Makevars and similar.
* R CMD INSTALL gains a new option --strip which (where supported)
strips installed shared object(s): this can also be achieved by
setting the environment variable _R_SHLIB_STRIP_ to a true value.
The new option --strip-lib attempts stripping of static and
shared libraries installed under lib.
These are most useful on platforms using GNU binutils (such as
Linux) and compiling with -g flags.
* There is more support for installing UTF-8-encoded packages in a
strict Latin-1 locale (and probably for other Latin locales):
non-ASCII comments in R code (and NAMESPACE files) are worked
around better.
UTILITIES:
* R CMD check now optionally checks makefiles for correct and
portable use of the SHLIB_OPENMP_*FLAGS macros.
* R CMD check now evaluates \Sexpr{} expressions (including those
in macros) before checking the contents of Rd files and so
detects issues both in evaluating the expressions and in the
expanded contents.
* R CMD check now lists missing packages separated by commas and
with regular quotes such as to be useful as argument in calling
install.packages(c(..)); from a suggestion by Marcel Ramos.
* tools::Rd2latex() now uses UTF-8 as its default output encoding.
* R CMD check now checks line endings of files with extension .hpp
and those under inst/include. The check now includes that a
non-empty file is terminated with a newline.
R CMD build will correct line endings in such files.
* R CMD check now tries re-building all vignettes rather than
stopping at the first error: whilst doing so it adds 'bookmarks'
to the log. By default (see the 'R Internals' manual) it
re-builds each vignette in a separate process.
It now checks for duplicated vignette titles (also known as
'index entries'): they are used as hyperlinks on CRAN package
pages and so do need to be unique.
* R CMD check has more comprehensive checks on the data directory
and the functioning of data() in a package.
* R CMD check now checks autoconf-generated configure files have
their corresponding source files, including optionally attempting
to regenerate them on platforms with autoreconf.
* R CMD build has a new option --compression to select the
compression used for the tarball.
* R CMD build now removes src/*.mod files on all platforms.
C-LEVEL FACILITIES:
* New pointer protection C functions R_PreserveInMSet and
R_ReleaseFromMSet have been introduced to replace UNPROTECT_PTR,
which is not safe to mix with UNPROTECT (and with
PROTECT_WITH_INDEX). Intended for use in parsers only.
* NAMEDMAX has been raised to 7 to allow further protection of
intermediate results from (usually ill-advised) assignments in
arguments to BUILTIN functions. Properly written package code
should not be affected.
* R_unif_index is now considered to be part of the C API.
* R_GetCurrentEnv() allows C code to retrieve the current
environment.
DEPRECATED AND DEFUNCT:
* Argument compressed of untar() is deprecated - it is only used
for external tar commands which increasingly for extraction
auto-detect compression and ignore their zjJ flags.
* var(f) and hence sd(f) now give an error for factor arguments;
they gave a deprecation warning since R 3.2.3, PR#16564.
* Package tools' vignetteDepends() has been deprecated (it called a
function deprecated since Feb 2016), being partly replaced by
newly exported vignetteInfo().
* The f77_f2c script has been removed: it no longer sufficed to
compile the .f files in R.
* The deprecated legacy support of make macros such as CXX1X has
been removed: use the CXX11 forms instead.
* Make macro F77_VISIBILITY is deprecated in favour of
F_VISIBILITY.
* Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS are
deprecated in favour of FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS
respectively.
* $.data.frame had become an expensive version of the default
method, so has been removed. (Thanks to Radford Neal for picking
this up and to Duncan Murdoch for providing a patch.)
BUG FIXES:
* replayPlot(r) now also works in the same R session when r has
been "reproduced" from serialization, typically after saving to
and reading from an RDS file.
* substr() and substring() now signal an error when the input is
invalid UTF-8.
* file.copy() now works also when its argument to is of length
greater than one.
* mantelhaen.test() no longer suffers from integer overflow in
largish cases, thanks to Ben Bolker's PR#17383.
* Calling setGeneric("foo") in a package no longer fails when the
enclosing environment of the implicit generic foo() is
.GlobalEnv.
* untar(file("<some>.tar.gz"), *) now gives a better error message,
suggesting to use gzfile() instead.
* Method dispatch uses more relevant environments when looking up
class definitions.
* The documentation for identify() incorrectly claimed that the
indices of identified points were returned in the order that the
points were selected. identify() now has a new argument order to
allow the return value to include the order in which points were
identified; the documentation has been updated. Reported by
Richard Rowe and Samuel Granjeaud.
* order(...., decreasing=c(TRUE, FALSE)) could fail in some cases.
Reported from StackOverflow via Karl Nordstr"om.
* User macros in Rd files now accept empty and multi-line
arguments.
* Changes in print.*(), thanks to Lionel Henry's patches in
PR#17398:
* Printing lists, pairlists or attributes containing calls with
S3 class no longer evaluate those.
* Printing S4 objects within lists and pairlists dispatches
with show() rather than print(), as with auto-printing.
* The indexing tags (names or [[<n>]]) of recursive data
structures are now printed correctly in complex cases.
* Arguments supplied to print() are now properly forwarded to
methods when printing lists, pairlists or attributes
containing S3 objects.
* The print parameters are now preserved when printing S3
objects or deparsing symbols and calls. Previously, printing
lists containing S3 objects or expressions would reset these
parameters.
* Printing lists, pairlists or attributes containing functions
now uses srcref attributes if present.
* Calling install.packages() with a length zero pkgs argument now
is a no-op (PR#17422).
* unlist(x) now returns a correct factor when x is a nested list
with factor leaves, fixing PR#12572 and PR#17419.
* The documentation help(family) gives more details about the aic
component, thanks to Ben Bolker's prompting.
* The documentation for attributes and `attributes<-` now gives x
as name of the first and main argument which the implementation
has been requiring, fixing PR#17434. For consistency, the first
argument name is also changed from obj to x for
`mostattributes<-`.
* strwidth() now uses par("font") as default font face (PR#17352).
* plot(<table>, log="x") no longer warns about log.
* The print() method for "htest" objects now formats the test
statistic and parameter directly and hence no longer rounds to
units _before_ the decimal point. Consequently, printing of
t.test() results with a small number of digits now shows
non-large df's to the full precision (PR#17444).
* kruskal.test() and fligner.test() no longer erroneously insist on
numeric g group arguments (PR#16719).
* Printing a news db via the browser now does a much better job
(PR#17433).
* print.aov() missed column names in the multivariate case due to
misspelling (reported by Chris Andrews).
* axis() now creates valid at locations also for small subnormal
number ranges in log scale plots.
* format.POSIXlt() now also recycles the zone and gmtoff list
components to full length when needed, and its internal C code
detects have_zone in more cases. In some cases, this changes its
output to become compatible with format.POSIXct().
* On Windows, detectCores() in package parallel now detects
processors in all processor groups, not just the group R is
running in (impacts particularly systems with more than 64
logical processors). Reported by Arunkumar Srinivasan.
* On Windows, socketSelect() would hang with more than 64 sockets,
and hence parallel::clusterApplyLB() would hang with more than 64
workers. Reported by Arunkumar Srinivasan.
* as(1L, "double") now does coerce (PR#17457).
* lm.influence(), influence.measures(), rstudent() etc now work
(more) correctly for multivariate models ("mlm"), thanks to
(anonymous) stackoverflow remarks.
* sample.int(2.9, *, replace=TRUE) again behaves as documented and
as in R < 3.0.0, namely identically to sample.int(2, ..).
* Fixes to convertColor() for chromatic adaptation; thanks to
Brodie Gaslam PR#17473.
* Using \Sexpr[stage=install]{..} to create an Rd section no longer
gives a warning in R CMD check; problem originally posted by
G'abor Cs'ardi, then reported as PR#17479 with a partial patch by
Duncan Murdoch.
* Parse data now include a special node for equal assignment.
* split.default() no longer relies on [[<-(), so it behaves as
expected when splitting an object by a factor with the empty
string as one of its levels. Thanks to Brad Friedman for the
report.
* Line numbers in messages about .Rd files are now more reliable,
thanks to a patch from Duncan Murdoch.
* In the numeric method for all.equal(), a numeric scale argument
is now checked to be positive and allowed to be of length > 1.
(The latter worked originally and with a warning in recent
years).
* Deferred string conversions now record the OutDec option setting
when not equal to the default. Reported by Michael Sannella.
* When y is numeric and f a factor, plot(y ~ f) nicely uses "y" and
"f" as y- and x-labels. The more direct boxplot(y ~ f) now does
too. The new argument ann = FALSE may be used to suppress these.
* Subassignment to no/empty rows of a data frame is more consistent
and typically a no-op in all cases instead of sometimes an error;
part of Emil Bode's PR#17483.
* Calls like formatC(*, zero.print = "< 0.001") no longer give an
error and are further improved via new optional argument
replace.zero. Reported by David Hugh-Jones.
* methods::formalArgs("<fn>") now finds the same function as
formals("<fn>"), fixing Emil Bode's PR#17499.
* The methods package better handles duplicated class names across
packages.
* The default method of seq() now avoids integer overflow, thanks
to the report and "cumsum" patch of Suharto Anggono's PR#17497.
* sub() no longer loses encodings for non-ASCII replacements
(PR#17509).
* Fix for rotated raster image on X11 device. (Partial fix for
PR#17148; thanks to Mikko Korpela).
* formula(model.frame(frml, ..)) now returns frml in all cases,
thanks to Bill Dunlap. The previous behavior is available as
DF2formula(<model.frame>).
* ar.ols() also returns scalar var.pred in univariate case
(PR#17517).
* normalizePath() now treats NA path as non-existent and normalizes
it to NA. file.access() treats NA file name as non-existent.
file.edit() and connection functions such as file() now treat NA
file names as errors.
* The internal regularize.values() auxiliary of approx(),
splinefun() etc now warns again when there are ties and the
caller did not specify ties. Further, it no longer duplicates x
and y unnecessarily when x is already sorted (PR#17515).
* strtoi("", base) now gives NA on all platforms, following its
documentation. Reported by Michael Chirico.
* In the definition of an S4 class, prototype elements are checked
against the slots of the class, with giving a prototype for an
undefined slot now being an error. (Reported by Bill Dunlap.)
* From setClassUnion(), if environment variable
_R_METHODS_SHOW_CHECKSUBCLASSES is set to true, the internal
.checkSubclasses() utility prints debugging info to see where it
is used.
* max.col(m) with an m of zero columns now returns integer NA
(instead of 1).
* axTicks() no longer returns small "almost zero" numbers (in
exponential format) instead of zero, fixing Ilario Gelmetti's
PR#17534.
* isSymmetric(matrix(0, dimnames=list("A","b"))) is FALSE again, as
always documented.
* The cairo_pdf graphics device (and other Cairo-based devices) now
clip correctly to the right and bottom border.
There was an off-by-one-pixel bug, reported by Lee Kelvin.
* as.roman(3) <= 2:4 and all other comparisons now work, as do
group "Summary" function calls such as max(as.roman(sample(20)))
and as.roman(NA). (Partly reported by Bill Dunlap in PR#17542.)
