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From jago at mclink.it Mon Dec 18 18:53:53 2000
From: jago at mclink.it (Stefano Iacus)
Date: Mon, 18 Dec 2000 18:53:53 +0100
Subject: Latest/last beta of R 1.1.1 for MacOS (rel Dec 10 2000)
Message-ID: <a05001905b663fcabe859@[159.149.74.61]>
Dear R&Mac developers(users),
at
http://www.eco-dip.unimi.it/R
you can find the latest (and last) beat version of R for MacOs
corresponding to R vers 1.1.1.
Release date is Dec 10 2000. It is no longer a pre-alpha version but
a beta one :)
In what follows you can find what's new in this version but please
remember that it is still a beta version intended mainly for R
developers and with the aim to collect as much feedback as possible.
Sometimes R application fails to allocate memory and it quits. This
is a known bug and it will be fixed in the next release.
I think that this is the last porting of R 1.1.1 and next version of
R for MacOS will be based on R ver 1.2.0 released on Dec 15 2000. I
hope this to be a complete porting and it will come with next year.
I would like to thank the R Core Team people for the invaluable help
given to me.
Stefano
p.s. I apologize for this long message.
----
Macintosh porting of R-1.1.1, beta 1, (Dec 10 2000).
What's new from R for Mac pre-alpha 2
======================================
* tempfile() is now supported. Temporary files are stored in a directory
"tmp" that it is assumed to be in the main R folder. If it doesn't
exist, R create it. All temporary files will be stored there.
* unlink() is implemented. It can delete only files and dirs created
from the current R session. Wildcards not allowed yet.
* Dynamic libraries are fully implemented grace to the code give to me
by Luke Tierney.
(There is a problem with DLLName. Every function must be searched
for global and not for a specific package when calling .C/.Fortran etc)
* Most of the packages have been compiled but the tclk one.
* tclk demos disabled
* Packages. The following packages have been compiled or simply added
to the base one:
ctest (ex:tested)
eda (ex:tested)
lqs (ex:tested)
modreg (ex:tested)
mva (ex:tested)
nls (ex:tested, does not work "SSlogis")
splines (ex:tested)
stepfun (ex:tested)
ts (file AnIndex to be built)
wavethresh (examples and help files to be built)
* Metric Information for graphics device partially working.
You can write expressions and symbols in plots but it is not yet
perfectly working.
* data(women) doesn't load! Can't understand why...yet.
* XDR loading/saving has been implemented. I use the code from B. Ripley
that (seems) to work fine with very little modifications.
* Load and Save of image is now implemented correctly.
* Load and Save implemented from menu too. If you save from menu an icon
will be added to the file. You can double-click on a R file to start the
application or load a file in R if the application is running. You can
also drag&drop the file on the R icon to launch R.
* Help files are now displayed correctly with colors as under Windows
What else still remains to do!
==============================
There are lots of things that have to be implemented and fixed.
Not all the avalaible packages have been compiled. If you have any
particular need please let me know and I will compile and made
available the package. There is not an automatic install procedure
for building packages under MacOS yet.
This current version containes wavethresh and multiv packages but no
help files and examples are avalaible yet.
If you need them you should only copy the directories "help" and "R-ex"
of the Windows distribution in their respectively directory under this
distribution.
Memory problems
===============
There is a strange behaviour of this porting of R with memory
that I'm not able to fix yet.
As the memory routines will be changed in R 1.2 I decided to
fix it in version 1.2 of the MacOS porting.
Anyway, the suggested memory parameters are the following: from
Finder get Information on the R application and change its
assigned memory to 42000k. From within R application preferences set
RVSize = 5M and RNSize = 500k.
Hystory
=======
What was in R for Mac pre-alpha 2 and 1
=======================================
* dir, setcwd, getcwd
* macdevice pdated to WasteLib 2.0
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_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Latest/last beta of R 1.1.1 for MacOS (rel Dec 10 2000)
|
<a05001905b663fcabe859@[159.149.74.61]>
|
Stefano Iacus
| 339 |
From Kurt.Hornik at ci.tuwien.ac.at Wed Apr 23 08:40:28 1997
From: Kurt.Hornik at ci.tuwien.ac.at (Kurt Hornik)
Date: Wed, 23 Apr 1997 08:40:28 +0200
Subject: ANNOUNCE: CRAN
Message-ID: <[email protected]>
This is the first announcement of the
Comprehensive R Archive Network
(CRAN)
CRAN is a collection of sites which carry identical material, consisting
of the R&R 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 (Austria)
and is currently being mirrored daily at
http://lib.stat.cmu.edu/R/CRAN (U.S.A.)
ftp://franz.stat.wisc.edu/pub/R (U.S.A.)
ftp://ftp.stat.math.ethz.ch/R-CRAN (Switzerland)
This list should grow within soon. If you want to become an official
CRAN mirror, please send me a note (Kurt.Hornik at ci.tuwien.ac.at).
Please use the CRAN site closest to you to reduce network load.
The structure of the CRAN tree is as follows.
src/base # Source distribution
src/contrib # Source for extensions
doc/ # Documentation
bin/<platform> # Binaries
`src/base' contains the official R source distribution as provided by
Ross Ihaka and Robert Gentleman.
`src/contrib' contains code for extension packages. Currently, there
are acepack, bootstrap, ctest, date, e1071, fracdiff, gee, jpn, oz,
snns, splines, and survival4. Look at the INDEX file in this directory
for more specific information. More packages are expected for the near
future.
`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.
`doc' is for additional documentation and information on R.
In the short run, the process of `submitting' to CRAN is very simple:
upload to
ftp://ftp.ci.tuwien.ac.at/incoming
and drop me a note (Kurt.Hornik at ci.tuwien.ac.at). Please indicate the
copyright situation (GPL, ...) in your submission.
In the long run, there will be a form to fill in, and some requirement
of authentication (PGPish, ...), and submission could maybe be done via
WWW. I am open to suggestions here.
*****************************************************************************
* 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-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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
|
ANNOUNCE: CRAN
|
Kurt Hornik
| 564 |
|
From Hadley.Wickham at r-project.org Fri Jan 3 18:57:59 2014
From: Hadley.Wickham at r-project.org (Hadley Wickham)
Date: Fri, 3 Jan 2014 11:57:59 -0600
Subject: The R Journal, Volume 5, Issue 2
Message-ID: <CABdHhvH19RkSnuUgVDuy1jUMeH2y0KZWuFAaCbB90ZtCAn82Yg@mail.gmail.com>
Dear all,
The latest issue of The R Journal is now available at
http://journal.r-project.org/archive/2013-2/
Many thanks to all contributors.
Hadley
--
Editor-in-chief, The R Journal
|
The R Journal, Volume 5, Issue 2
|
<CABdHhvH19RkSnuUgVDuy1jUMeH2y0KZWuFAaCbB90ZtCAn82Yg@mail.gmail.com>
|
Hadley Wickham
| 345 |
From guido at hal.stat.unipd.it Sun Apr 29 13:52:24 2001
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Sun, 29 Apr 2001 13:52:24 +0200
Subject: R 1.2.3 for Windows available
Message-ID: <[email protected]>
A Windows binary distribution of R 1.2.3 is available at
http://sirio.stat.unipd.it/RWin
It will be mirrored at a CRAN site near you in a couple of days.
See below for a list of Windows-specific changes.
guido masarotto
(for the R-core team)
Windows-specific changes to R
=============================
rw1023
======
Alternative installers based on Inno Setup 2.0.x, either SetupR.exe or
miniR* (which fits on four floppies).
The location of R_HOME and the version can optionally be recorded in
the Registry (and will be used by the DCOM interface). The Inno Setup
installers register the installation, and unregister on
uninstallation. rwinst.exe has an option to register. Program
rw1023\bin\RSetReg.exe will register, and rw1023\bin\RSetReg.exe /U
will unregister.
The windows() device no longer rounds width and height to the nearest inch.
You can override the settings Windows reports for pixels per inch
(sometimes it is seriously adrift). See ?windows.
File `extract-usage' needed for codoc was missing from rw1022sp.zip.
The default memory limit (as reset by --max-mem-size) is set to at
least 16Mb, to allow R to start on machines with 8Mb of RAM.
link.html.help() has been re-written using connections and so is
several times faster.
Rcmd INSTALL now allows Windows-style paths to a tar file.
rproxy.dll is now built for StatConnector version 0.99: earlier versions
are no longer supported.
A Windows-specific bug in bitmap() which caused output to appear twice
has been fixed.
Rcmd check now stops when package-specific tests fail (not just
reports on the console).
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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 1.2.3 for Windows available
|
Guido Masarotto
| 241 |
|
From bates at stat.wisc.edu Thu Jan 31 18:09:57 2002
From: bates at stat.wisc.edu (Douglas Bates)
Date: 31 Jan 2002 11:09:57 -0600
Subject: bin/windows updated on cran.r-project.org and cran.us.r-project.org
Message-ID: <[email protected]>
The bin/windows directory on the master CRAN site, cran.r-project.org,
and on the U.S. mirror, cran.us.r-project.org, has been updated with the
R-1.4.1 binary files that Brian Ripley announced recently.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
bin/windows updated on cran.r-project.org and cran.us.r-project.org
|
Douglas Bates
| 13 |
|
From Friedrich.Leisch at ci.tuwien.ac.at Tue May 9 13:15:42 2000
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Tue, 9 May 2000 13:15:42 +0200 (CEST)
Subject: contributed documentation
Message-ID: <[email protected]>
Hi,
as promised I have started a ``user contributed documentation''
section on CRAN. It currently contains a Spanish version of the
``Notes on R'' by Andr?s Gonz?lez and Silvia Gonz?lez and ``Data
Analysis and Graphics Using R'' by John Maindonald.
All contributions are welcome!
Please note that I had a little accident last week (shoulder
dislocation) such that CRAN maintainance will be a bit slower for the
next 2-3 weeks ...
Best,
Fritz
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 10715
Technische Universit?t Wien Fax: (+43 1) 58801 10798
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
-------------------------------------------------------------------
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
contributed documentation
|
Friedrich Leisch
| 315 |
|
From P.Dalgaard at biostat.ku.dk Mon Jun 23 12:07:36 2008
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Mon, 23 Jun 2008 12:07:36 +0200
Subject: R 2.7.1 re-released
Message-ID: <[email protected]>
There was a minor problem with the date in the previously released
version. It has been replaced with a new file.
The updated md5sums are
565b06a1f3f11020399934cc7b47a59d R-2.7.1.tar.gz
565b06a1f3f11020399934cc7b47a59d R-latest.tar.gz
--
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 2.7.1 re-released
|
Peter Dalgaard
| 600 |
|
From p.dalgaard at biostat.ku.dk Mon Nov 15 16:41:04 2004
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 15 Nov 2004 16:41:04 +0100
Subject: R-2.0.1 is released
Message-ID: <[email protected]>
Whoops!
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.0.1.tar.gz
(Notice the R-2 subdir)
I also forgot to sign it on behalf of The R Core Team.
--
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-2.0.1 is released
|
Peter Dalgaard
| 387 |
|
From Friedrich.Leisch at ci.tuwien.ac.at Tue Sep 11 18:52:42 2001
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Tue, 11 Sep 2001 18:52:42 +0200
Subject: New package pixmap
Message-ID: <[email protected]>
A new package called `pixmap' has been released on CRAN. From the
DESCRIPTION file:
Package: pixmap
Version: 0.2-1
Title: Bitmap Images (``Pixel Maps'')
Depends: R (>= 1.3)
Author: Friedrich Leisch and Roger Bivand
Maintainer: Friedrich Leisch <Friedrich.Leisch at ci.tuwien.ac.at>
Description: Functions for import, export, plotting and other
manipulations of bitmapped images.
License: GPL version 2.
The package is intended to provide the central low-level support for
reading/writing/plotting bitmapped images. It replaces the read.pnm
and write.pnm functions of package e1071. Currently only PNM images
are supported for import/export, but we want to add other filter real
soon.
A rich class structure is already in place, allowing for grey, rgb and
indexed images together with conversions between all three
formats. The classes allow images also to have a coordinate system
attached, such that, e.g., locator() can be used meaningfully on
geographical maps.
This is a first release, all comments and feedback are more than
welcome (thanks to Jonathan Marchini for valuable feedback on the
first development version).
Best,
Fritz Leisch
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 10715
Technische Universit?t Wien Fax: (+43 1) 58801 10798
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
-------------------------------------------------------------------
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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
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
New package pixmap
|
Friedrich Leisch
| 273 |
|
From dmurdoch at pair.com Fri Apr 18 03:29:05 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Thu, 17 Apr 2003 21:29:05 -0400
Subject: R 1.7.0 Windows binary build released
Message-ID: <[email protected]>
I've just finished uploading the Windows binary of R 1.7.0 to CRAN.
It should move to the public areas and the mirrors in a day or two.
It will appear in <http://cran.r-project.org/bin/windows/base> and the
corresponding directory on a mirror near you.
Duncan Murdoch
|
R 1.7.0 Windows binary build released
|
Duncan Murdoch
| 166 |
|
From verz@ni @ending from m@th@c@i@cuny@edu Wed Aug 8 15:55:37 2018
From: verz@ni @ending from m@th@c@i@cuny@edu (John Verzani)
Date: Wed, 8 Aug 2018 09:55:37 -0400
Subject: [ANN] New issue of The R Journal
Message-ID: <CADx-4xCkTFEKFZxryVfSvwwQ7+kHt9O1Lup-Tkm840UxHiLaQw@mail.gmail.com>
Dear All,
The latest issue of The R Journal is now available at:
https://journal.r-project.org/archive/2018-1/.
Many thanks to all contributors - especially reviewers and authors.
Regards,
John Verzani
CUNY/College of Staten Island
[[alternative HTML version deleted]]
|
[ANN] New issue of The R Journal
|
<CADx-4xCkTFEKFZxryVfSvwwQ7+kHt9O1Lup-Tkm840UxHiLaQw@mail.gmail.com>
|
John Verzani
| 687 |
From edd at debian.org Mon Feb 23 05:19:29 2009
From: edd at debian.org (Dirk Eddelbuettel)
Date: Sun, 22 Feb 2009 22:19:29 -0600
Subject: R/Finance 2009: Applied Finance with R -- Registration now open
Message-ID: <[email protected]>
R/Finance 2009: Applied Finance with R
April 24 & 25, Chicago, IL, US
The first annual R/Finance conference for applied finance using R , the
premier free software system for statistical computation and graphics,
will be held this spring in Chicago, IL, USA on Friday April 24 and
Saturday April 25.
The two-day conference will cover topics as diverse as portfolio theory,
time-series analysis, as well as advanced risk tools, high-performance
computing, and econometrics. All will be discussed within the context of
using R as a primary tool for financial risk management and trading.
Assembled to talk over the two days are some of the industry's most
recognizable authorities within the world of R and quantitative finance.
R/Finance 2009 is organized by a leading group of R package authors and
community contributors, and hosted by the International Center for Futures
and Derivatives [ICFD] at the University of Illinois at Chicago.
Conference registration is now open. Special advanced registration pricing is
available, as well as discounted pricing for academic and student
registrations.
More details and registration information can be found at the website at
http://www.RinFinance.com
For the program committee:
Gib Bassett, Peter Carl, Dirk Eddelbuettel, John Miller,
Brian Peterson, Dale Rosenthal, Jeffrey Ryan
--
Three out of two people have difficulties with fractions.
|
R/Finance 2009: Applied Finance with R -- Registration now open
|
Dirk Eddelbuettel
| 646 |
|
From maechler at stat.math.ethz.ch Tue Jun 1 15:54:54 1999
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 1 Jun 1999 15:54:54 +0200
Subject: libraries and repeated measurements code
In-Reply-To: <[email protected]> (message from Martin
Maechler on Tue, 1 Jun 1999 10:47:27 +0200 (MET DST))
References: <[email protected]>
Message-ID: <[email protected]>
This was Jim Lindsey <jlindsey at luc.ac.be>, not me.
Sorry for the wrong "From:".
{(as list manager I've forwarded his posting to R-announce which bounced
because it came from jlindsey at alpha.luc.ac.be instead of jlindsey at luc.ac.be)}
Martin
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Send "info", "help", or "[un]subscribe"
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_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
libraries and repeated measurements code
|
Martin Maechler
| 484 |
|
From n@m@t|o|| @end|ng |rom ucd@v|@@edu Fri Sep 13 18:56:11 2019
From: n@m@t|o|| @end|ng |rom ucd@v|@@edu (Norman Matloff)
Date: Fri, 13 Sep 2019 09:56:11 -0700
Subject: R Journal, Vol. 11, Issue 1
Message-ID: <CAKbPKxsjXrJMxOStvBHsryHO=hqc1+xdffNQR3pnH3GkTxNmpw@mail.gmail.com>
After a long delay, the issue was put online on Wednesday evening. As noted
in the editorial, we are taking measures to help ensure that future issues
will be more timely.
Norm Matloff
[[alternative HTML version deleted]]
|
R Journal, Vol. 11, Issue 1
|
<CAKbPKxsjXrJMxOStvBHsryHO=hqc1+xdffNQR3pnH3GkTxNmpw@mail.gmail.com>
|
Norman Matloff
| 676 |
From keitt at nceas.ucsb.edu Sat Nov 13 03:18:57 1999
From: keitt at nceas.ucsb.edu (Timothy H. Keitt)
Date: Fri, 12 Nov 1999 18:18:57 -0800
Subject: postgresql package for R
Message-ID: <[email protected]>
A preliminary release of my postgres package for R is at
http://www.nceas.ucsb.edu/~keitt/R/postgres.tgz
It allows one to read and write data frames to and from a postgres
database, execute queries and has an experimental "proxy" interface that
allows you to access postgres tables using the standard, local data
frame model. All accesses to the data frame generate the appropriate
queries and returns the data from the database. (The proxy interface is
broken at the moment.) I'm mostly looking for a few testers (hopefully
with postgresql experience) to try it out.
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/
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Send "info", "help", or "[un]subscribe"
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_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
postgresql package for R
|
Timothy H. Keitt
| 504 |
|
From jago at mclink.it Sat Apr 28 17:05:24 2001
From: jago at mclink.it (Stefano)
Date: Sat, 28 Apr 2001 17:05:24 +0200
Subject: R for Mac Special Interest Group
Message-ID: <[email protected]>
R for Mac Special Interest Group
Alog with the forthcoming 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
| 243 |
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From ihaka at stat.auckland.ac.nz Wed Apr 23 11:36:33 1997
From: ihaka at stat.auckland.ac.nz (Ross Ihaka)
Date: Wed, 23 Apr 1997 21:36:33 +1200 (NZST)
Subject: Version 0.49 Addendum
Message-ID: <[email protected]>
I should mention that this version of R has been verified to configure
and compile on the following platforms:
PLATFORM COMPILER
alpha-dec-osf3.2 cc
hppa1.1-hp-hpux9.07 gcc or c89
i386-unknown-freebsd2.1.5 gcc
i686-unknown-linux gcc
mips-sgi-irix6.2 cc
sparc-sun-solaris2.5.1 gcc
sparc-sun-sunos4.1.4 gcc
We'd be interested in any other successes.
Ross
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|
Version 0.49 Addendum
|
Ross Ihaka
| 566 |
|
From guido at sirio.stat.unipd.it Mon Dec 21 13:14:43 1998
From: guido at sirio.stat.unipd.it (Guido Masarotto)
Date: Mon, 21 Dec 1998 13:14:43 +0100
Subject: R 0.63.1 for Windows
Message-ID: <[email protected]>
A new version of R for Windows is available from CRAN in directory
bin/windows/windows-NT. This supersedes rw0630, rw63-io, bdr0631 and earlier
versions. It runs on Windows 95, 98, NT4 (on i386), at least.
There are two executables, Rgui.exe and Rterm.exe.
NEW FEATURES
Will run from NT command line.
No `tricks' are needed for animated graphics.
The windows are much more responsive.
R commands can be interrupted by Esc.
Rterm allows batch mode operation and can also be run in
inferior-R-mode under NTEmacs.
There is a history mechanism for graphics plots.
Graphics can be copied to the clipboard.
Commands history is saved between session (only by Rgui.exe).
Saved images and user profile are called .RData and .Rprofile as under Unix
(before they were RData and Rprofile).
PACKAGES:
Pre-compiled packages for this (and hopefully all subsequent versions)
are available at CRAN/bin/windows-NT/contrib.
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|
R 0.63.1 for Windows
|
Guido Masarotto
| 562 |
|
From bates at stat.wisc.edu Fri Oct 10 19:03:09 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: 10 Oct 2003 12:03:09 -0500
Subject: Debian (testing) packages for R-1.8.0
Message-ID: <[email protected]>
Packages of R-1.8.0 for the Debian testing (or sarge) distribution are
now available on http://cran.us.r-project.org/bin/linux/debian and
should appear on other mirrors in a day or two.
|
Debian (testing) packages for R-1.8.0
|
Douglas Bates
| 189 |
|
From Kurt.Hornik at ci.tuwien.ac.at Mon Apr 12 09:03:52 1999
From: Kurt.Hornik at ci.tuwien.ac.at (Kurt Hornik)
Date: Mon, 12 Apr 1999 09:03:52 +0200 (CEST)
Subject: CRAN uploads
Message-ID: <[email protected]>
I just uploaded updated versions of the packages
cluster
polynom
to CRAN. Both pass `R CMD check' now.
-k
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|
CRAN uploads
|
Kurt Hornik
| 475 |
|
From pgilbert at bank-banque-canada.ca Wed Nov 24 16:46:05 1999
From: pgilbert at bank-banque-canada.ca (Paul Gilbert)
Date: Wed, 24 Nov 1999 10:46:05 -0500
Subject: DSE package for multi-variate time series
Message-ID: <[email protected]>
A new version of my DSE package for multi-variate time series analysis
is
now available at <www.bank-banque-canada.ca/pgilbert>. I am trying to
sort
out some minor glitches with the new R 0.90 graphics before I submit it
to CRAN. Much of the underlying code has been re-worked and reorganized
in the
new version. In particular, the use of model and data constructors has
been
more formalized and the internal structure of these objects, while still
documented, is considered "opaque."
I have separated out a "syskern" package which tries to provide a kernel
of
routines to isolate OS differences and a few Splus and R differences.
For most
people, the most interesting part of this is probably the approach to
RNG,
which provides a convenient way to generate the same random experiments
in R
and Splus.
I have also separated out a "tframe" package which provides a kernel of
routines for programming time series methods. These allow a programmer
to
write most code in a way that is independent of the time representation
(i.e.
the class of the time series data). So, for example, the use of tsp() is
avoided
because it is specific to certain classes of time series.
The changes to the underlying structure necessitated a substantial
re-write of
the user's guide, so I am taking the opportunity to bring the guide
up-to-date
with respect to R. A draft of the guide is available at the above web
site in
postscript and pdf files. The first nine sections, which cover material
in the previous version of the guide, are now mostly complete and I hope
correct. I would certainly appreciate comments. Some later sections,
which
cover new material, are still missing or incomplete.
The help has largely been converted to integrate with R's help. I have
not yet worked through all the examples, many of which were written with
fictitious data in mind, so it will be some time before "R CMD check
dse" works, however, most of my tests work in both Linux and Solaris.
These include:
random.number.test()
tframe.function.tests()
dse1.function.tests()
dse2.function.tests()
dse3.function.tests()
dse4.function.tests()
guide.example.tests.part1()
guide.example.tests.part2()
which cover a large part of the package. The comparison tolerances on
some of
the tests had to be relaxed in order to pass with R on Linux and R and
Splus 3.3
in Solaris. I would appreciate feedback about how the tests work on
other
platforms.
Paul Gilbert
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|
DSE package for multi-variate time series
|
Paul Gilbert
| 510 |
|
From bates at stat.wisc.edu Thu Aug 22 18:05:18 2002
From: bates at stat.wisc.edu (Douglas Bates)
Date: 22 Aug 2002 11:05:18 -0500
Subject: CD's of R from CheapBytes
Message-ID: <[email protected]>
CheapBytes, a vendor of Linux CDs, now offers a CD of R. See
www.cheapbytes.com
-> "Enter the store"
-> CheapBytes CDs
-> CheapBytes "R" Project CD-R
or use the direct link
http://cart.cheapbytes.com/cgi-bin/cart/0070010796?I2uHEGKI;;13
which says, in part,
CheapBytes includes binary files for the following platforms:
* Debian
o Potato
o Woody
* Linux PPC
* Mandrake Linux 8.1
* Red Hat
o Version 6.x
o Version 7.x
* SuSE 7.2
* Windows
Their price is $4.99/CD plus a flat fee of $5 for shipping up to 18 CDs
within the U.S.A. or Canada. Prices for shipping to other countries
are listed on www.cheapbytes.com -> .27777778 Do the Math
This announcement is not an endorsement. In general the R-announce
list is for announcements about the development of R and the
availability of new code. We made an exception in announcing this
product because it is, to our knowledge, the first commercially
available CD of R.
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|
CD's of R from CheapBytes
|
Douglas Bates
| 58 |
|
From ripley at stats.ox.ac.uk Sun Apr 11 10:04:44 1999
From: ripley at stats.ox.ac.uk (Prof Brian D Ripley)
Date: Sun, 11 Apr 1999 09:04:44 +0100 (BST)
Subject: R-0.64 versions of packages
Message-ID: <[email protected]>
Versions of
KernSmooth
VR5.3pl037
boot
gee
rpart
sm (delete src/Makefile: I'll get the version on CRAN changed)
tree
for R-0.64 are now on CRAN. Please note that spatial (in the VR bundle)
and sm really do need 0.64 as we use the platform-independent file
handling, and sm uses chull.
This will be the last version of the VR5.x software for the second
edition, as a new more `R friendly' third edition is due out in July. The
software for that is now available for pretest (including for R-0.64 on
UNix and Windows) at
http://www.stats.ox.ac.uk/pub/MASS3
It is almost completely backwards compatible (just no support for
survival4) with eariler versions but has new datasets and functions.
Some, such as ppr and lqs, are already in R.