* reformulate("x", response = "sin(y)") no longer produces extra
back quotes, PR#17359, and gains new optional argument env.
* When reading console input from stdin with re-encoding (R
--encoding=enc < input) the code on a Unix-alike now ensures that
each converted input line is terminated with a newline even if
re-encoding fails.
* as.matrix.data.frame() now produces better strings from logicals,
thanks to PR#17548 from Gabe Becker.
* The S4 generic signature of rowSums(), rowMeans(), colSums() and
colMeans() is restricted to "x".
* match(x, tab) now works for long _character_ vectors x, thanks to
PR#17552 by Andreas Kersting.
* Class unions are unloaded when their namespace is unloaded
(PR#17531, adapted from a patch by Brodie Gaslam).
* selectMethod() is robust to ANY-truncation of method signatures
(thanks to Herve Pages for the report).
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.6.0 is released
|
Peter Dalgaard
| 673 |
|
From pgilbert at bank-banque-canada.ca Fri Jan 16 17:50:36 1998
From: pgilbert at bank-banque-canada.ca (Paul Gilbert)
Date: Fri, 16 Jan 1998 11:50:36 -0500
Subject: DSE time series package
Message-ID: <[email protected]>
===============================================================
ANNOUNCEMENT
===============================================================
An R version of my multivariate time series package (DSE) is now available at
CRAN/src/contrib/devel/dse.v.98.1alphaR.tar.gz and it should be reflected
at the mirrors shortly. The User's Guide is available at
http://www.bank-banque-canada.ca/pgilbert
HTML help documentation is distributed with the code and is also available
at the above web site. (The web page is a bit out of date but I hope to fix
that soon.)
The tar file includes two other packages which may be of interest by themselves.
The first, called syskern, provides a kernel of functions for S/R programmers
which is intended to help write code which is independent of operating system
differences and some small differences between S and R.
The second, called tframe, provides a kernel of functions for programming time
series methods relatively independently of the representation of time.
This is intended to make it easier to write code which can use any new/better
time representations when they appear. It also provides plotting, windowing,
and some other utility functions which are specifically intended for time
series.
The DSE library implements an object oriented approach to time series
models (using classes and methods in R/S). This means that different
model representations can be implemented with fairly simple extensions
to the library. The original library included multi-variate state space
and ARMA (including VAR) models. The current version implements Troll
models as another class. These are run by completely separate software
(Troll from Intex Inc.) as if they were an integral part of the
library. Models and data are passed back and forth to Troll and the
results can be analyzed with already existing functions in the
library. This also serves as an example for including other classes
and methods. [The Troll interface is not yet functional in R.]
Methods for simulating, estimating, and converting among different
model representations form the basic part of the library. Methods for
studying estimation methods and for examining the forecasting properties
of models are also documented in the User Guide.
Relative to commercial packages the library is especially useful for
time series research (such as studying estimation methods) and for
teaching. For usual time series applications there may be commercial
packages which are preferable.
A list server for questions and discussion of problems has also been set up.
To subscribe to the list send a message to
with a line in the body:
subscribe boc_dse Your Name
Subsequent message submissions to the list should be sent to
boc_dse at bank-banque-canada.ca
Caveats for R
I have tested the package with R0.61.1 in Solaris and R0.61 in Linux. I would
appreciate feedback about other OSs. The install procedures are currently Unix
specific (I believe) but if anyone attempts installing in Windows I would be
especially interested in knowing how to do this.
The package has been put in the devel area of CRAN because there are still
some things I would like to fix (although it is mostly working well), and
because the documentation has not been revised. I would appreciate any early
feedback as I would like to fix as many problems as possible before moving
this out of the devel category.
The package is divided into several parts, some logical and some because
the current version of R does not support large libraries.
Beware that some documentation in the code, in the HTML based help system,
and in the Brief Users' Guide is still somewhat specific to S and is not
correct for R (particularly with respect to installation). See the READ.ME
file for instruction to install in R.
Paul Gilbert
pgilbert at bank-banque-canada.ca
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|
DSE time series package
|
Paul Gilbert
| 520 |
|
From gregory_r_warnes at groton.pfizer.com Mon Sep 23 22:00:33 2002
From: gregory_r_warnes at groton.pfizer.com (Warnes, Gregory R)
Date: Mon, 23 Sep 2002 16:00:33 -0400
Subject: New version of gregmisc package
Message-ID: <[email protected]>
I forgot to note that Marc Schwartz contributed barplot2() and CrossTable().
-Greg
> -----Original Message-----
> From: Warnes, Gregory R
> Sent: Monday, September 23, 2002 2:35 PM
> To: 'r-announce at lists.R-project.org'
> Subject: New version of gregmisc package
>
>
>
>
> Version 0.6.0 of the gregmisc package has just been released
> on CRAN.
>
>
> Description:
> ===========
>
> Package: gregmisc
> Description: Misc Functions written/maintained by Gregory R. Warnes
> Title: Greg's Miscellaneous Functions
> Version: 0.6.0
> Date: 2002/09/23
> Maintainer: Gregory R. Warnes <Gregory_R_Warnes at groton.pfizer.com>
> Author: Gregory R. Warnes. Includes code provided by Ben Bolker,
> Bendix Carstensen, Don MacQueen, William Venables, and Marc
> Schwartz
> License: GPL (version 2 or later)
>
> Index:
>
> CrossTable Cross Tabulation with Tests for Factor
> Independence
> aggregate.table Create 2-Way Table of Summary Statistics
> bandplot Plot x-y Points with Locally Smoothed Mean and
> Standard Deviation
> barplot2 Enhanced Bar Plots
> boxplot.n Produce a Boxplot Annotated with the Number of
> Observations
> ci Compute Confidence Intervals
> combinations Enumerate the Combinations or Permutations of
> the Elements of a Vector
> combine Combine R Objects With a Column Labeling the
> Source
> contrast.lm Compute (and test) arbitrary contrasts for
> regression objects
> estimable Compute and test estimable linear functions of
> the fitted coefficients (including contrasts)
> of regression objects
> factorial Compute factorial function
> glh.test Test a General Linear Hypothesis for a
> Regression Model
> hist2d Compute and Plot a 2-Dimensional Histogram
> interleave Interleave Rows of Data Frames or Matrices
> lowess Scatter Plot Smoothing
> nobs Compute the Number of Non-missing
> Observations
> plotCI Plot Error Bars
> plotmeans Plot Group Means and Confidence Intervals
> quantcut Create a Factor Variable Using the
> Quantiles of
> a Continuous Variable
> rename.vars Rename variables in a dataframe
> reorder Reorder the Levels of a Factor
> running Apply a Function Over Adjacent Subsets of a
> Vector
> space Space points in an x-y plot so they don't
> overlap.
> undocumented Undocumented functions
> wapply Compute the Value of a Function Over a Local
> Region Of An X-Y Plot
>
> Changelog Since 0.5.5
> =====================
>
> - Added barplot2():
>
> barplot2 is an enhanced version of barplot that can add confidence
> intervals for each bar, color plot region separately from the
> background area, draw "height" axis grid lines *behind* the bars,
> and log-scale the data axis. Contributed by Mark Schwartz
>
> - Added CrossTable():
>
> CrossTable is an implementation of a cross-tabulation function
> with output similar to S-Plus crosstabs() and SAS Proc Freq with
> Chi-square and Fisher tests of the independence of table factors
>
> - Permit combinations() to be used when r>n provided
> repeat.allowed=TRUE
>
> - Renamed 'concat' function to 'combine' to avoid name conflict with
> an existing S-Plus function.
>
> - Misc fixes to files for compatibility with R 1.6.0
>
> - Correction of some documentation typos
>
>
>
>
> LEGAL NOTICE
> Unless expressly stated otherwise, this message is
> confidential and may be privileged. It is intended for the
> addressee(s) only. Access to this E-mail by anyone else is
> unauthorized. If you are not an addressee, any disclosure or
> copying of the contents of this E-mail or any action taken
> (or not taken) in reliance on it is unauthorized and may be
> unlawful. If you are not an addressee, please inform the
> sender immediately.
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
> -.-.-.-.-.-.-.-.-
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> http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !) To:
> r-announce-request at stat.math.ethz.ch
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> _._._._._._._._._
>
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|
New version of gregmisc package
|
Warnes, Gregory R
| 64 |
|
From bates at stat.wisc.edu Thu Jan 31 20:24:58 2002
From: bates at stat.wisc.edu (Douglas Bates)
Date: 31 Jan 2002 13:24:58 -0600
Subject: R and R-recommended 1.4.1 Debian packages available
In-Reply-To: <[email protected]>
References: <[email protected]>
<[email protected]>
Message-ID: <[email protected]>
Dirk Eddelbuettel <edd at debian.org> writes:
> Debian packages of R-1.4.1 and R-1.4.1-recommended [1] have been uploaded for
> i386 and are currently available at http://incoming.debian.org. These will
> run on any current "testing" (aka "woody") or "unstable" (aka "sid")
> distribution.
Dirk's Debian packages are now installed on the cran.us.r-project.org
site and will be mirrored tonight to the main CRAN site. If you are
running Debian GNU/Linux and have lines like
deb-src http://cran.us.r-project.org/bin/linux/debian woody main
deb http://cran.us.r-project.org/bin/linux/debian woody main
in your /etc/apt/sources.list file, you should be able to install
these packages with
apt-get update
apt-get install r-base r-recommended r-doc-pdf
or upgrade your current R packages with
apt-get update
apt-get upgrade
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
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(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
R and R-recommended 1.4.1 Debian packages available
|
Douglas Bates
| 14 |
|
From chong at stat.purdue.edu Mon Mar 3 09:52:03 2003
From: chong at stat.purdue.edu (Chong Gu)
Date: Mon Mar 3 09:52:03 2003
Subject: gss_0.8-2
Message-ID: <[email protected]>
A new version of gss, version 0.8-2, is on CRAN now. Numerous new
functionalities have been added since my last r-announce post.
An ssanova1 suite has been added since version 0.7-4. It implements
low-dimensional approximations of the smoothing spline ANOVA models
of the ssanova suite. ssanova1 scales much better than ssanova with
large sample sizes.
A gssanova1 suite is added for non Gaussian regression. Similar to
ssanova1, it provides better scalability than gssanova. Direct
cross-validation is used in gssanova1 instead of the indirect CV of
gssanova. Currently, only three families are supported: binomial,
poisson, and Gamma; other families of gssanova will be added to
gssanova1 in the (near?) future.
An sshzd suite is added to fit hazard models using right-censored
lifetime data with possible left-truncation and covariates. It
estimates log hazard as "bivariate" smooth functions of time and
covariates through penalized full likelihood. It only takes static
covariates but accommodates interactions between time and covariates,
going beyond the proportional hazard models.
Utilities are provided for the calculation of a certain
Kullback-Leibler projection of cross-validated fits to "reduced model"
spaces, for the "testing" of model terms. Projection code is provide
for ssanova1, gssanova1, ssden, and sshzd fits.