Windows versions:
=================
I have split the Windows contributed collection into current and
rw063x sections: the mirroring on CRAN caught the middle of the change
but should be complete by tomorrow when we plan to release rw0640.
One nice new feature is the larger packages can have their help and
examples files stored in zip archives, thereby saving a lot of space on
some file systems.
--
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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|
R-0.64 versions of packages
|
Prof Brian D Ripley
| 474 |
|
From cbuerkle at bio.indiana.edu Mon Nov 23 23:32:57 1998
From: cbuerkle at bio.indiana.edu (Alex Buerkle)
Date: Mon, 23 Nov 1998 17:32:57 -0500 (EST)
Subject: [R] R-0.63 rpms are now built for linuxppc
In-Reply-To: <[email protected]>
Message-ID: <[email protected]>
Using Martin Plummer's source rpms, I have started putting together binary
rpms for linuxppc.
The current rpms are:
R-base-0.63-3.ppc.rpm
R-VR-5.3pl030-1.ppc.rpm
R-contrib-1998.11.20-1.ppc.rpm
These are (or will be) found at:
1) CRAN/bin/linux/linuxppc/
2) ftp://biocserver.cwru.edu/pub/linuxppc/
(science apps for linuxppc ftp site)
3) ftp://ftp.linuxppc.org/pub/linuxppc/linuxppc-R4/contrib/RPMS/
(and its mirrors)
I hope these are useful to someone else.
-- Alex
~^^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^
C. Alex Buerkle Ph: 812-855-9018
Jordan Hall 142 Fax: 812-855-6705
Department of Biology
Indiana University
Bloomington, IN 47405 cbuerkle at bio.indiana.edu
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|
[R] R-0.63 rpms are now built for linuxppc
|
Alex Buerkle
| 560 |
|
From guido at hal.stat.unipd.it Wed Jun 27 15:56:43 2001
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Wed, 27 Jun 2001 15:56:43 +0200
Subject: R-1.3.0 for Windows
Message-ID: <[email protected]>
A binary distribution of R-1.3.0 to run on Windows 95, 98, NT4.0 and 2000 on
Intel/clone chips is available at
http://sirio.stat.unipd.it/RWin
It will be mirrored at a CRAN site near you in a couple of days.
See below for a list of Windows-specific changes.
guido masarotto
(for the R-core team)
Windows-specific changes to R
=============================
rw1030
======
SetupR.exe and miniR* now include the nine `recommended' packages,
so the miniR* distribution needs six floppies rather than four.
Rgui has a new menu `Packages' with items to load packages, to install
packages from CRAN or from local zip files, and to update packages.
The packages list shown by help.start() now includes all packages in
all libraries, but the search index is still confined to the system
library.
The installers set up a file association for *.RData files, so
double-clicking on a *.RData file launches R in that directory and
loads the *.RData file. Also, a *.RData file can be dropped onto a
shortcut to Rgui (or Rterm) on the desktop or in Windows Explorer.
Drag-and-drop of images (.RData and .rda) and source files (.R)
onto the Rgui.exe console window is now supported.
Profiling (as described in `Writing R Extensions') is now available.
There is a new `Save as PDF' option on the graphics device menu.
bringToTop() can specify the console window in Rgui (as -1).
The default graphics device is now windows() only in interactive use:
otherwise it is postscript(). (This affects the DCOM interface, which
is not interactive use.)
Support for earlier (pre-Feb 2000) mingw compilers has been dropped:
you must use a compiler system that supports --shared and has an
in-memory dlltool.
Rcmd check has been changed to be more robust to reported problems
with Perl's system() command under 16-bit versions of Windows. It now
works for us under Windows 98. (It has always worked under NT4 and
2000.)
Rcmd SHLIB no longer adds a version tab to the DLL, as this seemed to
cause some people problems under Windows 95/98/ME.
The correct file version information should now appear on Windows 2000
Version tab under Properties (working around a Windows 2000 bug).
rwinst.exe is no longer part of the distribution: use the newer
installers to install R, and the Packages menu in Rgui.exe to install
pre-compiled packages, or use an external unzip program.
The old-style Windows help is no longer part of the standard distribution,
but can be made from the sources. It is no longer tested.
Make targets such as test-Reg have been moved to directory rw1030\tests.
The default internet module modules\internet.dll is built using basic
WinSock calls. There is an alternative modules\internet2.dll which uses
WinInet calls (and so needs Internet Explorer installed) which can be
used as a replacemnet.
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|
R-1.3.0 for Windows
|
Guido Masarotto
| 252 |
|
From fharrell at virginia.edu Sun Apr 7 22:41:24 2002
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Sun, 7 Apr 2002 16:41:24 -0400
Subject: Hmisc 1.0 Available
Message-ID: <[email protected]>
After taking much longer than I had hoped, the Hmisc library version 1.0 is now available for Linux/Unix/Windows. The web page for Hmisc is
http://hesweb1.med.virginia.edu/biostat/s/Hmisc.html from which you can download the ready-to-install package. See http://hesweb1.med.virginia.edu/biostat/s/help/Hmisc/html/Overview.html
for an overview of the library. R users will be particularly interested in the semi-advanced LaTeX table-making functions by Heiberger and Harrell, and in sas.get, summary.formula (for moderate-level table making and graphical summaries), summarize, and extensions to Lattice graphics that allow for error bars, bands, filled bands, and automatic legend drawing. There are many utility functions, such as labcurve for labeling curves where they are most separated or for drawing legends in the most empty region of a plot. There are many high-level and some low-level graphics functions and some sample size/power functions.
The Design library will not be far behind. For both libraries, the last things to work will be the examples, as my help files currently contain much example code and its printed output that will not execute.
Please send error reports directly to me, with simple examples causing failure if possible.
I wish to thank several people who, besides the helpful group of
R-core members, assisted in porting the Hmisc library to R:
Xiao Gang Fan <xiao.gang.fan1 at libertysurf.fr> kindly creates Windows
distributions of the library from my Linux/Unix version.
Patrick Connolly <P.Connolly at hortresearch.co.nz> wrote an R version of
the print.char.matrix function that allows the summary.formula
function to print boxed tables. Patrick's function will be of general
interest to many users [in S-Plus, print.char.matrix is used to print
the output from crosstabs].
Paul Murrell <paul at stat.auckland.ac.nz> wrote the grid package and
Deepayan Sarkar <deepayan at stat.wisc.edu> wrote the lattice package.
Paul and Deepayan displayed amazing patience in answering many of my
questions, and they made imrovements in their packages to allow me to
better use them in Hmisc.
Don MacQueen <macq at llnl.gov> provided major fixes to sas.get for R for
POSIX date, time, and date/time variables and for use of scan.
Peter Malewski <malewski.peter at mh-hannover.de> and Tom Short
<TShort at epri-peac.com> provided information about several errors in a
pre-release of Hmisc.
Thanks to all developers and contributors to R.
Sincerely,
Frank Harrell
--
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
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|
Hmisc 1.0 Available
|
Frank E Harrell Jr
| 21 |
|
From guido at hal.stat.unipd.it Thu Apr 20 11:19:25 2000
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Thu, 20 Apr 2000 10:19:25 +0100
Subject: New Windows binaries available
Message-ID: <[email protected]>
Windows binaries at CRAN (in bin/windows/Windows-NT/base) have been updated
to R-1.0.1. See below for a list of Windows-specific changes.
Happy Easter,
guido masarotto
Windows-specific changes to R
=============================
The installer, rwinst.exe, now checks for ZIP files as well as zip files,
as some browsers manage to map filenames to uppercase.
There are batch files Rd2txt.bat Rdconv.bat Rdindex.bat Sd2Rd.bat
which are the equivalent of the Unix `R CMD foo' utilities mentioned in
`Writing R Extensions'. To use these you must have R_HOME set as an
environment variable (using the form P:/R/rw1001). There is also a
shell script Rd2dvi.sh which you can use if you have sh.exe (as
used to compile packages) and latex etc. The environment variable
XDVI sets the previewer, defaulting to xdvi.bat.
A file `Makevars' in the `src' directory of a package can be used to
add to/override the MakeDll makefile used to make foo.dll, as on Unix.
(See `Creating shared libraries', section 3.4 of `Writing R Extensions'.)
Under rare conditions (lots of very short input lines) the history buffer
could overrun and so cause crashes. This has been possible since rw0623,
but first caused reported problems in rw1000 and has now been fixed.
Certain HP printer drivers (e.g. the 6/6MP-Postscript driver) reset the
FPU and so were causing crashes. This has been circumvented in this
version by restoring the settings before and after each page.
Building on a non-default drive should be more reliable, as Perl is
used to find the current drive.
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|
New Windows binaries available
|
Guido Masarotto
| 313 |
|
From p.dalgaard at biostat.ku.dk Tue Oct 3 12:30:47 2006
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 03 Oct 2006 12:30:47 +0200
Subject: R-2.4.0 is released
Message-ID: <[email protected]>
I've rolled up R-2.4.0.tar.gz a short while ago. This version contains
several changes and additions, mostly incremental, but some larger
changes to S4 methods have been added, as well as namespace sealing.
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-2.4.0.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.
There is no longer 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:
a8efde35b940278de19730d326f58449 AUTHORS
eb723b61539feef013de476e68b5c50a COPYING
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
bdb43ae25511ed02c58bce1ff0e93337 FAQ
70447ae7f2c35233d3065b004aa4f331 INSTALL
4426b6244f014353965fa09f85d8fd5b NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
f32379469d8712e9f5dd6435d30127d3 R-2.4.0.tar.gz
433182754c05c2cf7a04ad0da474a1d0 README
020479f381d5f9038dcb18708997f5da RESOURCES
4eaf8a3e428694523edc16feb0140206 THANKS
This is the relevant part of the NEWS file
CHANGES IN R VERSION 2.4.0
USER-VISIBLE CHANGES
o The startup message now prints first the version string and
then the copyright notice (to be more similar to R --version).
o save() by default evaluates promise objects. The old behaviour
(to save the promise and its evaluation environment) can be
obtained by setting the new argument 'eval.promises' to FALSE.
(Note that this does not apply to promises embedded in
objects, only to top-level objects.)
o The functions read.csv(), read.csv2(), read.delim(),
read.delim2() now default their 'comment.char' argument to "".
(These functions are designed to read files produced by other
software, which might use the # character inside fields, but
are unlikely to use it for comments.)
o The bindings in the base environment/namespace (currently the
same thing) are now locked. This means that the values of
base functions cannot be changed except via
assignInNamespace() and similar tricks.
o [[ on a factor now returns a one-element factor (and not an
integer), as.list() on a factor returns a list of one-element
factors (and not of character vectors), and unlist() on a list
of factors returns a factor (and not an integer vector).
These changes may affect the results of sapply() and lapply()
applied to factors.
o mauchly.test() now returns the W statistic (for comparability
with SAS and SPSS), rather than the z (which was accidentally
not named in the output)
o sort(x, decreasing = FALSE, ...) is now a generic function.
This means that 'partial' is no longer the second argument,
and calls which used positional matching may be incorrect: we
try to detect them.
o See the section on 'Changes to S4 methods': all packages
depending on 'methods' need to be re-installed.
NEW FEATURES
o agrep(), grep(), strwrap(), strtrim(), substr() and
related functions now coerce arguments which should be
character via as.character() rather than internally (so method
dispatch takes place, e.g. for factors).
chartr(), charfold(), tolower() and toupper() now coerce their
main argument if necessary to a character vector via
as.character().
Functions which work element-by-element on character vectors
to give a character result now preserve attributes including
names, dims and dimnames (as suggested by the Blue Book
p. 144). Such functions include charfold(), chartr(), gsub(),
strtrim(), sub(), substr(), tolower() and toupper(). (Note
that coercion of a non-character argument may lose the
attributes.)
agrep(value = TRUE) preserves names for compatibility with
grep().
nchar() has always preserved dims/dimnames (undocumented
before) and now also preserves names.
o .Deprecated and .Defunct take a new parameter, msg, that allows
for the specification of the message printed and facilitates
deprecation of calling sequences etc.
o .Fortran() will map 'name' to lower case, and will work with
'name' containing underscores.
o The default is now .saveRDS(compress = TRUE)
o The :: operator now also works for packages without name spaces
that are on the search path.
o [[ on a list does not duplicate the extracted element unless
necessary. (It did not duplicate in other cases, e.g. a
pairlist.)
o argsAnywhere() works like args() on non-exported functions.
o as.data.frame() gains a '...' argument.
o Added an as.data.frame() method for class "ftable".
o as.list(<an expression>) is now handled by internal code and
no longer loses attributes such as names.
as.list(<a list>) no longer duplicates (unnecessarily).
o as.POSIX[cl]t can now convert character strings containing
fractional seconds.
o attach() can now attach a copy of an environment.
o available.packages() and installed.packages() gain a 'fields'
argument thanks to Seth Falcon.
o axis.POSIXct() uses a different algorithm for ranges of 2 to 50
days that will mark days at midnight in the current timezone
(even if the graph crosses a DST change).
o body<-() and formals<-() default to envir = environment(fun),
that is they do not by default change the environment.
(Previously they changed it to parent.frame().)
o New function combn(x, m, ..) for computing on all combinations of
size 'm' (for small 'm' !).
o The cumxxx() functions now handle logical/integer arguments
separately from numeric ones, and so return an integer result
where appropriate.
o data.frame() has a new argument 'stringsAsFactor'. This and
the default for read.table(as.is=) are set from the new global
option 'stringsAsFactors' via the utility function
default.stringsAsFactors().
o dev.interactive() now has an optional argument 'orNone'.
o df() now has a noncentrality argument 'ncp', based on a
contribution by Peter Ruckdeschel.
o example() gains an argument 'ask' which defaults to "TRUE when
sensible", but the default can be overridden by setting option
'example.ask'.
o expand.grid() now has an argument 'KEEP.OUT.ATTRS' which can
suppress (the potentially expensive) "out.attrs" attribute. It no
longer returns an extraneous 'colnames' attribute.
o The subset and subassign methods for factors now handle factor
matrices, and dim() can be set on a factor.
o There is now a format() method for class "ftable".
o head(x, n) and tail(x, n) now also work for negative arguments,
thanks to Vincent Goulet.
o head.matrix() and tail.matrix() are no longer hidden, to be used
for building head() and tail() methods for other classes.
o If help() finds multiple help files for a given topic, a menu
of titles is used to allow interactive choice.
o help.search() now rebuilds the database if 'package' specifies a
package not in the saved database.
o hist(*, plot = FALSE) now warns about unused arguments.
o history() gains a 'pattern' argument as suggested by Romain
Francois.
o integer(0) now prints as that rather than "numeric(0)" (it
always deparsed as "integer(0)").
o interaction(..., drop=TRUE) now gives the same result as
interaction(...)[,drop=TRUE] (it used to sometimes give a
different order for the levels).
o lag.plot() produces a conventional plot (not setting mfrow) if
only one plot is to be produced.
o lapply() does much less copying. Vector X are handled without
duplication, and other types are coerced via as.list(). (As a
result, package 'boot' runs its examples 4% faster.)
lapply(<a pairlist>) now coerces to a list (rather than traverse
the pairlist from the beginning for each item).
o legend() has new parameters 'box.lwd' and 'box.lty'.
o lines() gains a simple method for isoreg() results.
o load() no longer coerces pairlists to lists (which was
undocumented, but has been happening since 1998).
o make.link() now returns an object of class "link-glm".
The GLM families accept an object of this class for their
'link' argument, which allows user-specified link functions.
Also, quasi() allows user-specified variance functions.
o mapply() uses names more analogously to lapply(), e.g..
o matplot() now accepts a 'bg' argument similarly to plot.default() etc.
o median() is now generic, and its default method uses mean()
rather than sum() and so is more widely applicable (e.g. to dates).
o Dummy functions memory.size() and memory.limit() are available
on Unix-alikes, for people who have not noticed that documentation
is Windows-specific.
o merge() works more efficiently when there are relatively few
matches between the data frames (for example, for 1-1
matching). The order of the result is changed for 'sort = FALSE'.
o merge() now inserts row names as a character column and not a
factor: this makes the default sort order more comprehensible.
o Raw, complex and character vectors are now allowed in model
frames (there was a previously undocumented restriction to
logical, integer and numeric types.). Character vectors in a
formula passed to model.matrix() are converted to factors and
coded accordingly.
o modifyList() utility, typically for housekeeping nested lists.
o x <- 1:20; y <- rnorm(x); nls(y ~ A*exp(-x^2/sig)) no longer
returns an unhelpful error message. In this and similar cases, it
now tries a wild guess for starting values.
o Ops.difftime() now handles unary minus and plus.
o Ops.Date() and Ops.POSIXt() now allow character arguments
(which are coerced to the appropriate class before comparison,
for Ops.POSIXt() using the current time zone).
o There is a new option(max.contour.segments = 25000) which can be
raised to allow extremely complex contour lines in contour()
and contourLines(). (PR#9205)
o options(max.print = N) where N defaults to 99999 now cuts printing
of large objects after about N entries. print(x, ..., max = N)
does the same for the default method and those building on
print.default().
options("menu.graphics") controls if graphical menus should be
used when available.
options("par.ask.default") allows the default for par("ask")
to be set for a newly-opened device. (Defaults to FALSE, the
previous behaviour.)
The way option("papersize") is set has been changed. On
platforms which support the LC_PAPER locale category, the
setting is taken first from the R_PAPERSIZE environment
variable at run time, then from the LC_PAPER category
("letter" for _US and _CA locales and "a4" otherwise). On
other platforms (including Windows and older Unixen), the
choice is unchanged.
o package.skeleton() gains arguments 'namespace' and
'code_files'.
o par(ask=TRUE) now only applies to interactive R sessions.
o parse() now returns up to 'n' expressions, rather than fill
the expressions vector with NULL. (This is now compatible
with S.)
o The 'version' argument for pdf() is now increased
automatically (with a warning) if features which need a higher
level are used.
o pie() now allows expressions for 'labels', and empty slices.
o There is a new '%.%' operator for mathematical annotations
(plotmath) which draws a centred multiplication dot
(a \cdot in LaTeX), thanks to Uwe Ligges.
o predict.lm() gains a 'pred.var' argument. (Wishlist PR#8877.)
o print.summary.{aov,glm,lm,nls} and print.{aov,glm} make use of
naprint() to report when na.action altered the model frame.
o print.table(T, zero.print=ch) now also replaces 0 by ch when T is
non-integer with integer entries.
o Recursive rapply() which is similar to lapply but used
recursively and can restrict the classes of elements to which
it is applied.
o r2dtable() has been moved to package 'stats'.
o New function read.DIF() to read Data Interchange Format files,
and (on Windows) this format from the clipboard.
o New experimental function readNEWS() to read R's own "NEWS" file
and similarly formatted ones.
o readLines() has a new argument 'warn' to suppress warnings:
the default behaviour is still to warn.
o reg.finalizer() has a new argument 'onexit' to parallel the
C-level equivalent R_RegisterFinalizerEx.
o rep() is now a primitive function and under some conditions
very much faster: rep.int() is still a little faster (but does
less). (Because it is primitive there are minor changes to the
call semantics: see the help page.)
o The 'row.names' of a data frame may be stored internally as an
integer or character vector. This can result in considerably
more compact storage (and more logical row names from rbind)
when the row.names are 1:nrow(x). However, such data frames
are not compatible with earlier versions of R: this can be
ensured by supplying a character vector as 'row.names'.
row.names() will always return a character vector, but direct
access to the attribute may not.
The internal storage of row.names = 1:n just records 'n', for
efficiency with very long vectors.
The "row.names" attribute must be a character or integer
vector, and this is now enforced by the C code.
o The "data.frame" and "matrix" methods for rowsum() gain an 'na.rm'
argument.
o Experimental support for memory-use profiling via Rprof(),
summaryRprof(), Rprofmem() and tracemem().
o save.image() [also called by sys.save.image() and hence from q()]
now defaults to saving compressed binary images. To revert to
the previous behaviour set option "save.image.defaults": see
?save.image.
o There is a new primitive seq.int() which is slightly more
restricted than seq() but often very much faster, and new
primitives seq_along() and seq_len() which are faster still.
o serialize(connection = NULL) now returns a raw vector (and not
a character string). unserialize() accepts both old and new
formats (and has since 2.3.0).
o setwd() now returns the previously current directory (invisibly).
o The function sort() is now sort.int(), with a new generic
function sort() which behaves in the same way (except for the
order of its argument list) for objects without a class, and
relies on the '[' method for objects with a class (unless a
specific method has been written, as it has for class "POSIXlt").
o sort.list() now implements complex vectors (PR#9039), and how
complex numbers are sorted is now documented.
o spline() and splinefun() now follow approx[fun] to have an argument
'ties = mean' which makes them applicable also when 'x' has
duplicated values.
o str(x) does not print the S3 "class" attribute when it is the
same as 'mode' (which is printed anyway, possibly abbreviated)
and it puts it beside mode for atomic objects such as S3 class
"table".
o str(<data.frame>) now outputs 'data.frame' instead of
`data.frame'; this may affect some strict (Package) tests.
o str() now takes also its defaults for 'vec.len' and 'digits.d'
from options('str') which can be set by the new strOptions().
o symnum() has a new argument 'numeric.x' particularly useful for
handling 0/1 data.
o Sys.getlocale() and Sys.setlocale() support LC_MESSAGES,
LC_PAPER and LC_MEASUREMENT if the platform does.
o Sweave has a new options 'pdf.encoding' and 'pdf.version' for
its Rweave driver.
o The character vector used by an output textConnection() has
a locked binding whilst the connection is open.
There is a new function textConnectionValue() to retrieve the
value of an output textConnection().
o traceback() gains a 'max.lines' argument.
.Traceback is no longer stored in the workspace.
o warning(immediate. = TRUE) now applies to
getOption("warn") < 0 and not just == 0.
o warnings() is now an accessor function for 'last.warning' (which
is no longer stored in the workspace) with a print() method.
o The internal internet download functions have some new
features from libxml 2.6.26.
o There is an option "HTTPUserAgent" to set the User Agent in R
download requests etc. Patch from S. Falcon.
o PCRE has been updated to version 6.7.
o The C function substituteList now has tail recursion expanded
out, so C stack overflow is less likely. (PR#8141, fix by
Kevin Hendricks)
o The (somewhat soft) 1023/4 byte limit on command lines is now
documented in 'An Introduction to R'.
o The maximum number of open connections has been increased from
50 to 128.
o There is a new manual 'R Internals' on R internal stuctures
plus the former appendices of 'Writing R Extensions'.
o The autoloads introduced at the package re-organization have been
almost completely removed: the one that remains is for ts().
o The setting of the various Java configuration variables has been
improved to refer to JAVA_HOME, and they are now documented in
the R-admin manual.
o It is (again) possible to calculate prediction intervals from
"lm" objects for the original data frame, now with a warning
that the intervals refer to future observations. Weighted
intervals have also been implemented, with user-specifiable
weights. Warnings are given in cases where the default
behaviour might differ from user expectations. See the
?predict.lm for details.
CHANGES TO S4 METHODS
o The default prototype object for S4 classes will have its own
internal type in 2.4.0, as opposed to being an empty list (the
cause of several errors in the code up to 2.3.1). Note that old
binary objects, including class definitions, will be
inconsistent with the type, and should be recreated.
o S4 method dispatch has been completely revised to use cached
generic functions and to search for the best match among
inherited methods. See ?Methods and
http://developer.r-project.org/howMethodsWork.pdf
o Objects created from an S4 class are now marked by an internal flag,
tested by isS4() in R and by macro IS_S4_OBJECT() in C. This
is an efficient and reliable test, and should replace all
earlier heuristic tests.
o Some changes have been made to automatic printing of S4
objects, to make this correspond to a call to show(), as per
'Programming with Data'.
o S4 generic and class definitions are now cached when the related
package is loaded. This should improve efficiency and also
avoid anomalous situations in which a class or generic cannot
be found.
o trace() now creates a new S4 class for the traced object if
required. This allows tracing of user-defined subclasses of
"function".
DEPRECATED & DEFUNCT
o The re-named tcltk functions tkcmd, tkfile.tail, tkfile.dir,
tkopen, tkclose, tkputs, tkread are now defunct.
o Argument 'col' of bxp() has been removed: use 'boxfill'.
o Use of NULL as an environment is now an error.
o postscriptFont() is defunct: use Type1Font().
o La.chol() and La.chol2inv() are defunct (they were the same as
the default options of chol() and chol2inv).
o La.svd(method = "dgesvd") is defunct.
o Files install.R and R_PROFILE.R in packages are now ignored
(with a warning).
o The following deprecated command-line options to INSTALL have
been removed (use the fields in the DESCRIPTION file instead):
-s --save --no-save --lazy --no-lazy --lazy-data --no-lazy-data
o Graphical parameter 'tmag' is obsolete.
o mauchley.test() (package 'stats') is now defunct.
o symbol.C() and symbol.For() are deprecated. They are required in
S for use with is.loaded(), but are not so required in R.
o load()ing an object saved in one of the formats used prior to
R 1.4.0 is deprecated. Such objects should be re-saved in the
current format.
o save(version = 1) is now deprecated.
C-LEVEL FACILITIES
o The convenience function ScalarLogical now coerces all
non-zero non-NA values to TRUE.
o The vector accessor functions such as INTEGER, REAL and
SET_VECTOR_ELT now check that they are called on the
correct SEXPTYPE (or at least on a compatible one). See
`Writing R Extensions' for the details and for a stricter
test regime.
o It is no longer possible to pass list variables to
.C(DUP = FALSE): it would have given rise to obscure garbage
collection errors.
o allocString is now a macro, so packages using it will need to
be reinstalled.
o R_ParseVector was returning with object(s) protected in the
parser if the status was PARSE_INCOMPLETE or PARSE_ERROR.
o There is a new function Rf_endEmbeddedR to properly terminate
a session started by Rf_initEmbeddedR, and both are now
available on Windows as well as on Unix-alikes. These and
related functions are declared in a new header <Rembedded.h>.