Further details are to be found in the documentations and the examples
therein. As always, feature suggestions and bug reports will be
sincerely appreciated.
Chong Gu
|
gss_0.8-2
|
Chong Gu
| 156 |
|
From edd at debian.org Tue Jun 18 04:37:12 2002
From: edd at debian.org (Dirk Eddelbuettel)
Date: Mon, 17 Jun 2002 21:37:12 -0500
Subject: Debian packages of R 1.5.1 available
Message-ID: <[email protected]>
Debian packages for r-base_1.5.1 and r-recommended_1.5.1 have been uploaded
to the main Debian archive and should hit the mirrors tomorrow. These
packages were built on i386, packages for the other architectures (alpha,
hppa, ia64, m68k, mips. mipsel, powerpc, s390, sparc) should become available
in the next few days.
Dirk
--
Good judgement comes from experience; experience comes from bad judgement.
-- Fred Brooks
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|
Debian packages of R 1.5.1 available
|
Dirk Eddelbuettel
| 40 |
|
From guido at hal.stat.unipd.it Wed Jul 7 12:20:29 1999
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Wed, 7 Jul 1999 11:20:29 +0100
Subject: Win9X/NT binaries updated
Message-ID: <[email protected]>
A binary distribution of R-0.64.2 for Windows is available at
CRAN/bin/windows/windows-NT.
There are few Windows-specific enhancements: rw0642 (and R-0.64.2) is
a bug-fixing release.
CHANGES
=======
If options(pager="console") then files are listed in the console
window, as happened prior to rw0640.
On request, we have enabled `pagerstyle = singlewindow' in MDI mode,
although we do not recommend this combination.
The file HOME\.Renviron is read (it was HOME\Renviron, and the
documentation used both names). Only the last line was successfully
processed in rw0641, but all lines are in this version.
unlink() on non-existent files no longer causes a crash.
The new function win.version() will report details of the run-time
Windows version, principally for use in bug.report().
bug.report() has a new argument wait: wait=FALSE gives a non-modal editor
screen.
Generally TAB will move between fields in dialog boxes, and return and
escape will work (selecting OK and Cancel) in the Change Directory
dialog box.
The installer will allow several packages to be selected, and will
install them in sequence. It should give more informative messages on
some error conditions. Usually return will select Next or Finish,
escape will select Cancel and B Back.
There is a new target `make check' for running the standard tests and
checking the standard packages (as on Unix).
Saving the content of a graphic device as GIF should work again
(saving of an image with less than 256 colours was broken in rw0641).
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Send "info", "help", or "[un]subscribe"
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_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Win9X/NT binaries updated
|
Guido Masarotto
| 492 |
|
From dmurdoch at pair.com Mon Apr 12 21:37:40 2004
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Mon, 12 Apr 2004 15:37:40 -0400
Subject: [R] R 1.9.0 is release
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
On 12 Apr 2004 14:05:25 +0200, Peter Dalgaard
<p.dalgaard at biostat.ku.dk> wrote :
>I've rolled up R-1.9.0.tgz a short while ago. This is a new version
>with a number of new features, most notably a substantial
>reorganization of the standard packages, a major update of the grid
>package, and the fact that underscore can now be used as a regular
>character in variable names.
I've just uploaded the Windows build. It should appear on CRAN and
the mirrors by tomorrow.
The main Windows-specific changes are the following:
- A "stay on top" option for windows.
- Rcmd can now be written R CMD, as on Unix.
- Tony Plate's "Paste commands only" to paste the commands from a
copied block of output
There are many other changes and bug fixes. Here's an extract from
the CHANGES file:
rw1090
======
Both Rterm and Rgui now give usage information via the --help or -h
command-line flag.
There is now a "Misc|Break to debugger" menu option, enabled
when a debugger is detected (somewhat fallibly), or infallibly by the
"--debug" command line option. This will cause a trap to an external
debugger, e.g. for running Rgui under gdb. If the menu item is
selected when not running under a debugger R is likely to crash.
If the "--debug" option is used, R will break to the debugger during
command line processing, allowing the startup process to be debugged.
Added "stay" argument to bringToTop(), to allow the user to specify
that a window should stay on top of other windows. Also added "stay
on top" item to the popup menus. All of these require R to be running
in SDI mode ("Rgui --sdi" or via the settings in file `Rconsole').
Changed windows() so that new windows fit within the MDI client
area.
Added winMenuNames() and winMenuItems() functions to query user menus.
Added menu items for www.r-project.org and CRAN on the help menu.
(Wishlist PR#6492)
Added "R" command to be similar to Unix invocation of scripts, e.g.
"R CMD INSTALL" is the same as "Rcmd INSTALL". Rcmd still exists for
backwards compatibility (and to avoid conflicts over the name `R').
All of R, R CMD and Rcmd now accept --help.
Rcmd Rd2dvi can now be specified as such rather than as Rcmd
Rd2dvi.sh.
Added "Paste commands only" to edit and popup menus in the Rgui
console.
This allows copying of a block of output, but pasting only the
commands
back to the console for re-execution. (Code contributed by Tony
Plate.)
Installation
------------
Parallel make (make -j2, say) can be used, but only usefully on
dual-processor (or perhaps hyperthreaded) hosts with at least 384Mb of
memory.
Installing now sorts in the C locale to ensure that a consistent sort
order is used. (Some aspects of sorting used to be done in the locale
of the host machine, but Perl and the cygwin-based tools used the
ASCII collation order.)
The long-untested support for making Windows .hlp files has been
withdrawn.
There is support for using K. Goto's fast BLAS. On a 2.6Ghz P4 with
1Gb RAM and A a 1000 x 1000 matrix we had the following timings
R BLAS ATLAS Goto
A %*% A 3.7 0.65 0.56
svd(A) 16.2 7.77 6.83
Note that using a fast BLAS is much less effective for smaller
matrices as are more common in statistical applications.
Faster assembler code for exponentiation is used.
Cross-building of R itself now works again. (It had been broken since
1.8.0.)
Building/installing packages
----------------------------
R CMD INSTALL/build/check map path names with spaces in to their short
forms.
R CMD INSTALL now supports versioned install via
--with-package-versions.
Installing (binary) package bundles now checks the MD5 sums and
reports success, just as for packages.
Added "* DONE" to the end of INSTALL logs so --install option to CHECK
will work. (This is a repository maintainer option; see
src/scripts/check.in for docs).
Internal changes
----------------
The fast bmp/png/jpeg code introduced in R 1.8.0 is used even for
256-color displays (as we have now been able to test it on such).
R's internal malloc etc are now remapped to Rm_malloc etc and only
used in allocating memory for R objects, the Wilcoxon tests and a few
other memory-intensive applications.
Improved malloc routines from the current version of Doug Lea's malloc
(as suggested by David Teller) should enable large memory areas to be
used more effectively, in particular those over 2Gb where OS support
has been enabled. The initially requested memory is no longer
reserved, but as this malloc is able to work with non-contiguous
memory chunks that should not matter.
The installer uses LZMA compression, so Inno Setup >= 4.1.5 is
required.
Version 1.2.5 of libpng is now used in binary builds.
Bug fixes
---------
Fixed list.files() to properly handle paths like "C:", etc.
Fixed unlink() to accept empty file list for Unix consistency.
Fixed handling of whitespace in Rd2dvi.sh processing of DESCRIPTION
files.
Fixed handling of "--max-mem-size" syntax error on command line.
In RGui, ^T would not transpose the first and second characters on a
line. (PR#5593)
Fixed junk character at start of a pipe(). (PR#5053)
R CMD SHLIB was computing dependencies for all C files, not just those
specified on the command line, and building the DLL from all *.o files
in the directory.
The sizes of metafiles in pixels were often coming out one pixel more
than requested, so the background was not quite all painted. Now we
over-estimate.
Rproxy.dll would cause a crash when transferring large amounts of
data.
Workaround for Microsoft's esoteric idea that date-times in 1970
before
1970-01-01 00:00:00 GMT are invalid, so as.POSIXct("1970-01-01
00:00:00") failed in timezones ahead of GMT.
Avoid possible segfault with browseURL() on urls of more than 264
chars
(although these are not guaranteed to work).
|
[R] R 1.9.0 is release
|
Duncan Murdoch
| 379 |
|
From dmurdoch at pair.com Fri Oct 10 03:23:12 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Thu, 09 Oct 2003 21:23:12 -0400
Subject: R 1.8.0 Windows binaries uploaded
Message-ID: <[email protected]>
I've just uploaded the 1.8.0 binary build for Windows. It should be
available on CRAN and the mirrors tomorrow.
Duncan Murdoch
|
R 1.8.0 Windows binaries uploaded
|
Duncan Murdoch
| 187 |
|
From thomas at biostat.washington.edu Mon Jan 15 20:03:35 2001
From: thomas at biostat.washington.edu (Thomas Lumley)
Date: Mon, 15 Jan 2001 11:03:35 -0800 (PST)
Subject: announce: survival5 bug fix
Message-ID: <Pine.GSO.4.21.0101151050480.18938-100000@atlas.biostat.washington.edu>
Anyone using the penalised partial likelihood routines in survival5 should
update their version.
A bug has been fixed in the S package: in coxph() models with penalised
likelihood and strata it was possible in some circumstances to get an
infinite loop or perhaps an incorrect answer.
The new version (2.3) is on cran.r-project.org and will percolate through
CRAN in the next few days.
-thomas
Thomas Lumley Asst. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
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|
announce: survival5 bug fix
|
<Pine.GSO.4.21.0101151050480.18938-100000@atlas.biostat.washington.edu>
|
Thomas Lumley
| 216 |
From chong at stat.purdue.edu Thu Jun 27 01:05:58 2002
From: chong at stat.purdue.edu (Chong Gu)
Date: Wed, 26 Jun 2002 18:05:58 -0500
Subject: gss_0.7-2
Message-ID: <[email protected]>
A new version of the gss package (gss_0.7-2.tar.gz) is on CRAN now. A
new ssden suite is added for density estimation with up to 4 numeric
r.v.'s; computation in higher dimension can be very slow as numerical
integrations are involved. Support for discrete variables will be
added in the future.
The utility provides limited support for the nonparametric estimation
of graphical models, as conditional independence structures can be
built in via selective inclusion of terms in ANOVA decompositions of
the log density.
d- and dc- functions are provided for the evaluation of pdf and
conditional pdf. p-, q-, pc-, qc- functions are provided for 1-D cdf,
quantiles, conditional cdf, and conditional quantiles, respectively.
r- function is missing.
Bug reports and feature suggestions will be appreciated.
Chong Gu
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|
gss_0.7-2
|
Chong Gu
| 52 |
|
From guido at hal.stat.unipd.it Mon Dec 18 12:09:57 2000
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Mon, 18 Dec 2000 12:09:57 +0100
Subject: R 1.2.0 for Windows
Message-ID: <[email protected]>
A binary distribution of R 1.2.0 to run on
Windows 95, 98, NT4.0 and 2000 on Intel/clone chips is available.