If R_TempDir is set when embedded R is initialized it is
assumed to point to a valid session temporary directory: see
`Writing R Extensions'.
o There is a new interface allowing one package to make C routines
available to C code in other packages. The interface consists
of the routines R_RegisterCCallable and R_GetCCallable. These
functions are declared in <R_ext/Rdynload.h>. This interface
is experimental and subject to change.
In addition, a package can arrange to make use of header
files in another (already installed) package via the
'LinkingTo' field in the DESCRIPTION file: see 'Writing R
Extensions'.
UTILITIES
o R CMD SHLIB now handles (as linker commands) -L*, -l* and *.a.
o R CMD check now:
- warns if there are non-ASCII characters in the R code (as
these will likely be syntax errors in some locale).
- tests Rd cross-references by default, and tests for
(syntactically) valid CITATION metadata.
- tests that the package can be loaded, and that the package
and namespace (if there is one) can each be loaded in
startup code (before the standard packages are loaded).
- tests for empty 'exec' or 'inst' directories.
- checks if $(FLIBS) is used when $(BLAS_LIBS) is.
- checks that all packages (except non-S4-using standard
packages) used in ::, :::, library() and require() calls are
declared in the DESCRIPTION file, and 'methods' is declared if
S4 classes or methods are set.
- throws an error if the standard packages 'methods' and
'stats4' are imported from in the NAMESPACE file and not
declared in the DESCRIPTION file.
o The test script produced by massage-Examples.pl no longer
creates objects in the base environment.
o New utilties R CMD Stangle and R CMD Sweave for extracting S/R
code from and processing Sweave documentation, respectively.
o The DESCRIPTION file of packages may contain an 'Enhances:'
field.
o An R CMD javareconf script has been added to allow Java
configuration to be updated even after R has been installed.
INSTALLATION
o The C function realpath (used by normalizePath()) is hidden on
some systems and we try harder to find it.
o There is a new option --enable-BLAS-shlib, which compiles the
BLAS into a dynamic library -lRblas and links against that.
For the pros and cons see the R-admin manual.
The defaults are now --without-blas (so you have explicitly to
ask for an external BLAS), and --enable-BLAS-shlib unless
a usable external BLAS is found or on AIX or on MacOS X 10.2
and earlier.
o MacOS X did not like having LSAME in both BLAS and LAPACK
libraries, so it is no longer part of the R-internal LAPACK.
We now require an external BLAS to provide LSAME: it seems
that nowadays all do.
o The configure test for 'whether mixed C/Fortran code can be
run' has been improved as on one system that test passed but
the Fortran run-time library was broken.
o A precious configure variable DEFS can be set to pass defines
(e.g. -DUSE_TYPE_CHECKING_STRICT) to C code when compiling R.
o There is now a test for visible __libc_stack_end on Linux
systems (since it is not visible on some recent glibc's
built from the sources).
o MacOS X 10.4 and higher now use two-level namespaces, single
module in a shared library and allow undefined symbols to be
resolved at run-time. This implies that common symbols are now
allowed in package libraries. --enable-BLAS-shlib is supported
for internal BLAS, external BLAS framework and external static
BLAS. An external dynamic library BLAS is NOT supported. (But
it can be easily used by replacing internal BLAS library file
later.) MacOS X < 10.4 does not support --enable-BLAS-shlib.
o Dynamic libraries and modules use a flat namespace on MacOS X
10.4 and higher if either Xcode tools don't support dynamic
lookup (Xcode < 2.3) or the FORCE_FLAT_NAMESPACE environment
variable is set. (The latter was introduced temporarily for
testing purposes and may go away anytime.)
o configure now defaults to 'run-time linking' on AIX
(and AIX < 4.2 is no longer allowed), using -bexpall rather
than export/import files. If this works, it allows R to be
built in the same way as other Unix-alikes, including with R
as a shared library and with a shared BLAS.
o The "mac.binary" package type now defaults to universal
binary. If a repository supports architecture-specific Mac
binaries, they can be requested by using "mac.binary.xxx" in
contrib.url(), where xxx is the desired architecture.
BUG FIXES
o The name of a Fortran symbol reported to be missing by
.Fortran() is now the actual name. (What was reported to be
an 'entry point' was missing the common leading underscore.)
o print() on a MBCS character string now works properly a
character at a time rather than a byte at time. (This does
not affect MBCSs like UTF-8 and the Windows DBCSes which have
non-ASCII lead bytes and always worked correctly.)
o glm() now recalculates the null deviance whenever there is an
offset (even if it is exactly zero to avoid a discontinuity in
that case, since the calculations with and without offset are
done by different algorithms).
o Amongst families, quasi() accepted an expression for link and
no other did. Now all accept an expression which evaluates to
a one-element character vector (although e.g. 'logit' is taken
as a name and not an expression).
o trace() now accepts arguments where= and signature= for the
old-style trace (no tracer or exit, edit==FALSE) and just
prints a message on entry. Also the undocumented feature of
where=function now works for generic functions as well.
o callNextMethod() failed for recursive use when the methods had
nonstandard argument lists. Now enforces the semantic rule
that the inheritance is fixed when the method containing the
callNextMethod() is installed. See Details in the documentation.
o UseMethod() looked for the defining environment of 'generic' as
if it were the current function, although some functions are
generic for methods of a different generic.
Lookup for S3 methods is confined to functions: previously a
non-function 'fun.class' could have masked a function of the
same name.
o Line types (lty) specified as hex strings were documented not to
allow zero, but some devices accepted zero and handled it in a
device-dependent way. Now it is an error on all devices.
(PR#8914)
o Subassignment for a time series can no longer extend the series:
it used to attempt to but failed to adjust the tsp attributes.
Now window() must be used.
o Function AIC() in package 'stats4' was not dispatching correctly
on S4 classes via logLik() because of namespace issues.
o Subsetting LANGSXPs could break the call-by-value illusion.
(PR#7924) (patch from Kevin Hendricks).
o parse() with n > 1 gave a syntax error if fewer than n statements
were available.
o parse() with n > 1 gave strange results on some syntax errors.
(PR#8815)
o lag.plot() now respects graphical parameters for the axes.
o Using a wrong link in family() now gives more consistent error
messages.
o sort.list(method="radix") works on factors again.
o object.size() is more accurate for vector objects (it takes into
account the smaller header and also the fixed sizes used in
the node classes for small vector objects).
o addmargins(T, ...) now returns a "table" when 'T' is a "table", as
its help page has always suggested.
o remove() now explicitly precludes removing variables from
baseenv() and throws an error (this was previously ignored).
o Saving the workspace at the end of a session now works as has
long been intended, that is it is saved only if something has
been added/deleted/changed during the current session.
o The search for bindings in <<-, ->> and assign(inherits=TRUE)
was omitting the base package, although this was not
documented. Now the base package is included (but most
bindings there are locked).
o dweibull(0, shape) was NaN not Inf for shape < 1. Also, the
help for dgamma and dweibull gave support as x > 0, but
returned non-zero values for x = 0. (PR#9080)
o Subsetting arrays no longer preserves attributes (it was
removed for matrices in 1998).
o The "factor" method of as.character() no longer maps level
"NA" to "<NA>" (a legacy of before there were NA character
strings).
o terms(keep.order=TRUE) was not returning a valid "order"
attribute.
o The DLL registration code was not freeing .External symbols.
o The internet download routines expected URLs of less than 4096
bytes, but did not check. Now this is checked, and http:// URLs
are allowed to be up to 40960 bytes.
o parse(n=-1) threw a stack-imbalance error, and parse(n=3) did
not cope correctly with EOF during input.
o Zero-column data frames had no names (rather than character(0)).
o by() and acf() could get confused when they used very long
expressions as names.
o residuals(<glm object>, type="working") was NA for cases with
zero weight (whereas they are well-defined even though the
case was not used during the fitting) and the actual value is
now returned. This allows residuals to be computed from fits
with 'y = FALSE'.
The residuals in a fitted "glm" object are computed more
accurately: the previous formula was subject to cancellation.
o loess() now checks the validity of its 'control' argument.
o rownames(<0-row matrix>, do.NULL=FALSE) was wrong. (PR#9136)
o apply() now works as documented when applied over 2 or more
margins with one of zero extent. (It used to drop dimensions.)
o head() and tail() now also work row-wise for "table" and "ftable"
objects.
o NextMethod() could throw an error/crash if called from a method
that was called directly rather than from a generic (so
.Method was unset).
o order(x, na.last = NA) failed for a zero-length x.
o grep(pat, x, value = TRUE, perl = L) preserved names for
L == TRUE && !is.na(pat) but not otherwise. Now it always does.
o [rc]bind() now find registered methods and not just visible ones.
o Printing a factor no longer ignores attributes such as names and
dim/dimnames.
o Command-line arguments after --encoding were ignored.
o The check for impossible confidence levels was off by one in
wilcox.test (PR#8557)
o [[ on an environment could create aliases. (PR#8457)
o pt() with a very small (or zero) non-centrality parameter could
give an unduly stringent warning about 'full precision was not
achieved'. (PR#9171)
o writeChar() could segfault if 'nchars' was given silly values.
o qt() and rt() did not work for vector 'ncp', and qt() did not
work for negative 'ncp'.
o ns() failed to work correctly when 'x' was of length one.
o identical() ignored tags on pairlists (including names of
attributes) and required an identical ordering for
attribute values in their pairlists. Now names are compared
on pairlists, and attribute sets are treated as unordered.
o If they were unused arguments supplied to a closure, only
the first non-empty one was reported, despite the message.
Unmatched empty arguments (such as f(1,,) for a function of
one argument) were ignored. They are now an error.
o Calling a builtin with empty arguments used to silently remove
them (and this was undocumented). Now this is an error unless
builtin is c() or list() or there are only trailing empty
arguments, when it is a warning (for the time being: this will
be made an error in R 2.5.0).
o install.packages() ignored 'configure.args' if the vector was
unnamed.
o biplot() now works if there are missing values in the data.
o biplot() now passes par() values to all four axes (not
just those on sides 1 and 2).
o [.acf now handles an empty first index.
o Deparsing uses backticks more consistently to quote
non-syntactic names.
o Assigning to the symbol in a for() loop with a
list/expression/pairlist index could alter the index. Now the
loop variable is explicitly read-only. (PR#9216)
o Using old.packages() (and hence update.packages()) on an empty
(or non-existent) library failed with an obscure message.
o plot.xy() could segfault if supplied with an invalid 'col'
argument. (PR#9221)
o menu() with graphics=TRUE attempted to use Tcl/Tk on unix even
if DISPLAY was not set (in which case Tk is not available and
so the attempt is bound to fail).
o The print() method for 'dist' objects prints a matrix even for
n = 2.
o The cumxxx functions were missing some PROTECTs and so could
segfault on long vectors (especially with names or where
coercion to numeric occurred).
o The X11() device no longer produces (apparently spurious)
'BadWindow (invalid Window parameter)' warnings when run from
Rcmdr.
o legend() assumed that widths and heights of strings were positive,
which they need not be in user coordinates with reversed axes.
(In part, PR#9236)
o The plot() methods for "profile.nls" objects could get
confused if 'which' had been used in the profile() call. (PR#9231)
o boxplot() did not passed named arguments (except graphics
parameters) to bxp() as documented. (PR#9183)
o Only genuinely empty statements act as 'return' in the
browser, not say those starting with a comment char. (PR#9063)
o summary.mlm() incorrectly used accessor functions to fake an
"lm" object. (PR#9191)
o prettyNum() was not preserving attributes, despite being
explicitly documented to. (PR#8695)
o It was previously undocumented what happened if a graphical
parameter was passed in both '...' and 'pars' to boxplot()
and bxp(), and they behaved differently. Now those passed in
'...' have precedence in both cases.
o A failed subassignment could leave behind an object '*tmp*'.
The fix also sometimes gives better error messages.
o Using SIGUSR1 on Unix now always terminates a session, and no
longer is caught by browser contexts and restarts (such as try()).
o In the 'graphics' package, in-line 'font=5' was being ignored
(report by Tom Cook).
o nls() looked for non-parameter arguments in a function call in
the wrong scope (from the body of nls).
o Printing of complex numbers could misbehave when one of the
parts was large (so scientific notation was used) and the
other was so much smaller that it had no significant digits
and should have been printed as zero (e.g. 1e80+3e44i).
o Using install.packages with type="mac.binary" and target path
starting with ~ failed with a cryptic message while unpacking.
o getwd() now works correctly when the working directory is
unavailable (e.g. unreadable).
o The alternative hypothesis in wilcox.test() was labelled by an
unexplained quantity 'mu' which is now spelled out.
The alternative hypothesis in ks.test() is clearer both in the
documentation and in the result. (PR#5360)
--
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-2.4.0 is released
|
Peter Dalgaard
| 459 |
|
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: [S] 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
--------------------------------------------------------------------
This message was distributed by s-news at lists.biostat.wustl.edu. To
...(s-news.. clipped)...