(now at ftp://ftp.stat.unipd.it/users/guido/RWin, from tomorrow,
at CRAN)
guido masarotto
(for the R-core team)
Windows-specific changes to R
=============================
This version has been compiled against msvcrt.dll not crtdll.dll.
This gives small speed increases and generally more accurate results.
Packages compiled against crtdll.dll will still work (as far as we are
aware), but for best results should be re-compiled. (A few packages
need to be re-compiled for 1.2.0 on all platforms, and any that used
malloc directly need to be recompiled on this one.)
This release has a number of changes to bring its behaviour closer to that
of Unix versions of R.
- The default font for graphics on windows(), win.printer() and
win.metafile() devices is now Arial: the font numbers for the
Times New Roman and Arial families have been interchanged.
- The history is only saved when the workspace is (to be compatible with
Unix versions of R) and whether it is restored is controlled by
option --no-restore-history (implied by --no-restore and --vanilla):
the default remains to restore.
- Environment variables R_HISTFILE and R_HISTSIZE can be set to specify
the name of the commands history file (default .Rhistory)
and its maximum size (in lines, default 512).
- More locale support is now enabled where supported by the version of
Windows in use. It means that sorting and comparison of character
strings will be locale-specific. You may not want this (the sort
order in `English_United Kingdom' is aAbB..., for example) and
setting Sys.setlocale("LC_COLLATE", "C") should give the previous
behaviour. Further, users of Windows 9x/ME should be able to use
their native character set for the names of R objects (as NT/2000
users always have: this is caused by the change to msvcrt.dll).
(For the benefit of those used to Unix, LC_ALL can be set in the
environment, although this is not usually supported by Windows,
and setting individual LC_* such as LC_COLLATE will also work.)
- It is possible to make DVI and HTML versions of the manuals:
see file INSTALL in the source distribution.
- New utility Rcmd.exe to emulate R CMD : see below.
- unlink() now works the same way on Windows and Unix. Thus on
Windows it no longer deletes empty directories, but has a new
argument recursive=TRUE to delete directories (empty or not).
- The startup code looks for .Renviron, a file pointed to by
environment variable R_ENVIRON and then .Renviron in the home
directory. This file can contain lines of the forms NAME=value
and NAME=${NAME1-value} to take the value of NAME1 if set (and not
empty), otherwise `value'.
- make check no longer makes R, just runs the tests (as make test
always has). Tests are run in the C locale.
Gui changes
-----------
- There are new console menu items `Load History' on the File menu and
`Clear console' on the Edit menu. (The current line is not cleared.)
- The menu items `Load/Save Image' are now called `Load/Save Workspace'.
- The Print menu item on the File menu of a console or pager now prints
the selection if there is one, and the whole (saved) contents otherwise.
- There is a new `Save to File' item on the File menu of a console or
pager which saves the selection if there is one, and the whole
(saved) contents otherwise.
- The Rgui console now uses the same history mechanism as Rterm. The
history limit is now just on the number of lines (rather than on the
number of lines and the total size). The mechanism has been altered
so that Rterm records repeated lines (as Rgui always did).
- There are some additional command-line editing commands in Rgui: see
the Help | Console information screen. (There is also one
addition, ^W, in Rterm: see README.rterm.)
- Selection works slightly differently: if the selection extends beyond
the last character on the line the (invisible) CRLF is made part of
the selection, but not if only up to the last character is selected.
- The data editor is no longer modal (which seems not to have worked
properly in the GraphApp toolkit) and this allows its popups to be
modal.
- The size of the console scroll buffer can be set in file Rconsole,
and resized (upwards) via the GUI preferences editor.
- The GUI console copes much better with receiving output (e.g. from
tcltk interactive functions) during input.
New utilities for preparing packages
------------------------------------
There are several new utilities in the rw1020sp.zip distribution.
The utilities Rd2dvi.sh Rd2txt Rdconv Rdindex Sd2Rd are no longer
batch files but accessed through a new front-end Rcmd.exe, so if this
is in your path (otherwise use ...\rw1020\bin\Rcmd) you can use
Rcmd Rd2dvi.sh [options] files
Rcmd Rd2txt file
Rcmd Rdconv [options] file
Rcmd Rdindex [options] files
Rcmd Sd2Rd [options] file
There are new utilities INSTALL, REMOVE, SHLIB which can be used
to install a source package, remove a package and make a DLL, and
implementations of the Unix R utilities BATCH, build and
check. Invoke these by
Rcmd INSTALL [options] pkgdir(s)
Rcmd REMOVE [options] pkg(s)
Rcmd SHLIB [options] file(s)
Rcmd build [options] pkgdir(s)
Rcmd check [options] pkgdir(s)
Rcmd BATCH [options] infile [outfile]
Use option --help with any of these for fuller details.
The default for options("papersize") is set according to the locale,
and so might be set to "letter" under US or Canadian versions of
Windows.
Rterm in interactive use sets the title of the window it is running
in, and unsets it when it terminates.
The Windows memory manager proved to be (far) too slow to work with
the new generational garbage collector, so it has been replaced. The
current memory manager rarely releases memory back to Windows (but
reuses memory very efficiently) so total memory usage will often grow
slowly over the course of a session. Memory used for transient large
objects will normally be returned at garbage collection. (Once memory
usage has gone over the 256Mb of address space that is initially
reserved, it is unlikely to be reduced much, but the allocated memory
will be reused.) You can compile R to use the Windows memory manager
if you need to.
New function memory.size() showing the amount of memory currently in
use or the maximum that has been used.
New command-line option --max-mem-size to set the maximum memory
allocation: it has a minimum allowed value of 10M. This is intended
to catch attempts to allocate excessive amounts of memory which may
cause other processes to run out of resources. The default is the
smaller of the amount of physical RAM in the machine and 256Mb.
DLLs for packages (including standard packages supplied with R)
automatically gain version information when compiled under this
version. (Use the Version tab on the Properties dialog box to see it,
or the new function DLL.version() within R.)
Windows (.hlp) help files now have hyperlinks to other objects within
the same package.
The windows() graphics device has a new argument `record' to set the
initial state of the recording flag, and this defaults to the setting
of the option "graphics.record" (and that defaults to FALSE).
The windows() graphics device has new options for what happens when it
is resized, which can be set from the command line of from the menu.
See ?windows for details.
New function bringToTop() to bring a graphics window to the top of the
windows stack (useful from menu actions, ...).
If the options setting for a pager or editor (or the editor argument
to edit.default) is a path containing a space, it is automatically
quoted if not already quoted.
The range of allowed text sizes in a windows/win.print device has been
increased, so smaller values of cex will work. (The smallest allowed
text size is 2pt not 8pt.)
Interactive use of Rterm.exe on Windows 2000 systems is now possible
(including under ESS).
Better rendering of wide (lwd > 1) and dashed (lty != "solid") lines
on the windows/win.print device.
The installer rwinst.exe when first asked to install a package tries
to find a current installation of R, first from R_HOME if set in the
environment, then from the PATH (it looks for ...\rw1020\bin).
make pkgcheck-foo will unzip zipped example files if needed.
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|
R 1.2.0 for Windows
|
Guido Masarotto
| 337 |
|
From plummer at iarc.fr Wed Dec 26 11:15:29 2001
From: plummer at iarc.fr (Martyn Plummer)
Date: Wed, 26 Dec 2001 11:15:29 +0100 (CET)
Subject: RPM binaries of R 1.4.0 for RedHat/Mandrake/Linuxppc
Message-ID: <[email protected]>
RPM based binary distributions of R 1.4.0 are avaiable on CRAN for the
following flavours of Linux:
Distribution Version Platform Packager
Red Hat 7.x intel Martyn Plummer <plummer at iarc.fr>
Red Hat 7.x alpha Naoki Takebayashi <ntakebay at bio.indiana.edu>
Red Hat 6.x intel Stephen Eglen <stephen at gnu.org>
Mandrake 8.1 intel Michele Alzetta <mikalzet at libero.it>
LinuxPPC ppc Alex Buerkle <buerkla at uwec.edu>
The RPMS are
R-base: The base distribution
R-recommended: Recommended packages
Given the recent problems with CRAN being cracked, I would like to
remind you that all of these binary distributions are signed with
gpg by their respective maintainers. To verify the gpg signature
of an rpm use a command like
rpm --checksig R-base-1.4.0-1.i386.rpm
First you must download the public key of the package maintainer
from a public key server (see the man page for gpg).
Martyn Plummer
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Send "info", "help", or "[un]subscribe"
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|
RPM binaries of R 1.4.0 for RedHat/Mandrake/Linuxppc
|
Martyn Plummer
| 295 |
|
From mikalzet at libero.it Tue Jun 26 21:13:02 2001
From: mikalzet at libero.it (mikalzet at libero.it)
Date: Tue, 26 Jun 2001 21:13:02 +0200 (CEST)
Subject: R-1.3.0 RPM for Mandrake 8.0
Message-ID: <[email protected]>
An RPM of R-1.3.0 for Mandrake 8.0 is available on CRAN.
I am no longer supporting Mandrake < 8; anyone needing
an RPM for Mandrake < 8 can quite easily build it
(contact me if you need instructions).
--
Michele Alzetta
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|
R-1.3.0 RPM for Mandrake 8.0
|
mikalzet at libero.it
| 251 |
|
From p.murrell at auckland.ac.nz Tue Oct 31 19:52:09 2006
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Wed, 01 Nov 2006 07:52:09 +1300
Subject: R News, volume 6, issue 4 is now available
Message-ID: <[email protected]>
Hi
The October 2006 issue of R News is now available on CRAN under the
Documentation/Newsletter link.
Paul
(on behalf of the R News Editorial Board)
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
|
R News, volume 6, issue 4 is now available
|
Paul Murrell
| 461 |
|
From p.murrell at auckland.ac.nz Fri Jun 2 00:11:01 2006
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Fri, 02 Jun 2006 10:11:01 +1200
Subject: DSC 2007 info
Message-ID: <[email protected]>
Hi
This is a second announcement and call for abstracts.
Please forward and circulate to other interested parties.
DSC 2007, a conference on systems and environments for statistical
computing, will take place in Auckland, New Zealand on February 15 & 16,
2007.
We invite abstracts on the development of software systems and computing
environments for interactive statistics. The workshop will focus on,
but is not limited to, open source statistical computing.
The deadline for submitting abstracts is 2006-10-15 (October 15th).
Please send abstracts (one page) to dsc2007 at stat.auckland.ac.nz
The workshop web page (including on-line registration) is now available
at http://www.stat.auckland.ac.nz/dsc-2007/
Paul
(on behalf of the Organising Committee)
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
|
DSC 2007 info
|
Paul Murrell
| 455 |
|
From pd@me@ @ending from cb@@dk Thu Dec 20 09:33:30 2018
From: pd@me@ @ending from cb@@dk (Peter Dalgaard)
Date: Thu, 20 Dec 2018 08:33:30 +0000
Subject: R 3.5.2 is released
Message-ID: <[email protected]>
The build system rolled up R-3.5.2.tar.gz (codename "Eggshell Igloo") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.5.2.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 3bba37aa1dd06de3f781200a8081302f
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 2e406d65b35c6e2f6f0cf07ce12f1697
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 591dcf615162127f904e4e461f330ce9
MD5 (R-latest.tar.gz) = 3e4b40b2bbd4a2f8133ac45dbef6a485
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 08158353102084599797db8c9ccf8e2a
MD5 (VERSION-INFO.dcf) = 2f0bb13198cfc16ce69d0c61d8cd57ad
MD5 (R-3/R-3.5.2.tar.gz) = 3e4b40b2bbd4a2f8133ac45dbef6a485
2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
98df47801c33cc4f4a4de98447cb2bd40e09c0920195f540a981ceed874714f2 FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
c1bb84ce9fb277e742e2545506c8d1233deb8d397c65329b9325162675a2516c NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
ca04f78ffe54afa326fe3ed40e7e1411aca0000ed2fa5ead97ddf51c6aa5b7bc NEWS.2
e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62 R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
2d2e85e85574c4430951f6b070c08cd5aff1602abfd1bb162bed6d89c436b11f THANKS
9d0e6e7f442952001c174cfc235cc4e6ec97f6e73865f605da30abf34f116fb0 VERSION-INFO.dcf
e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62 R-3/R-3.5.2.tar.gz
This is the relevant part of the NEWS file:
CHANGES IN R 3.5.2:
PACKAGE INSTALLATION:
* New macro CXX_VISIBILITY analogous to C_VISIBILITY (which several
packages have been misusing for C++ code) for the default C++
compiler (but not necessarily one used for non-default C++
dialects like C++14).
TESTING:
* The random number generator tests in tests/p-r-random-tests.R no
longer fail occasionally as they now randomly sample from
"certified" random seeds.
BUG FIXES:
* The "glm" method of drop1() miscalculated the score test
(test="Rao") when the model contained an offset.
* Linear multiple empty models such as lm(y ~ 0) now have a
correctly dimensioned empty coefficient matrix; reported by Brett
Presnell.
* vcov(<empty mlm>) and hence confint() now work (via a consistency
change in summary.lm()).
* confint(<multiple lm()>) now works correctly; reported on R-devel
by Steven Pav.
* quade.test() now also works correctly when its arguments are not
yet sorted along groups, fixing PR#15842.
* Installation on a Unix-alike tries harder to link to the pthread
library where required (rather than relying on OpenMP to provide
it: configuring with --disable-openmp was failing on some Linux
systems).
* The data.frame method for print(x) is fast now also for large
data frames x and got an optional argument max, thanks to
suggestions by Juan Telleria.
* hist() no longer integer overflows in very rare cases, fixing
PR#17450.
* untar() ignored a character compressed argument: however many
external tar programs ignore the flags which should have been set
and automagically choose the compression type, and if appropriate
gzip or bzip2 compression would have been chosen from the magic
header of the tarball.
* zapsmall(x) now works for more "number-like" objects.
* The tools-internal function called from R CMD INSTALL now gets a
warnOption = 1 argument and only sets options(warn = warnOption)
when that increases the warning level (PR#17453).
* Analogously, the tools-internal function called from R CMD check
gets a warnOption = 1 argument and uses the larger of that and
getOption("warn"), also allowing to be run with increased warning
level.
* Parse data now have deterministic parent nodes (PR#16041).
* Calling match() with length one x and POSIXlt table gave a
segfault (PR#17459).
* Fork clusters could hang due to a race condition in cluster
initialization (makeCluster()).
* nextn(n) now also works for larger n and no longer loops
infinitely for e.g, n <- 214e7.
* cooks.distance() and rstandard() now work correctly for multiple
linear models ("mlm").
* polym() and corresponding lm() prediction now also work for a
boundary "vector" case fixing PR#17474, reported by Alexandre
Courtiol.
* With a very large number of variables terms() could segfault
(PR#17480).
* cut(rep(0, 7)) now works, thanks to Joey Reid and Benjamin Tyner
(PR#16802).
* download.file(*, method = "curl", cacheOK = FALSE) should work
now on Windows, thanks to Kevin Ushey's patch in PR#17323.
* duplicated(<dataframe with 'f'>) now works, too, thanks to
Andreas Kersting's PR#17485; ditto for anyDuplicated().
* legend(*, cex = 1:2) now works less badly.
* The print() method for POSIXct and POSIXlt now correctly obeys
getOption("max.print"), fixing a long-standing typo, and it also
gets a corresponding optional max argument.
* Unserialization of raw vectors serialized in ASCII representation
now works correctly.
* <data frame>[TRUE, <new>] <- list(c1, c2) now works correctly,
thanks to Suharto Anggono's PR#15362 and Emil Bode's patch in
PR#17504.
* seq.int(*, by=by, length=n) no longer wrongly "drops fractional
parts" when by is integer, thanks to Suharto Anggono's report
PR#17506.
* Buffering is disabled for file() connections to non-regular files
(like sockets), as well as fifo() and pipe() connections. Fixes
PR#17470, reported by Chris Culnane.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.5.2 is released
|
Peter Dalgaard
| 690 |
|
From jago at mclink.it Mon Sep 3 01:08:15 2001
From: jago at mclink.it (Stefano Iacus)
Date: Mon, 3 Sep 2001 01:08:15 +0200
Subject: R-1.3.1 for both MacOS version released
Message-ID: <[email protected]>
Version 1.3.1 of R(s) for MacOS have been released.
They will be mirrored starting from tomorrow at CRAN.
For the Carbon version (MacOS 8.6 to 9.2 and OSX) refer to
http://cran.r-project.org/bin/macos/rm131
and for the Darwin/X11 version refer to
http://cran.r-project.org/bin/macosx/rx131
(this last was already announced by Jan de Leeuw and now mirrored at
CRAN).
Stefano M. Iacus
What follows are specific changes to Carbon R.
rm131
=====
* Added the "Config" menu
* Fixed a bug in the lapack module. Complex functions are now
available.
* Added MPW makefiles to build standard libraries and modules
* Added experimental script to build R via Apple's MRC compiler
* Now R needs a new shared library "f2c" lib that will increase
portability for all fortran based packages
* Added support for apple events. R begins to be a scriptable
application. Very limited support by now but will increase soon.
Some demo scripts have been added.
* link.html.help() function has been added by picking windows code.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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|
R-1.3.1 for both MacOS version released
|
Stefano Iacus
| 269 |
|
From maechler at lynne.stat.math.ethz.ch Thu May 21 11:01:46 2015
From: maechler at lynne.stat.math.ethz.ch (Martin Maechler)
Date: Thu, 21 May 2015 11:01:46 +0200
Subject: The R Foundation announces new mailing list 'R-package-devel'
Message-ID: <[email protected]>
New Mailing list: R-package-devel -- User R Packages Development
At last week's monthly meeting, the R foundation has decided to
create a new mailing list in order to help R package authors in
their package development and testing.
The idea is that some experienced R programmers (often those
currently helping on R-devel or also R-help) will help package
authors and thus unload some of the burden of the CRAN team
members.
Please read the detailed description of the mailing list here,
https://stat.ethz.ch/mailman/listinfo/r-package-devel
or also the more extended announcement of the list on R-devel,
archived at
https://stat.ethz.ch/pipermail/r-devel/2015-May/071208.html
For the R foundation,
Martin Maechler, Secretary General
|
The R Foundation announces new mailing list 'R-package-devel'
|
Martin Maechler
| 201 |
|
From rgentlem at jimmy.harvard.edu Fri Mar 21 16:01:47 2003
From: rgentlem at jimmy.harvard.edu (Robert Gentleman)
Date: Fri, 21 Mar 2003 10:01:47 -0500
Subject: ArrayAnalyzer and Bioconductor
Message-ID: <[email protected]>
Today, Insightful Corporation (www.insightful.com) is announcing the
availability of S+ArrayAnalyzer, a new, integrated module for S-PLUS
based on collaboration with the BioConductor Project
(www.bioconductor.org) - an open source and open development software
project for the analysis and comprehension of genomic data.
The collaboration between Insightful and BioConductor delivers
benefits to both commercial and academic researchers analyzing
microarray experiments:
- BioConductor's advanced analytics for genomic data will be available
to a wider audience via a commercially supported product from
Insightful, a long-established vendor with fully staffed tech
support, training, and consulting.
- S+ArrayAnalyzer adds numerous features that can improve productivity
for many users, such as installation, more data access and import
options, a guided-workflow interface, interactive graphs with
hyperlinked annotation, Web deployment of applications.
- Insightful will sponsor a graduate student position in the
BioConductor project to help drive continued advancements and
innovation in both the open source and commercial offerings.
- A new differential expression library (lpetest), written by
Insightful and the University of Virginia, will be ported to R and
made available on the Comprehensive R Archive Network (CRAN) and
BioConductor in Summer 2003.
Spokespeople for BioConductor see the collaboration as helping ensure
the distribution and high-level end-user support of key research tools
to the broadest possible population of researchers. These people
include: S.Dudoit, Division of Biostatistics, University of
California, Berkeley; R.A. Irizarry, Department of Biostatistics,
Johns Hopkins University; V.J. Carey, Harvard Medical School;
R. Gentleman, Harvard School of Public Health.
Shawn Javid, Insightful's CEO had this to add, "The collaboration with
BioConductor is a blueprint for how Insightful can work with the open
source community to bring highly innovative data analysis applications
to the widest possible user base. This cooperation improves the
analytic solutions available to our common base of S programmers and
the non-statisticians who benefit from using applications developed
with S-PLUS and R."
S+ArrayAnalyzer is available now with pricing for commercial and
academic organizations available by calling (800)569-0123 x479, or via
email at pharmasales at insightful.com
|
ArrayAnalyzer and Bioconductor
|
Robert Gentleman
| 161 |
|
From guido at sirio.stat.unipd.it Fri Nov 6 09:30:25 1998
From: guido at sirio.stat.unipd.it (Guido Masarotto)
Date: Fri, 6 Nov 1998 09:30:25 +0100
Subject: R-0.62.4 for MsWindows (again)
Message-ID: <[email protected]>
I apologize but I made an error and just sent the message with the
same 'subject' without saying that the files can be found
in the R/bin/ms-windows/win-32-devel directory at CRAN
(in this moment only at the Wien site, I suppose).
In addition, please, replay to this message not to the one before.
guido
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-0.62.4 for MsWindows (again)
|
Guido Masarotto
| 555 |
|
From ht at heatherturner.net Thu Jun 23 12:13:41 2011
From: ht at heatherturner.net (Heather Turner)
Date: Thu, 23 Jun 2011 11:13:41 +0100
Subject: The R Journal Vol. 3/1 now published
Message-ID: <[email protected]>
Dear All,
The first issue of the third volume of The R Journal is now available at
http://journal.r-project.org/current.html.
Thanks to everyone involved.
Heather
--
Editor in chief
Heather.Turner at r-project.org
|
The R Journal Vol. 3/1 now published
|
Heather Turner
| 401 |
|
From guido at hal.stat.unipd.it Tue Apr 13 10:08:52 1999
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Tue, 13 Apr 1999 09:08:52 +0100
Subject: R-0.64.0 for Win9X/WinNT
Message-ID: <[email protected]>
Windows binaries and source at CRAN (binaries/windows/Windows-NT/base)
have been updated to R-0.64.0.