.
|
[S] Gstat: multivariable geostatistics for S (R and S-Plus)
|
Edzer J. Pebesma
| 160 |
|
From james.lindsey at luc.ac.be Wed Oct 17 12:49:29 2001
From: james.lindsey at luc.ac.be (Jim Lindsey)
Date: Wed, 17 Oct 2001 12:49:29 +0200 (MET DST)
Subject: stochastic course notes with R
Message-ID: <[email protected]>
I have just put the postscript file for the first draft of a
manuscript of a course on The Statistical Analysis of Stochastic
Processes in Time, as well as the R code to do all of the examples, on
my web page at
www.luc.ac.be/~jlindsey/manuscripts.html
The chapters are
Part I Basic principles
1. What is a stochastic process?
2. Normal theory models and extensions.
Part II Categorical state space
3. Survival processes.
4. Recurrent events.
5. Discrete-time Markov chains.
6. Event histories.
7. Dynamic models.
8. More complex dependencies.
Part III Continuous state space
9. Time series.
10. Growth curves.
11. Dynamic models.
12. Repeated measurements.
Although it contains chapters on survival analysis and time series, as
far as I have been able to see, the ts and survival libraries are not
capable of performing the analyses that I required, except for some of
the simple plots.
As a reminder, the following books all have complete R code available
on my web page as well:
Introductory Statistics. A Modelling Approach. OUP, 1995 0-19-852345-9
(also instructor's manual can be downloaded)
Models for Repeated Measurements. (2nd edn) OUP, 1999 0-19-850559-0
Nonlinear Models in Medical Statistics. OUP, 2001 0-19-850812-3
Of course, all four require my R libraries available at
www.luc.ac.be/~jlindsey/rcode.html
Comments and criticisms are very welcome.
Jim
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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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|
stochastic course notes with R
|
Jim Lindsey
| 276 |
|
From Friedrich.Leisch at ci.tuwien.ac.at Thu Oct 30 09:35:32 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Thu, 30 Oct 2003 09:35:32 +0100
Subject: R News Volume 3/2
Message-ID: <[email protected]>
We have published the 2003/2 issue of R News on
http://cran.R-project.org/doc/Rnews
where you can download the newsletter as PDF or Postscript file. It
will propagate to the CRAN mirrors within a day or two.
Contents of this issue:
R Help Desk
Integrating grid Graphics Output with Base Graphics Output
A New Package for the General Error Distribution
Web-based Microarray Analysis using Bioconductor
Sweave, Part II: Package Vignettes
R Foundation News
Recent Events
Book Reviews
Changes in R 1.8.0
Changes on CRAN
Crossword Solution
Correction to ``Building Microsoft Windows Versions of R and R
packages under Intel Linux''
For the editorial board,
Fritz Leisch
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 10715
Technische Universit?t Wien Fax: (+43 1) 58801 10798
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
|
R News Volume 3/2
|
Friedrich.Leisch at ci.tuwien.ac.at
| 191 |
|
From tlumley at u.washington.edu Wed Oct 6 20:00:08 2004
From: tlumley at u.washington.edu (Thomas Lumley)
Date: Wed, 6 Oct 2004 11:00:08 -0700 (PDT)
Subject: R Newsletter
Message-ID: <[email protected]>
Issue 4/2 of the R Newsletter is up on www.r-project.org.
This issue is especially commended to your attention since it has an
article by Brian Ripley describing the largest change in R 2.0.0, lazy
loading of packages.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
|
R Newsletter
|
Thomas Lumley
| 385 |
|
From dicook at iastate.edu Fri Mar 9 22:26:24 2007
From: dicook at iastate.edu (Dianne Cook)
Date: Fri, 9 Mar 2007 15:26:24 -0600
Subject: useR! 2007 --- Call for papers and posters
Message-ID: <[email protected]>
R Users and Developers,
The first North American useR! will be held at Iowa State University,
Ames, Iowa, August 8?10, 2007. Information about the meeting can be
found at http://www.user2007.org/.
We are now ready to accept paper and poster submissions.
Papers are encouraged in all areas, but particular emphasis is given
to work describing newly created or improved R packages. Papers will
be refereed and a best paper/presentation award is likely. Your full
paper needs to be submitted by April 23, 5:00PM CST, to be considered
for the meeting.
There will also be the opportunity to present your work as a poster
instead of a paper. Poster submissions will be in the form of an
abstract and needs to be submitted by June 30.
Submit full papers, and poster abstracts, to submissions at user2007.org.
useR! Program Committee
user2007 at iastate.edu
|
useR! 2007 --- Call for papers and posters
|
Dianne Cook
| 413 |
|
From chong at stat.purdue.edu Tue Jul 6 18:40:14 1999
From: chong at stat.purdue.edu (Chong Gu)
Date: Tue, 6 Jul 1999 11:40:14 -0500
Subject: New smoothing spline package gss
Message-ID: <[email protected]>
Dear fellow R users,
I just uploaded a new package gss to ftp.ci.tuwien.ac.at. The package
name gss stands for General Smoothing Spline.
In the current version (0.4-1), it handles nonparametric multivariate
regression with Gaussian, Binomial, Poisson, Gamma, Inverse Gaussian,
and Negative Binomial responses. I am still working on code for
density estimation and hazard rate estimation to be made available in
future releases.
On the modeling side, gss uses tensor-product smoothing splines to
construct nonparametric ANOVA structures using cubic spline, linear
spline, and thin-plate spline marginals. The popular
(main-effect-only) additive models are special cases of nonparametric
ANOVA models. The syntax of gss functions resembles that of the lm
and glm suites.
Among new features that are not available from other spline packages
are the standard errors needed for the construction of Wahba's Bayesian
confidence intervals for smoothing spline fits, so you may want to try
out gss even if you only wants to calculate a univariate cubic spline
or a single term thin-plate spline.
For those familiar with smoothing splines, gss is a front end to
RKPACK, which encodes O(n^3) generic algorithms for reproducing kernel
based smoothing spline calculation.
Reports on bugs and suggestions for improvements/new features are most
welcome.
Chong Gu
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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 smoothing spline package gss
|
Chong Gu
| 491 |
|
From keitt at nceas.ucsb.edu Sat Jan 8 22:29:24 2000
From: keitt at nceas.ucsb.edu (Timothy H. Keitt)
Date: Sat, 08 Jan 2000 13:29:24 -0800
Subject: RPgSQL 0.3
Message-ID: <[email protected]>
A new version of the RPgSQL package is available at
http://www.nceas.ucsb.edu/~keitt/R/ (also uploaded to CRAN). I added a
configure script. Hopefully this will solve any installation problems.
T.
--
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
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
RPgSQL 0.3
|
Timothy H. Keitt
| 343 |
|
From bates at stat.wisc.edu Tue Feb 29 13:28:20 2000
From: bates at stat.wisc.edu (Douglas Bates)
Date: 29 Feb 2000 06:28:20 -0600
Subject: R-1.0 is available via rsync
Message-ID: <[email protected]>
You can now obtain the R-1.0 sources via rsync from
rsync.r-project.org as the r-release module. For example,
rsync -aC rsync.r-project.org::r-release ./R-1.0.0
will create a copy of the source tree (minus the CVS subdirectories)
in the subdirectory R-1.0.0
The module r-release-patched incorporates any patches that may be made
to the current released version. The module r-devel is a copy of the
unstable, development version of the CVS tree.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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-1.0 is available via rsync
|
Douglas Bates
| 308 |
|
From P.Dalgaard at biostat.ku.dk Fri Sep 25 12:25:18 2009
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Fri, 25 Sep 2009 12:25:18 +0200
Subject: R 2.10.0 is scheduled for October 26
Message-ID: <[email protected]>
This is to announce that we plan to release R version 2.10.0 on Monday,
October 26, 2009.
Release procedures start today. The detailed schedule can
be found on http://developer.r-project.org
The source tarballs will be made available daily (barring build
troubles), starting September 28, and the tarballs can be picked up at
http://cran.r-project.org/src/base-prerelease/
a little later.
Binary builds are expected to appear soon thereafter.
For the Core Team
Peter Dalgaard
--
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 2.10.0 is scheduled for October 26
|
Peter Dalgaard
| 661 |
|
From pd.mes at cbs.dk Mon Oct 31 11:22:44 2016
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 31 Oct 2016 10:22:44 +0000
Subject: [R] R 3.3.2 is released
Message-ID: <[email protected]>
The build system rolled up R-3.3.2.tar.gz (codename "Sincere Pumpkin Patch") 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-3.3.2.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) = 342856fe28ac8af7c8d48db1f6dde8e2
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 3edf7e6a206a1303ed50979fb21d2ab7
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = 2437014ef40641cdc9673e89c040b7a8
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = f80d02e7ba9729a927e1c9cf7b435b32
MD5 (VERSION-INFO.dcf) = c643e0eb5a8e98b034f76287c574be32
MD5 (R-3/R-3.3.2.tar.gz) = 2437014ef40641cdc9673e89c040b7a8
This is the relevant part of the NEWS file
CHANGES IN R 3.3.2:
NEW FEATURES:
* extSoftVersion() now reports the version (if any) of the readline
library in use.
* The version of LAPACK included in the sources has been updated to
3.6.1, a bug-fix release including a speedup for the
non-symmetric case of eigen().
* Use options(deparse.max.lines=) to limit the number of lines
recorded in .Traceback and other deparsing activities.
* format(<AsIs>) looks more regular, also for non-character atomic
matrices.
* abbreviate() gains an option named = TRUE.
* The online documentation for package methods is extensively
rewritten. The goals are to simplify documentation for basic
use, to note old features not recommended and to correct
out-of-date information.
* Calls to setMethod() no longer print a message when creating a
generic function in those cases where that is natural: S3
generics and primitives.
INSTALLATION and INCLUDED SOFTWARE:
* Versions of the readline library >= 6.3 had been changed so that
terminal window resizes were not signalled to readline: code has
been added using a explicit signal handler to work around that
(when R is compiled against readline >= 6.3). (PR#16604)
* configure works better with Oracle Developer Studio 12.5.
UTILITIES:
* R CMD check reports more dubious flags in files
src/Makevars[.in], including -w and -g.
* R CMD check has been set up to filter important warnings from
recent versions of gfortran with -Wall -pedantic: this now
reports non-portable GNU extensions such as out-of-order
declarations.
* R CMD config works better with paths containing spaces, even
those of home directories (as reported by Ken Beath).
DEPRECATED AND DEFUNCT:
* Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
are included by R headers from C++ as from R 3.3.0, so it should
no longer be needed).
BUG FIXES:
* The check for non-portable flags in R CMD check could be stymied
by src/Makevars files which contained targets.
* (Windows only) When using certain desktop themes in Windows 7 or
higher, Alt-Tab could cause Rterm to stop accepting input.
(PR#14406; patch submitted by Jan Gleixner.)
* pretty(d, ..) behaves better for date-time d (PR#16923).
* When an S4 class name matches multiple classes in the S4 cache,
perform a dynamic search in order to obey namespace imports.
This should eliminate annoying messages about multiple hits in
the class cache. Also, pass along the package from the
ClassExtends object when looking up superclasses in the cache.
* sample(NA_real_) now works.
* Packages using non-ASCII encodings in their code did not install
data properly on systems using different encodings.
* merge(df1, df2) now also works for data frames with column names
"na.last", "decreasing", or "method". (PR#17119)
* contour() caused a segfault if the labels argument had length
zero. (Reported by Bill Dunlap.)
* unique(warnings()) works more correctly, thanks to a new
duplicated.warnings() method.
* findInterval(x, vec = numeric(), all.inside = TRUE) now returns
0s as documented. (Reported by Bill Dunlap.)
* (Windows only) R CMD SHLIB failed when a symbol in the resulting
library had the same name as a keyword in the .def file.
(PR#17130)
* pmax() and pmin() now work with (more ?) classed objects, such
as "Matrix" from the Matrix package, as documented for a long
time.
* axis(side, x = D) and hence Axis() and plot() now work correctly
for "Date" and time objects D, even when "time goes backward",
e.g., with decreasing xlim. (Reported by William May.)
* str(I(matrix(..))) now looks as always intended.
* plot.ts(), the plot() method for time series, now respects cex,
lwd and lty. (Reported by Greg Werbin.)
* parallel::mccollect() now returns a named list (as documented)
when called with wait = FALSE. (Reported by Michel Lang.)
* If a package added a class to a class union in another package,
loading the first package gave erroneous warnings about
"undefined subclass".
* c()'s argument use.names is documented now, as belonging to the
(C internal) default method. In "parallel", argument recursive
is also moved from the generic to the default method, such that
the formal argument list of base generic c() is just (...).
* rbeta(4, NA) and similarly rgamma() and rnbinom() now return
NaN's with a warning, as other r<dist>(), and as documented.
(PR#17155)
* Using options(checkPackageLicense = TRUE) no longer requires
acceptance of the licence for non-default standard packages such
as compiler. (Reported by Mikko Korpela.)
* split(<very_long>, *) now works even when the split off parts are
long. (PR#17139)
* min() and max() now also work correctly when the argument list
starts with character(0). (PR#17160)
* Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
thanks to Michael Schubmehl's PR#17158.
* bartlett.test() used residual sums of squares instead of
variances, when the argument was a list of lm objects. (Reported
by Jens Ledet Jensen).
* plot(<lm>, which = *) now correctly labels the contour lines for
the standardized residuals for which = 6. It also takes the
correct p in case of singularities (also for which = 5).
(PR#17161)
* xtabs(~ exclude) no longer fails from wrong scope, thanks to
Suharto Anggono's PR#17147.