Pre-compiled packages for this version of R are provided by
Brian D. Ripley and available CRAN/binaries/Windows-NT/contrib.
Brian Ripley is also mantaining a FAQ for this version of R
(linked in the main R FAQ at CRAN or available directly
at http:/www.stats.ox.ac.uk/pub/R/rw-FAQ.html).
WINDOWS NEWS:
============
R-0.64 uses platform-independent code for file handling. Files are
displayed under a pager in a separate window rather than in the
console.
Environment variables can be set as NAME=value on the command line,
including in a short-cut.
Content of the pager and of the Rgui's console can be printed
by File | Print.
The help, latex and example files can be stored in zip files to save
space; this is used for the base package.
The menus are enabled/disabled and check-marked correctly under NT.
We hope to have solved the 'rw0633 font dimension problem' shown
under some NT version.
read.fwf works if you have Perl installed.
help(, offline=TRUE) will work if you have latex installed and
customize RHOME/bin/helpPRINT.bat. The optional rw0640l.zip
contains the latex sources.
The sockets code is compiled in, but we have not tested it.
system() has new arguments `invisible' and `minimized'.
=================================================================
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-0.64.0 for Win9X/WinNT
|
Guido Masarotto
| 476 |
|
From maechler at stat.math.ethz.ch Tue Nov 26 18:39:45 2002
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 26 Nov 2002 18:39:45 +0100
Subject: R-announce moved from majordomo to [procmail+mailman]
Message-ID: <[email protected]>
I have moved the R-announce mailing list from the Majordomo
software to a combination of procmail & mailman an hour or so ago.
You find a link in the footer of this message giving an URL
where you can modify your subscription, look at the archives
(everything from the beginning in 1997) and more.
CHANGE: Postings to R-announce are now moderated, ie.
they have to be approved by a list maintainer
unless they come from one of a small set of R developers.
Note that *everyone* subscribed to R-help also gets R-announce
messages without a need to subscribe.
Notice that the "Sender:" field of these e-mails has changed
from owner-r-announce to r-announce-admin. Those who use
mail-filtering rules may wish to adapt.
We expect faster mail delivery and an easier user (and
maintainer!) interface. Feedback welcome, to me privately or R-help.
The R-help mailing list (and its "digest") version will move to
mailman too.
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
|
R-announce moved from majordomo to [procmail+mailman]
|
Martin Maechler
| 105 |
|
From ihaka at stat.auckland.ac.nz Wed Apr 23 11:25:23 1997
From: ihaka at stat.auckland.ac.nz (Ross Ihaka)
Date: Wed, 23 Apr 1997 21:25:23 +1200 (NZST)
Subject: Version 0.49 Released
Message-ID: <[email protected]>
The newest version of R for Unix (version 0.49) is now available
(or soon will be) from the following sites.
NORTH AMERICA:
http://lib.stat.cmu.edu/R/Alpha
EUROPE:
ftp://ftp.stat.math.ethz.ch/R/
ftp://statlab.uni-heidelberg.de/pub/mirrors/auckland/R/
JAPAN:
ftp://ftp.u-aizu.ac.jp/pub/lang/R/
NEW ZEALAND:
ftp://stat.auckland.ac.nz/pub/R/
Please obtain a copy from site close to you. Note that New Zealand
is not close to anywhere other than itself :-).
This version adds considerable functionality and (we hope) stability
to R. Most notably, the object system is now very close to that
of S and we now have a fairly full implementation of complex
arithmetic.
The jump in version number (from 0.16) relects the fact that we
feel that this version of R represents quite a jump toward what we
hope will be in our eventual 1.0 release. However the version is
numbered 0.49 rather than the 0.50 we touted because it falls a
little short of what we really want for 0.50.
Immediate development of R will focus on creating a coherent way
of loading and unloading "libraries" and creating a good framework
for documentation (can you say "SGML" - I knew you could).
A (partial) list of changes from 0.16.1 follows. A list of known
problems is kept in the file "TASKS" in the distribution and a list
of problems we think are solved is in "TASKS.OLD"
R + R
-------------------------------------------------------------------
CHANGES IN VERSION R VERSION 0.49 ALPHA
NEW FEATURES
o The ``object'' system has been changed substantially. The
behavior of both "UseMethod" and "NextMethod" should match that
in S. Group methods for "Math", "Ops" and "Summary" are
available.
o Complex arithmetic is now implemented. Many mathematical
functions are now defined for complex arguments (e.g. sqrt,
exp, log, sin, cos, tan, asin, acos, atan). There is no
complex gamma function or log gamma function yet. The summary
functions "mean", "sum", "prod", "cumsum" and "cumprod" work
correctly when (some of) their arguments are complex. Other
functions such as "solve" are not "complex aware" yet, but do
print warning messages about coercion of complex values
to real by the dropping of imaginary parts.
S and R do not return identical results in all cases:
S> atan(tan(1i))
[1] 0-1i
R> atan(tan(1i))
[1] 0+1i
[ Is this just a difference on the branch cut boundary? ]
o The full set of S graphics symbols is now available with pch=0:18.
In addition, there is a special set of R plotting symbols which
can be obtained with pch=29:25.
pch=19 solid circle
pch=20 bullet
pch=21 circle
pch=22 square
pch=23 diamond
pch=24 triangle point-up
pch=25 triangle point down
The symbols 21:25 can be colored and filled with different colors.
For example, the expression
points(x, y, pch=21, col="red", bg="yellow")
will plot the points using a symbol consisting of a red circle with
a yellow interior.
o There is a new "family" argument to the postscript graphics driver
which can be set to any of "AvantGarde", "Bookman", "Courier",
"Helvetica", "Helvetica-Narrow", "NewCenturySchoolbook", "Palatino"
or "Times". In addition, setting font=5 will cause the "Symbol"
family to be used. This is still experimental and it is hard to
see it being useful without some sort of math capability.
[ Such a facility is "on the drawing board". ]
o The graphics parameter "las" is now implemented and can be used
to rotate axis labels. E.g. plot(1:10, las=1) .
o The hyperbolic and inverse hyperbolic functions cosh, sinh, tanh,
acosh, asinh and atanh are now implemented for both real and complex
arguments. (Q: are the underlying functions available on all
platforms, or do we need compatibility fixes?)
o "log" has changed so that it will accept an optional "base" argument.
"log2" and "log10" are implemented this way.
o "atan" can now either be invoked as atan(x) or atan(x,y).
o The behavior of "fft" has been modified to match that of S
(i.e. it returns a complex value. There is also a function
"mvfft" which performs a "vector transform" when passed a matrix
(i.e. it applies the fft to each column, rather than doing a
2d spatial transform).
o A new functon "polyroot" can be used to find the roots of
polynomials with (real or) complex coefficients.
o Vectors and lists are now "stretchy". This means that the
following is legal
x <- 1:10
x[20] <- 12
[ Note that there is a bug in S. When you try this kind of
extension - the "dim" and "dimname" attributes are not dropped,
leading to "invisible" elements in the result. ]
o Symbolic differention is now available using the functions "D"
and "deriv". The results are slightly difference in appearance
from those of S (which tends to put in a few too many parentheses),
but should provide identical semantics. To see the nature of the
difference, try the expression
D(expression(tan(x)/x^2),"x")
in both systems.
These functions are implemented as internal code in R (what's the
point in having a nice little underlying lisp if you don't use it
for obvious list processing applications?).
o A new function "grep" has been implemented. It performs regular
expression matching based on POSIX 1003.3. The function uses the
"regex" library written by Henry Spencer (the same one that Perl
uses). Grep is now used to provide a pattern matching facility
in "objects" and "ls". In addition, there are functions "sub"
and "gsub" which operate the same way as those in "nawk". Note
that "\" must be escaped to get it into a string, so if you want
a literal "\" you must type "\\\\" :-(.
o A new "methods" function written by Martin Maechler replaces the
older less sophisticated one. This has also been converted to use
the new "grep" function.
o A new version of model.frame from Thomas Lumley is included.
o Factors and ordered factors are now "objects" with class attributes
which match those in S. This change is primarily so that applications
written for S will work in R. The underlying implementation for
factors and ordered factors still uses special underlying types.
o R will now do conditioning plots as described in the S "Models" book.
Some thought is going into "doing trellis".
o Thomas Lumley's "require" and "provide" functions for library
organization added.
o There is a new graphical parameter "gamma" which is designed to
let users apply a ``gamma'' correction for their graphics
displays. Most monitors produce a color intensity which is
related to voltage by the equation
intensity = voltage ^ gamma
with gamma about 2.5 for most PC monitors. A typical symptom
of this non-linearity is that a colorwheel produced by
piechart(rep(1,48), col=48)
shows a marked over representation of the red, green and blue
and blue primaries. If this is the case try
par(gamma=1/2.5)
and redraw the color wheel. Vary gamma till you have a "nice"
spectrum. This is experimental and feedback would be welcome.
(If this is useful we will do the same for postscript).
BUG FIXES & ENHANCEMENTS
o The internals of the postscript device drivers have been rewritten
in preparation for "doing equations". The Adobe font metrics
are no longer processed during the build process. The original
files are now processed directly by the driver. The postscript
emitted by the drivers should conform to the Adobe 3.0 standard.
o Typos and logic errors in "crossprod" pointed out by Arne Kovac
have been fixed.
o "round" now works using IEEE rounding on platforms which support it.
E.g.
> round(.5 + -3:7)
[1] -2 -2 0 0 2 2 4 4 6 6 8
o A change to the PostScript graphics device driver change should
stop plots from rotating unexpectedly when viewed with ghostview
and other postscript viewers.
o Patches from Kurt Hornik for "structure" and "help" have been applied.
o "names" applied to 1-d arrays now does the "right thing" i.e. it
returns the first component of the "dimnames" attribute rather than
NULL. Subsetting a 1-d array as a vector will produce a "names"
attribute on the result.
o "atan" will now accept either 1 or 2 arguments ("atan2" still exists).
o "nchar" and "format" preserve "dim" and "dimname" attributes where
possible.
o There were problems with arguments in "switch". These have been
fixed. There appears to be a bug in S with the expression
z <- switch(1, a=, b=10, 20)
mode(z)
They appear to return a "missing argument". We die with an error
message. What is the right thing to do here?
o Problems deparsing arguments of the form "a"= and a=, have been fixed.
o The default graphics line width is now 1 rather than 0.
o "as.is" problem in "read.table" pointed out by Peter Dalgaard fixed.
o paste(list(character(0),""), 1:2) no longer causes a segfault.
"as.character" applied to a list now returns the vector obtained
by deparsing each element of the list.
o "attach" now attaches objects at pos=2 when directed.
o Memory usage was measured in 1000 byte chunks with the -v flag.