* Reference class calls to methods() did not re-analyse previously
defined methods, meaning that calls to methods defined later
would fail. (Reported by Charles Tilford).
* findInterval(x, vec, left.open = TRUE) misbehaved in some cases.
(Reported by Dmitriy Chernykh.)
--
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] R 3.3.2 is released
|
Peter Dalgaard
| 130 |
|
From P.Dalgaard at biostat.ku.dk Mon Oct 26 16:20:58 2009
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Mon, 26 Oct 2009 16:20:58 +0100
Subject: R 2.9.0 is released
Message-ID: <[email protected]>
I've rolled up R-2.10.0.tar.gz some hours ago. This is a development
release which contains a number of new features, notably a brand new
HTML based dynamic help system.
Also, a number of mostly minor bugs have been fixed. See the full list
of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.10.0.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:
70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
b80eafe743ef130e129c6d004793492f NEWS
7abcbbc7480df75a11a00bb09783db90 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
9ec5df24a0d6ecb04a9817275b825027 FAQ
4486934883b1dbcd5400135e22b26a75 R-2.10.0.tar.gz
4486934883b1dbcd5400135e22b26a75 R-latest.tar.gz
This is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.10.0
SIGNIFICANT USER-VISIBLE CHANGES
o Package help is now converted from Rd by the R-based converters
that were first introduced in 2.9.0. This means
- Packages that were installed by R-devel after 2009-08-09
should not be used with earlier versions of R, and most
aspects of package help (including the runnable examples)
will be missing if they are so used.
- Text, HTML and latex help and examples for packages
installed under the new system are converted on-demand from
stored parsed Rd files. (Conversions stored in packages
installed under R < 2.10.0 are used if no parsed Rd files
are found. It is recommended that such packages be
re-installed.)
o HTML help is now generated dynamically using an HTTP server
running in the R process and listening on the loopback
interface.
- Those worried about security implications of such a server
can disable it by setting the environment variable
R_DISABLE_HTTPD to a non-empty value. This disables
help.start() and HTML help (so text help is shown instead).
- The Java/Javascript search engine has been replaced by an
HTML interface to help.search(). help.start() no longer has
an argument 'searchEngine' as it is no longer needed.
- The HTML help can now locate cross-references of the form
\link[pkg]{foo} and \link[pkg:foo]{bar} where 'foo' is an
alias in the package, rather than the documented (basename
of a) filename (since the documentation has been much
ignored).
NEW FEATURES
o polygon(), pdf() and postscript() now have a parameter
'fillOddEven' (default FALSE), which controls the mode used for
polygon fills of self-intersecting shapes.
o New debugonce() function; further,
getOption("deparse.max.lines") is now observed when debugging,
from a code suggestion by John Brzustowski. (PR#13647/8)
o plot() methods for "stepfun" and hence "ecdf" no longer plot
points by default for n >= 1000.
o [g]sub(*, perl=TRUE) now also supports '\E' in order to *end*
\U and \L case changes, thanks to a patch from Bill Dunlap.
o factor(), `levels<-`(), etc, now ensure that the resulting factor
levels are unique (as was always the implied intention). Factors
with duplicated levels are still constructible by low-level means,
but are now declared illegal.
o New print() (S3) method for class "function", also used for
auto-printing. Further, .Primitive functions now print and
auto-print identically. The new method is based on code
suggestions by Romain Fran?ois.
o The print() and toLatex() methods for class "sessionInfo" now
show the locale in a nicer format and have arguments to
suppress locale information.
o In addition to previously only round(), there are other 'Math'
group (S3) methods for 'difftime', such as floor(), signif(),
abs(), etc.
o For completeness, old.packages() and available.packages() allow
'type' to be specified (you could always specify 'available'
or 'contriburl').
o available.packages() by default only returns information on
the latest versions of packages whose version requirements are
satisified by the currently running R.
o tools::write_PACKAGES() has a new argument 'latestOnly', which
defaults to TRUE when only the latest versions in the
repository will be listed in the index.
o getOption() has a new argument 'default' that is returned if
the specified option is not set. This simplifies querying a
value and checking whether it is NULL or not.
o parse() now warns if the requested encoding is not supported.
o The "table" method of as.data.frame() gains a 'stringsAsFactors'
argument to allow the classifying factors to be returned as
character vectors rather than the default factor type.
o If model.frame.default() encounters a character variable where
'xlev' indicates a factor, it now converts the variable to a
factor (with a warning).
o curve() now returns a list containing the points that were drawn.
o spineplot() now accepts axes = FALSE, for consistency with
other functions called by plot.factor().
o The Kendall and Spearman methods of cor.test() can optionally
use continuity correction when not computing exact p-values.
(The Kendall case is the wish of PR#13691.)
o R now keeps track of line numbers during execution for
code sourced with options(keep.source = TRUE). The source
reference is displayed by debugging functions such as traceback(),
browser(), recover(), and dump.frames(), and is stored as an
attribute on each element returned by sys.calls(). [Experimental]
o More functions now have an implicit (S4) generic definition.
o quantile.default() now disallows factors (wish of PR#13631)
and its help documents what numeric-like properties its input
need to have to work correctly.
o weighted.mean() is now generic and has "Date", "POSIXct" and
"POSIXlt" methods.
o Naming subscripts (e.g. x[i=1, j=2]) in data.frame methods for
[ and [[ now gives a warning. (Names are ignored in the
default method, but could have odd semantics for other
methods, and do for the data.frame ones.)
o as.data.frame() has an "aovproj" method. (Wish of PR#13505)
o as.character(x) for numeric x no longer produces strings such as
"0.30", i.e., with trailing zeros. This change also renders
levels construction in factor() more consistent.
o codocClasses(), which checks consistency of the documentation of
S4 class slots, now does so in considerably more cases. The
documentation of inherited slots (from superclasses) is now
optional. This affects 'R CMD check <pkg>' when the package
defines S4 classes.
o codoc() now also checks S4 methods for code/documentation
mismatches.
o for(), while(), and repeat() loops now always return NULL as
their (invisible) value. This change was needed to address a
reference counting bug without creating performance penalties
for some common use cases.
o The print() method for ls.str() results now obeys an optional
'digits' argument.
o The 'method' argument of glm() now allows user-contributed methods.
o More general reorder.default() replaces functionality of
reorder.factor() and reorder.character().
o The function aspell() has been added to provide an interface to
the Aspell spell-checker.
o Filters RdTextFilter() and SweaveTeXFilter() have been added
to the tools package to provide support for aspell() or other
spell checkers.
o xtabs() with the new option 'sparse = TRUE' now returns a sparse
Matrix, using package 'Matrix'.
o contr.sum() etc gain an argument 'sparse' which allows sparse
matrices to be returned.
contrasts() also gains a 'sparse' argument which it passes to the
actual contrast function if that has a formal argument 'sparse'.
'contrasts(f, .) <- val' now also works when 'val' is a sparse
Matrix. It is planned that model.matrix() will work with such
factors 'f' in the future.
o readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the
NEWS file. However, it is safer to use only ASCII code there
because not all editors recognize BOMs.
o New utility function inheritedSlotNames() for S4 class programming.
o tabulate() now allows NAs to pass through (and be ignored).
o If debug() is called on an S3 generic function then all methods
are debugged as well.
o Outlier symbols drawn by boxplot() now obey the 'outlwd'
argument. Reported by Jurgen Kluge.
o svd(x) and eigen(x) now behave analogously to qr(x) in
accepting logical matrices x.
o File NEWS is now in UTF-8, and has a BOM (often invisible) on
the first line, and Emacs local variables set for UTF-8 at the
end. RShowDoc("NEWS") should display this correctly, given
suitable fonts.
o terms.formula(simplify = TRUE) now does not deparse the LHS and
so preserves non-standard responses such as `a: b` (requested
by Sundar Dorai-Raj).
o New function news() for building and querying R or package news
information.
o z^n for integer n and complex z is more accurate now if
|n| <= 65536.
o factor(NULL) now returns the same as factor(character(0))
instead of an error, and table(NULL) consequently does
analogously.
o as.data.frame.vector() (and its copies) is slightly faster
by avoiding a copy if there are no names (following a
suggestion of Tim Hesterberg).
o writeLines(), writeBin() and writeChar() have a new argument
'useBytes'. If false, character strings with marked encodings
are translated to the current locale (as before) but if true
they are written byte-by-byte.
o iconv() has a new argument 'mark' which can be used (by
experts) to suppress the declaration of encodings.
o DESCRIPTION 'LinkingTo' specs are now recognized as installation
dependencies, and included in package management computations.
o Standardized DESCRIPTION 'License' specs are now available for
package management computations.
o "\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8
encoded string even in non-UTF-8 locales (this has been
implemented on Windows since R 2.7.0). The semantics have
been changed slightly: a string containing such escapes is
always stored in UTF-8 (and hence is suitable for portably
including Unicode text in packages).
o New as.raw() method for "tclObj" objects (wish of PR#13578).
o Rd.sty now makes a better job of setting email addresses,
including using a monospaced font.
o textConnection() gains an 'encoding' argument to determine how
input strings with marked encodings will be handled.
o R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf.
o R CMD check now checks links where a package is specified
(\link[pkg]{file} or \link[pkg:file]{topic}), if the package
is available. It notes if the package is not available, as in
many cases this is an error in the link.
o identical() gains three logical arguments, which allow for even
more differentiation, notably '-0' and '0'.
o legend() now can specify the 'border' color of filled boxes,
thanks to a patch from Frederic Schutz.
o Indexing with a vector index to [[]] has now been extended to
all recursive types.
o Pairlists may now be assigned as elements of lists. (Lists
could always be created with pairlist elements, but [[<-
didn't support assigning them.)
o The parser now supports C-preprocessor-like #line directives,
so error messages and source references may refer to the original
file rather than an intermediate one.
o New functions findLineNum() and setBreakpoint() work with the
source references to find the location of source lines and set
breakpoints (using trace()) at those lines.
o Namespace importing is more careful about warning on masked
generics, thanks to a patch by Yohan Chalabi.
o detach() now has an argument 'character.only' with the same
meaning as for library() or require().
o available.packages() gains a 'filters' argument for specifying
the filtering operations performed on the packages found in the
repositories. A new built-in 'license/FOSS' filter only
retains packages for which installation can proceed solely based
on packages which can be verified as Free or Open Source
Software (FOSS) employing the available license specifications.
o In registering an S3 class by a call to setOldClass(), the data
part (e.g., the object type) required for the class can be
included as one of the superclasses in the Classes argument.
o The argument 'f' to showMethods() can be an expression evaluating
to a generic function, allowing methods to be shown for
non-exported generics and other nonstandard cases.
o sprintf() now supports '%o' for octal conversions.
o New function Sys.readlink() for information about symbolic
links, including if a file is a symbolic link.
o Package 'tools' has new functions checkRdaFiles() and
resaveRdaFiles() to report on the format of .rda/.RData data
files, and to re-save them in a different compressed format,
including choosing the most compact format available.
A new INSTALL option, --resave-data, makes use of this.
o File ~/.R/config is used in preference to ~/.Rconfig, and
these are now documented in 'R Installation and Administration'.
o Logic operations with complex numbers now work, as they were always
documented to, and as in S.
o arrows() and segments() allow one of x1 or y1 to be omitted to
simplify the specification of vertical or horizontal lines
(suggestion of Tim Hesterberg).
o approxfun() is faster by avoiding repeated NA checks (diagnosis
and patch by Karline Soetaert & Thomas Petzoldt).
o There are the beginnings of a Nynorsk translation by Karl Ove
Hufthammer.
o stripchart() allows par 'bg' to be passed in for the
background colour for pch = 21 (wish of PR#13984).
o New generic function .DollarNames() to enable class authors
to customize completion after the $ extractor.
o load(), save(), dput() and dump() now open a not-yet-open
connection in the appropriate mode (as other functions using
connections directly already did).
REGULAR EXPRESSIONS
o A different regular expression engine is used for basic and
extended regexps and is also for approximate matching. This is
based on the TRE library of Ville Laurikari, a modifed copy of
which is included in the R sources.
This is often faster, especially in a MBCS locale.
Some known differences are that it is less tolerant of invalid
inputs in MBCS locales, and in its interpretation of undefined
(extended) regexps such as "^*". Also, the interpretation of
ranges such as [W-z] in caseless matching is no longer to map
the range to lower case.
This engine may in future be used in 'literal' mode for fixed
= TRUE, and there is a compile-time option in src/main/grep.c
to do so.
o The use of repeated boundary regexps in gsub() and gregexpr() as
warned about in the help page does not work in this engine (it
did in the previous one since 2005).
o Extended (and basic) regexps now support same set of options as
for fixed = TRUE and perl = TRUE, including 'useBytes' and
support for UTF-8-encoded strings in non-UTF-8 locales.
o agrep() now has full support for MBCS locales with a modest
speed penalty. This enables help.search() to use approximate
matching character-wise rather than byte-wise.
o [g]sub use a single-pass algorithm instead of matching twice
and so is usually faster.
o The perl = TRUE versions now work correctly in a non-UTF-8 MBCS
locale, by translating the inputs to UTF-8.
o useBytes = TRUE now inhibits the translation of inputs with
marked encodings.
o strsplit() gains a 'useBytes' argument.
o The algorithm used by strsplit() has been reordered to batch by
elements of 'split': this can be much faster for fixed = FALSE
(as multiple compilation of regexps is avoided).
o The help pages, including ?regexp, have been updated and
should be consulted for details of the new implementations.