This has been changed to 1024 byte chunks.
o Dependency on the "OSF sprintf bug" has been removed.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
|
Version 0.49 Released
|
Ross Ihaka
| 565 |
|
From p.dalgaard at biostat.ku.dk Tue Apr 19 01:17:12 2005
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 19 Apr 2005 01:17:12 +0200
Subject: Re-release of R 2.1.0
Message-ID: <[email protected]>
Due to a mishap in the build procedure, the originally released
sources erroneously had "2.2.0" in several places within the
"configure" file. A re-released version has been put up in
http://biostat.ku.dk/~pd/R-release/
and should find its way to CRAN and its mirrors some time tomorrow.
The new files have md5 sums as follows:
94d55d512a9ba36caa9b7df079bae19f COPYING
d8045f3b8f929c1cb29a1e3fd737b499 COPYING.LIB
70447ae7f2c35233d3065b004aa4f331 INSTALL
8b78e12b100a6834fdada2dfaab98ab0 NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
fb47b1fdef4323031e24d541a2f36b2b R-2.0.1.tar.gz
270f7a7382e8cb10a353148598f91096 R-2.1.0.tar.gz
d8a2d5461c16aa37b1418c0500423bec R-2.1.0.tar.gz-split.aa
9a8e7b5988fc4e43b56561cbb6853534 R-2.1.0.tar.gz-split.ab
dfb0600d8726613ac5a424bbd054c243 R-2.1.0.tar.gz-split.ac
150903071850a951722713560834029a R-2.1.0.tar.gz-split.ad
cb416f351d0c9c75a86c27998d691372 R-2.1.0.tar.gz-split.ae
d8e01f2b68d2f689444901ae1957c396 R-2.1.0.tar.gz-split.af
3949c2649d595683fe26212dc292f4b1 R-2.1.0.tar.gz-split.ag
4e984f0b2dacf5d52657b04e874756d9 R-2.1.0.tar.gz-split.ah
c0f6e6135e54bd5d8917c804ec4b9b15 R-2.1.0.tar.gz-split.ai
270f7a7382e8cb10a353148598f91096 R-latest.tar.gz
56a780cdec835c5c598f8dfc0738f7f3 README
AFAIK, the Windows build doesn't use "configure", so should be OK.
Source builds get (at least) Makeconf wrong, causing the following
symptom:
> library(MASS)
Warning message:
package 'MASS' was built under R version 2.2.0
In that case, you'll need to rebuild with the corrected "configure".
You can get the file separately from
https://svn.r-project.org/R/tags/R-2-1-0/configure
Apologies for the inconvenience.
-pd
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
Re-release of R 2.1.0
|
Peter Dalgaard
| 389 |
|
From jfox at mcmaster.ca Wed Jan 9 19:07:06 2002
From: jfox at mcmaster.ca (John Fox)
Date: Wed, 09 Jan 2002 13:07:06 -0500
Subject: new version of sem package
In-Reply-To: <a0501040bb7da2378d939@[163.1.41.88]>
Message-ID: <[email protected]>
Dear R-announce list members,
I've just uploaded to CRAN a substantially revised version (0.6-0) of the
sem (structural-equations model) package. The new version uses a formula
for the gradient to fit generalized SEMs, and also allows symbolic
specification of the model.
As always, comments and suggestions are appreciated.
John
-----------------------------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
email: jfox at mcmaster.ca
phone: 905-525-9140x23604
web: www.socsci.mcmaster.ca/jfox
-----------------------------------------------------
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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|
new version of sem package
|
John Fox
| 1 |
|
From luke at stat.uiowa.edu Thu Mar 26 15:17:29 2009
From: luke at stat.uiowa.edu (luke at stat.uiowa.edu)
Date: Thu, 26 Mar 2009 09:17:29 -0500 (CDT)
Subject: Travel funding for DSC/useR 2009 for young researchers at U.S.
institutions
Message-ID: <[email protected]>
*** Travel and Accommodation Support ***
[Deadline extended to April 15, 2009]
Funds from the U.S. National Science Foundation may be available to
provide partial support for travel and accommodation for some graduate
students and junior faculty at U.S. post-secondary institutions to
attend DSC 2009 and useR 2009. If you wish to apply for this support,
please send an application to luke at stat.uiowa.edu. Your application
should include
a brief CV
a copy of your abstract if you have submitted a paper or a poster
a statement that demonstrates your eligibility, your need for
support, and an amount of support requested
students should include a brief letter of support from their
supervisor
faculty or post-doc applicants should include a brief statement
about other funding sources
The allocation will be based on merit and need; women and minority
candidates are encouraged to apply.
Applications must be made by April 15 (2009-04-15) and successful
applicants will be notified by email soon thereafter.
Please visit the conference web pages at
http://www.r-project.org/dsc-2009/ and
http://www.agrocampus-rennes.fr/math/useR-2009/
for conference details.
--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke at stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
|
Travel funding for DSC/useR 2009 for young researchers at U.S. institutions
|
luke at stat.uiowa.edu
| 650 |
|
From p.dalgaard at biostat.ku.dk Fri Dec 4 15:22:23 1998
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 04 Dec 1998 15:22:23 +0100
Subject: R-0.63.1 is released
Message-ID: <[email protected]>
I've put up R-0.63.1.tgz up for FTP from Auckland some minutes ago.
As usual, don't get it from there unless you are desperate, but wait
for it to be mirrored at a CRAN site near you within a day or two.
For those who *are* desperate, I've left a copy in
ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.63.1.tgz
(Be gentle, that's my desktop PC!)
The person who fetched R-0.63 *from New Zealand* last time might
prefer ftp.stat.auckland.ac.nz, though...
There's also a version split in two for floppies and a patch file if
you prefer that.
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 0.63.1
NEW FEATURES
o new function mosaicplot().
o xy.coords(.) has a "recycle = FALSE" argument, used in text().
o RNGtype() allows to choose different Random Number Generators.
__EXPERIMENTAL__
o print.default(.) now also works with a `right = TRUE' argument.
{{ print.matrix(.) is bound to become deprecated... }}
o new help page `Memory' on the usage of command line options
--vsize and --nsize. Error message if R runs out of memory
points to help(Memory).
o rowsum() and improved na.omit() added from survival4
o backsolve(.) has new arguments "upper.tri = TRUE, transpose = FALSE"
o hist() has new "right = TRUE" argument;
"right = FALSE" gives [a,b) intervals
o help() has "htmlhelp" argument, allowing to suppress htmlhelp after
help.start(). This is desired for ESS.
o quantile(.) has an "names = TRUE" argument for speed.
It is much better documented now.
BUG FIXES
o build-help --dosnames should now also work for text help,
latex and examples.
o seq() should work better now (fuzz-factor 1e-7 inserted)
o multiple arguments to return caused value to be a pairlist
o data.frame choked on long names from deparse()
o data.edit now works (dataedit doesn't need pairlist()s anymore)
o as.pairlist(NULL) is ok
o ts(1:5, start=2, end=4) now work. Further plot(ts(..), ts(..))
o eigen() returns $vectors in any case [S compat].
o apply(cbind(1,1:9, 2, quantile) doesn't drop quantile names anymore
o array(1, dim=(1:3)[c(F,F,F)]) is now valid == array(1,NULL) == c(1);
the same for array(a,d, list())
o fix problem with step() and offsets
o drop attributes on matrix subsetting
o kappa(.) now works [dtrco now in load table (ROUTINES)].
o pmin() and pmax() now preserve attributes.
o handle null models arising in drop1(), step, etc.
o partial matching problem with $ indexing
o matplot(.) works with lwd (vectors)
o par("cex.axis") now has the desired effect...
o which(.) now omits NAs in its argument.
o rbind.data.frame caused character-to-factor coercion a bit too often
o couple of messups in dotplot
o z[[1]] <- ~x probl fixed as suggested by J.Lindsey
o do_modelframe could lose contrast attributes
o "make check" needed standardisation of locale
o unlist(...,recursive=F) got names wrong
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-0.63.1 is released
|
Peter Dalgaard BSA
| 561 |
|
From plummer at iarc.fr Mon Oct 28 12:41:28 2002
From: plummer at iarc.fr (Martyn Plummer)
Date: 28 Oct 2002 12:41:28 +0100
Subject: RPMS of R for Red Hat 8.0
Message-ID: <1035805364.993.100.camel@xena>
A binary RPM package of R 1.6.0 for Red Hat 8.0 should now be available
on a CRAN mirror near you. I apologize for the delay, but it took some
time to get a copy of the new Red Hat release.
I shall continue to support Red Hat 7.x.
For the security conscious: in order to check the GPG signature on this
package, you must first import my public key (1024D/97D3544E) into the
RPM database. See the man page for rpm. This is a change from previous
releases of Red Hat.
Martyn
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
RPMS of R for Red Hat 8.0
|
<1035805364.993.100.camel@xena>
|
Martyn Plummer
| 80 |
From pd.mes at cbs.dk Fri Aug 14 11:21:48 2015
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 14 Aug 2015 11:21:48 +0200
Subject: R 3.2.2 is released
Message-ID: <[email protected]>
The build system rolled up R-3.2.2.tar.gz (codename "Fire Safety") this morning.
The list below details the changes in this release. The main point of this release is to enable package installation via secure HTTP, since ordinary HTTP is increasingly being considered a security risk.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = eb97a5cd38acb1cfc6408988bffef765
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = e74e64dde0f92181957d46a0f8538e8b
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 5ff829377f0de5cdb0ad30bb42977611
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = 57cef5c2e210a5454da1979562a10e5b
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb
MD5 (VERSION-INFO.dcf) = 55826f7f976cd9623577e5a9ac694c47
MD5 (R-3/R-3.2.2.tar.gz) = 57cef5c2e210a5454da1979562a10e5b
This is the relevant part of the NEWS file
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.
|
R 3.2.2 is released
|
Peter Dalgaard
| 205 |
|
From snw at mcs.st-and.ac.uk Sun May 5 20:05:12 2002
From: snw at mcs.st-and.ac.uk (Simon Wood)
Date: Sun, 5 May 2002 19:05:12 +0100 (BST)
Subject: mgcv 0.8 released
Message-ID: <Pine.GSO.4.21.0205051856200.21846-100000@dolphin>
mgcv version 0.8-0 is now on CRAN. mgcv provides generalized additive
models with automatic smoothing parameter selection. Models may include
smooths of more than one variable. This release fixes one platform
dependent problem that could result in convergence problems/ unstable
models, provides facilities for using multi-dimensional smooths with very
large data sets, provides a mechanism for conditioning smooths on factors,
allows terms like s(x)+s(y)+s(x,y) in formulae and has improved
convergence diagnostics. Full details are at:
www.ruwpa.st-and.ac.uk/simon/mgcv.html
______________________________________________________________________
> Simon Wood snw at st-and.ac.uk http://www.ruwpa.st-and.ac.uk/simon.html
> The Mathematical Institute, North Haugh, St. Andrews, Fife KY16 9SS UK
> Direct telephone: (0)1334 463799 Indirect fax: (0)1334 463748
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
mgcv 0.8 released
|
<Pine.GSO.4.21.0205051856200.21846-100000@dolphin>
|
Simon Wood
| 34 |
From bates at stat.wisc.edu Mon Nov 22 21:19:17 1999
From: bates at stat.wisc.edu (Douglas Bates)
Date: 22 Nov 1999 14:19:17 -0600
Subject: Release 0.90.0 is also available via rsync
Message-ID: <[email protected]>
The 0.90.0 release of R is also available via anonymous rsync from
rsync.r-project.org. To create a copy of the release tree in a
subdirectory called R-0.90.0 of the current directory you can use
rsync -rC rsync.r-project.org::r-release R-0.90.0
The development tree is also available via anonymous rsync as
rsync.r-project.org::r-devel
The -C option in the rsync command is to cause it to skip the CVS
directories.
Once you have a copy of the tree, you can keep it up to date with an
rsync command like the above. Further information on rsync is
available at http://rsync.samba.org/rsync/
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
Release 0.90.0 is also available via rsync
|
Douglas Bates
| 508 |
|
From pd.mes at cbs.dk Tue Jan 1 19:07:39 2013
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Tue, 1 Jan 2013 19:07:39 +0100
Subject: R version 3.0.0
Message-ID: <[email protected]>
This is no secret to those who read the NEWS file of the development version regularly, as the following has been in place since December 12th:
\section{\Rlogo CHANGES IN R-devel}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item It is intended that this version will be released as \R
3.0.0.
....
However, it seems reasonable to supplement this with a more direct public announcement.
The intended timing is to follow the annual release schedule and have R 3.0.0 around April 1 and a finalizing 2.15.3 a month earlier.
Major R releases have not previously marked great landslides in terms of new features. Rather, they represent that the codebase has developed to a new level of maturity. This is not going to be an exception to the rule.
Version 1.0.0 was released at a point in time when we felt that we had reached a level of completeness and stability high enough to characterize a full statistical system, which could be put to production use.
Version 2.0.0 came out after strong enhancements of the memory management subsystem as well as several major features, including Sweave.
Version 3.0.0, as of this writing, contains only really major new feature: The inclusion of long vectors (containing more than 2^31-1 elements!). More changes are likely to make it into the final release, but the main reason for having it as a new major release is that R over the last 8.5 years has reached a new level: we now have 64 bit support on all platforms, support for parallel processing, the Matrix package, and much more.
On behalf of the R Core Team,
Peter D.
Happy New Year!
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R version 3.0.0
|
Peter Dalgaard
| 427 |
|
From p.dalgaard at biostat.ku.dk Thu Jun 1 11:04:12 2006
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 01 Jun 2006 11:04:12 +0200
Subject: R 2.3.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.3.1.tar.gz a short while ago. This version contains
several minor fixups and removes a couple of bad bugs. See the full list
of changes below.
You can get it (in a short while) from
http://cran.r-project.org/src/base/R-2/R-2.3.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
There is also a version split for floppies. (This will be the last
time we build those.)
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
c663533d4d6c86f2a192c2b86f5bac12 AUTHORS
eb723b61539feef013de476e68b5c50a COPYING
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
7eac2a82dfd523caf7e73eb08ab530a4 FAQ
70447ae7f2c35233d3065b004aa4f331 INSTALL
a592ca1b1582f94d3f468dd7ccb38c18 NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
a1d6d8081af4c71006a6e5a3ed54e4da R-2.3.1.tar.gz
0ae4891a63b3d7ebf82b1ff70c4f2dcb R-2.3.1.tar.gz-split.aa
142e3ecbde7d47b85dcad45782ee3b52 R-2.3.1.tar.gz-split.ab
f6fafac0e6c03dd1523d09960e56c7ca R-2.3.1.tar.gz-split.ac
8a076dd800893b56184819570b8b2863 R-2.3.1.tar.gz-split.ad
5ed399fa2181575ba67c11c81e33dba5 R-2.3.1.tar.gz-split.ae
6074ecc86fad61d679eea80515ab9944 R-2.3.1.tar.gz-split.af
7ba58cf3d6d55044738439518432d846 R-2.3.1.tar.gz-split.ag
e32d05cb40e79b49489ba09cf8fa654c R-2.3.1.tar.gz-split.ah
8e9f7675844031803a2076a73271b2c1 R-2.3.1.tar.gz-split.ai
12a494e22ddd220c4cefdb60cc532308 R-2.3.1.tar.gz-split.aj
a1d6d8081af4c71006a6e5a3ed54e4da R-latest.tar.gz
433182754c05c2cf7a04ad0da474a1d0 README
020479f381d5f9038dcb18708997f5da RESOURCES
4eaf8a3e428694523edc16feb0140206 THANKS
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 2.3.1
NEW FEATURES
o In lm() and glm(), offsets are allowed to be length 1 (and
if so are replicated to the number of cases).
o The \uxxxx notation for Unicode characters in input strings
can now be used on any platform which supports MBCS, even if
the current locale is not MBCS (provided that the Unicode
character is valid in the current character set).
o The quasibinomial() family now allows the "cauchit" link. (PR#8851)
o edit.data.frame() no longer (silently) coerces character columns
to factor.
C-LEVEL FACILITIES
o The variables controlling stack checking are made available via
Rinterface.h to front-ends embedding R: see 'Writing R Extensions'
o R_SignalHandlers (defined in Rinterface.h) can be set to 0 to
suppress the R signal handlers in front-ends embedding R.
INSTALLATION CHANGES
o There have been a number of changes to help installation on
platforms that no one had beta-tested.
- Changes related to older header files, e.g. on Redhat 8.0/9.
- Problems with 'make install' on older (<3) versions of bash
on Solaris and elsewhere.
- AIX 5.2/gcc issues with needing -lm when making modules X11
and vfonts.
- Some versions of Solaris and AIX had a fcntl.h that
redefined 'open' to be 'open64' and thereby broke
compilation of src/main/connections.c and elsewhere.
o 'make uninstall' works better on a build using a named
subarchitecture.
BUG FIXES
o min(), max(), sum() and prod() gave nonsensical answers with
an empty list or raw argument.
o sum() on a data frame did not allow multiple arguments. (PR#8385)
o charmatch() and pmatch() did not specify they applied only to
character vectors. Now they do, and attempt to coerce 'x' and
'target' to character before attempting matching.
o The Summary() methods for data.frame, Date, POSIXct, POSIXlt
and difftime all required an argument which can match 'x',
although the generics did not.
o regexpr() now accepts 0-length 'text' inputs.
o help.search() no longer errors out on a wrongly installed package
(with no "hsearch.rds" file).
o The LaTeX version of the package reference manual was omitting
some topics, and was not sorting the foo-package topic first.
o Serializing (e.g. via save()) is better protected against C
stack overflow, which will now abort the conversion but no
longer crashes the R process on some platforms.
o rbind()ing dataframes with a single row could lead to a
corrupt data frame (a problem with the fix to PR#8506).
o plot(lm(y ~ 1)) now works also for 'which = 5'.
o dbeta(0, 1, a, 0) now correctly gives 'a' (limit) instead of 0,
and dbeta(0, a, b, ncp) now returns Inf instead of NaN.
o demo(Hershey) was failing on the Cyrillic octal codes in locales
(e.g. UTF-8) in which these are invalid.
o mean() on an integer (or logical) vector was treating NAs as
actual values (unless na.rm = TRUE).
o mean() on a complex vector was calculated incorrectly in
code to improve precision (PR#8842, John Peters).
o Graphical parameters bg, cex, col, lty, and lwd were being
checked as being of length one even by functions such as
title() that ignored them. (Functions such as lines() and
points() allow them to be of length > 1, so they might be
passed through ... to other high-level graphical functions
which then used to reject them.)
o str() now is fast again for large character vectors.
o edit() would default the environment of a function to .BaseEnv,
instead of to .GlobalEnv.
o lm() and glm() coerce their 'weights' and 'offset' values to
vector to avoid problems with specifying them as 1D or n x 1
arrays.
o image() with one or both axes on log scales would give a
spurious warning; contour() would give an error.
o legend() with log axes would place the title in the wrong place.
o edit.data.frame() was not returning factors edited with
factor.mode="numeric" to factors.
o edit.matrix() tried to set rownames and colnames from the
original matrix even if the sizes had been altered, and
ignored changes made to the column names. edit.row.names has
a more sensible default (if the rownames are non-NULL).
o bindingIsLocked() was returning invalid values of a logical
vector on some platforms.
o merge.data.frame() did not make the column names unique (by
appending elements of 'suffixes') when performing a Cartesian
product. (PR#8676)
o rbind.data.frame() matches up the names of columns (which was
undocumented), but failed to do so when checking if it was
dealing with a factor column. (PR#8868)
If rbind() was used on data frames with duplicated names it
produced a corrupt data frame.
o dt(x, df, ncp= not.0) now longer gives erratic values for
|x| < ~1e-12. (PR#8874)
o \code{\linkS4class{.}} now works.
o ccf() aligns time series by ts.intersect() rather than
ts.union() and so is less likely to need a non-default
na.action. (PR#8893)
o optim(method="CG") could return a value that did not
correspond to $par for very badly behaved functions on which
the second phase of the line search failed. (PR#8786)
o print.ts() could fail on a corrupt time series: it now warns and
does the best it can.
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.3.1 is released
|
Peter Dalgaard
| 454 |
|
From pdalgd at gmail.com Wed Jun 30 18:05:38 2010
From: pdalgd at gmail.com (Peter Dalgaard)
Date: Wed, 30 Jun 2010 18:05:38 +0200
Subject: [R] The R Journal, Vol.2 Issue 1
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
Peter Dalgaard wrote:
> The first issue of the second volume of The R Journal will shortly be
> available at journal at r-project.org/current.html. Thanks to everyone
As no less than 16 people has informed me, that of course wants to be
http://journal.r-project.org/current.html
(That's what you get for doing editorial duties while on holiday in
Barcelona....., -ed.)
> involved.
>
> Peter Dalgaard
> Editor-in-chief
>
>
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[R] The R Journal, Vol.2 Issue 1
|
Peter Dalgaard
| 366 |
|
From murdoch at stats.uwo.ca Tue Nov 5 14:46:53 2002
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 05 Nov 2002 08:46:53 -0500
Subject: Windows binary for R 1.6.1 on CRAN
Message-ID: <[email protected]>
I've just uploaded a Windows binary of R 1.6.1 to CRAN. It should be
visible at <http://cran.r-project.org/bin/windows/base/> by tomorrow,
and will hopefully show up on the mirrors around the same time.
Besides the (mostly bug fix) changes in all versions of R, this
Windows version contains the following changes:
- Changed titles on help windows so topic name shows when minimized.
- Dependencies were not being generated properly in packages using
C++.
- share/R/firstlib.R was not being included in the binary
distribution.
Important for downloaders: the main file to download is called
rw1061.exe. (This file was called SetupR.exe before 1.6.0.) The
series of rw*.zip files is no longer being distributed. The mini-R
files are as before.
Duncan Murdoch
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Windows binary for R 1.6.1 on CRAN
|
Duncan Murdoch
| 91 |
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