HELP & Rd FILE CHANGES
o A new dynamic HTML help system is used by default, and may be
controlled using tools::startDynamicHelp(). With this enabled,
HTML help pages will be generated on request, resolving links
by searching through the current .libPaths(). The user
may set option("help.ports") to control which IP port is used
by the server.
o help.start() no longer sets options(htmlhelp = TRUE) (it used
to on Unix but not on Windows). Nor does it on Unix reset the
"browser" option if given an argument of that name.
Arguments 'update' and 'remote' are now available on all
platforms: the default is update = FALSE since the http server
will update the package index at first use.
o help() has a new argument 'help_type' (with default set by the
option of that name) to supersede 'offline', 'htmlhelp' and
'chmhelp' (although for now they still work if 'help_type' is
unset). There is a new type, "PDF" to allow offline PDF
(rather than PostScript).
A function offline_help_helper() will be used if this exists
in the workspace or further down the search path, otherwise
the function of that name in the 'utils' name space is used.
o Plain text help is now used as the fallback for HTML help (as
it always was for Compiled HTML help on Windows).
o It is possible to ask for static HTML pages to be prebuilt via
the configure option --enable-prebuilt-html. This may be
useful for those who wish to make HTML help available outside
R, e.g. on a local web site.
o An experimental tag \Sexpr has been added to Rd files, to
evaluate expressions at build, install, or render time.
Currently install time and render time evaluation are
supported.
o Tags \if, \ifelse and \out have been added to allow
format-specific (or more general, using \Sexpr) conditional
text in man pages.
o The parse_Rd() parser has been made more tolerant of coding
errors in Rd files: now all syntax errors are reported as
warnings, and an attempt is made to continue parsing.
o parse_Rd() now has an argument 'fragment' (default FALSE) to
accept small fragments of Rd files (so that \Sexpr can output
Rd code which is then parsed).
o parse_Rd() now always converts its input to UTF-8. The Rd2*
rendering functions have a new parameter, 'outputEncoding',
which controls how their output is encoded.
o parse_Rd() no longer includes the newline as part of a
"%"-style comment.
o There have been various bug fixes and code reorganization in
the Rd renderers Rd2HTML, Rd2latex, Rd2txt, and Rd2ex.
All example files are now created with either ASCII or UTF-8
encoding, and the encoding is only marked in the file if there
is any non-UTF-8 code (previously it was marked if the help
file had non-ASCII contents, possibly in other sections).
o print.Rd() now adds necessary escape characters so that
printing and re-parsing an Rd object should produce an
equivalent object.
o parse_Rd() was incorrectly handling multiple backslashes in
R code strings, converting 4n+3 backslashes to 2n+1 instead
of 2n+2.
o parse_Rd() now recognizes the \var tag within a quoted string
in R-like text.
o parse_Rd() now treats the argument of \command as LaTeX-like,
rather than verbatim.
COMPRESSION
o New function untar() to list or unpack tar archives, possibly
compressed. This uses either an external 'tar' command or an
internal implementation.
o New function tar() to create (possibly compressed) tar archives.
o New functions memCompress() and memDecompress() for in-memory
compression and decompression.
o bzfile() has a 'compress' argument to select the amount of
effort put into compression when writing.
o New function xzfile() for use with xz-compressed files. (This
can also read files compressed by some versions of 'lzma'.)
o gzfile() looks at the file header and so can now also read
bzip2-ed files and xz-compressed files.
o There are the new options of save(compress = "bzip2") and "xz"
to use bzip2 or xz compression (which will be slower, but can
give substantially smaller files). Argument compression_level
gives finer control over the space/time tradeoffs.
load() can read such saves (but only as from this version of R).
o R CMD INSTALL/check and tools::writePACKAGES accept a wider
range of compressed tar archives. Precisely how wide depends
on the capabilities of the host system's 'tar' command: they
almost always include .tar.bz2 archives, and with modern
versions of 'tar' other forms of compression such as lzma and
xz, and arbitrary extensions.
o R CMD INSTALL has a new option --data-compress to control the
compression used when lazy-loading data. New possibilities are
--data-compress=bzip2 which will give ca 15% better
compression at the expense of slower installation times, and
--data-compress=xz, often giving even better compression on
large datasets at the expense of much longer installation
times. (The latter is used for the recommended packages: it is
particularly effective for 'survival'.)
o file() for open = "", "r" or "rt" will automagically detect
compressed files (from gzip, bzip2 or xz). This means that
compressed files can be specified by file name (rather than
via a gzfile() connection) to read.table(), readlines(),
scan() and so on.
o data() can handle compressed text files with extensions
.{txt,tab,csv}.{gz,bz2,xz} .
DEPRECATED & DEFUNCT
o png(type="cairo1") is defunct: the value is no longer recognized.
o tools::Rd_parse() is defunct (as this version of R uses only
Rd version 2).
o Use of ~/.Rconf (which was deprecated in favour of ~/.Rconfig
in 2004) has finally been removed.
o Bundles of packages are deprecated. See 'Writing R
Extensions' for the steps needed to unbundle a bundle.
o help() arguments 'offline', 'htmlhelp' and 'chmhelp' are
deprecated in favour of 'help_type'.
o clearNames() ('stats') is deprecated for unname().
o Basic regular expressions (extended = FALSE) are deprecated in
strsplit, grep and friends. There is a precise POSIX standard
for them, but it is not what recent RE engines implement, and
it seems that in almost all cases package authors intended
fixed = TRUE when using extended = FALSE.
o methods::trySilent() is deprecated for try(*, silent=TRUE) or
- more efficiently and flexibly - something like
tryCatch(*, error = function(e) e).
o index.search() is deprecated: there are no longer directories of
types other than 'help'.
INSTALLATION
o cairo >= 1.2 is now required (1.2.0 was released in July 2006)
for cairo-based graphics devices (which remain optional).
o A suitable iconv() is now required: support for configure option
--without-iconv has been withdrawn (it was deprecated in R 2.5.0).
o Perl is no longer 'essential'. R can be built without it, but
scripts R CMD build, check, Rprof and Sd2d require it.
o A system 'glob' function is now essential (a working
Sys.glob() has been assumed since R 2.9.0 at least).
o C99 support for MBCS is now required, and configure option
--disable-mbcs has been withdrawn.
o Having a version of 'tar' capable of automagically detecting
compressed archives is useful for utils::untar(), and so 'gtar'
(a common name for GNU tar) is preferred to 'tar': set
environment variable TAR to specify a particular 'tar' command.
INTERNATIONALIZATION
o There is some makefile support for adding/updating translations
in packages: see po/README and 'Writing R Extensions'.
There is support for the use of 'dngettext' for C-level
translations in packages: see 'Writing R Extensions'.
BUG FIXES
o Assigning an extra 0-length column to a data frame by
DF[, "foo"] <- value now works in most cases (by filling with
NAs) or fails. (It used to give a corrupt data frame.)
o validObject() avoids an error during evaluation in the case
of various incorrect slot definitions.
o n:m now returns a result of type "integer" in a few more
boundary cases.
o The 'zap.ind' argument to printCoefmat() did not usually work as
other code attempted to ensure that non-zero values had a
non-zero representation.
o printCoefmat() formatted groups of columns together, not just
the cs.ind group but also the zap.ind group and a residual
group. It now formats all columns except the cs.ind group
separately (and zaps the zap.ind group column-by-column). The
main effect will be see in the output from print.anova, as
this grouped SS-like columns in the zap.ind group.
o R_ReplDLLinit() initializes the top-level jump so that some
embedded applications on Windows no longer crash on error.
o identical() failed to take the encoding of character strings
into account, so identical byte patterns are not necessarily
identical strings, and similarly Latin-1 and UTF-8 versions of
the same string differ in byte pattern.
o methods(f) used to warn unnecessarily for an S4 generic 'f' which
had been created based on an existing S3 generic.
o The check for consistent ordering of superclasses was not
ignoring all conditional relations (the symptom was usually
spurious warnings for classes extending "array").
o Trying to assign into a raw vector with an index vector
containing NAs could cause a segfault. Reported by Herv? Pag?s.
o Rscript could segfault if (by user error) its filename argument
was missing. Reported by Martin Morgan.
o getAnywhere() (and functions that use it, including argument
completion in the console) did not handle special built-in
functions. Reported by Romain Francois.
o order() was missing a PROTECT() call and so could segfault when
called on character data under certain (rare) circumstances
involving marked non-native encodings.
o prettyNum(z, drop0trailing=TRUE) did not work correctly when z
was a complex vector. Consequently, str(z, ...) also did
not. (PR#13985)
o 'make distclean' removed too many files in etc/ if
builddir = srcdir.
o R CMD replaced TEXINPUTS rather than appending to it (as
documented and intended).
o help.start() no longer fails on unix when "browser" is a
function.
o pbeta(x, *, log.p = TRUE) is sometimes more accurate, e.g., for
very small x.
o Unserializing a pre-2.8 workspace containing pure ASCII character
objects with a LATIN1 or UTF-8 encoding would corrupt the CHARSXP
cache.
--
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
| 663 |
|
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
| 99 |
|
From pd.mes at cbs.dk Mon Dec 6 11:19:37 2010
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 6 Dec 2010 11:19:37 +0100
Subject: R 2.12.1 scheduled for December 16
Message-ID: <[email protected]>
This is to announce that we plan to release R version 2.12.1 on Thursday,
December 16, 2010.
Those directly involved should review the generic schedule at
http://developer.r-project.org/release-checklist.html
The source tarballs will be made available daily (barring build
troubles) via
http://cran.r-project.org/src/base-prerelease/
For the R Core Team
Peter Dalgaard
--
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 2.12.1 scheduled for December 16
|
Peter Dalgaard
| 372 |
|
From p.dalgaard at biostat.ku.dk Fri Nov 1 12:41:54 2002
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 01 Nov 2002 12:41:54 +0100
Subject: R-1.6.1 is released
Message-ID: <[email protected]>
I've rolled up R-1.6.1.tgz a short while ago. This is a minor upgrade,
fixing an assortment of minor bugs, and one major one: 1.6.0
introduced a memory leak in deparsing, causing much trouble for people
running simulations.
You can get it from the developer site at
http://cvs.r-project.org/pub/CRAN/src/base/R-1.6.1.tgz
or wait for it to be mirrored at a CRAN site near you. Binaries for
various platforms will appear in due course.
There is also a version split for floppies, but due to the inclusion
of recommended packages as binary .tar.gz files, I'm no longer
providing a patch file.
For the R Core Team,
Peter D.
Here's the relevant part of the NEWS file:
CHANGES IN R VERSION 1.6.1
NEW FEATURES
o Added a few "trivial and obviously missing" functions to tcltk:
tkchooseDirectory, tkpopup, tkdialog, tkread
o barplot() has a new argument `axis.lty', which if set to 1
allows the pre-1.6.0 behaviour of plotting the axis and tick
marks for the categorical axis. (This was apparently not
intentional, but axis() used to ignore lty=0.)
The argument `border' is no longer ".NotYetUsed".
BUG FIXES
o hist(<datetime>, cex.axis = f) now works for x-axis too.
o prompt() gave wrong \usage{.} for long argument default expressions.
o summary(x) gives more information when `x' is a logical
(or a data frame with a logical column which is now quite customary).
o seq.POSIXt(from, to, length.out= . ) could give too long results
o summaryRprof() was counting nested calls to the same function
twice.
o Printing of objects of mode "expression" did strange things if
there were "%" characters in the deparsed expression (PR#2120).
o as.matrix.data.frame converted missings to "NA" not character NA.
(PR#2130)
o spec.pgram() was only interpolating zero freq for one series. (PR#2123)
o help(randu) had % unescaped in the example. (PR#2141)
o Making html links would fail if packages-head.html was not
writeable. (PR#2133)
o Sweave.sty was not installed to $R_HOME/share/texmf when
builddir != srcdir. On Windows backslashes in latex paths have
to be replaced by slashes.
o A memory leak in deparsing was introduced when eliminating
static variables (thanks to Achim Zeileis for spotting this).
A similar problem in loading workspaces has been corrected.
o TclInterface.Rd incorrectly used \synopsis for \usage so that
the usage section wasn't output.
o Readline stack off-by-one error. (PR#2165)
o R_ExpandFileName had a memory leak in the case libreadline was
used under Unix-alikes.
o sys.save.image() now closes all connections so it will work even
if the connection list has become full.
o loess() had an unstated limit of four predictors: this is now
documented and enforced.
o ${R_HOME}/etc/Renviron.site is now not read if R_ENVIRON is
set, as documented. Previously it was read unless R_ENVIRON
pointed to an actual file.
o Startup.Rd described the proceesing under Unix-alikes but
incorrectly implied it happened that way on the Windows and
MacOS ports. Neither use Renviron.site, for example.
o besselK(x,*) now returns 0 instead of Inf for large x. (PR#2179)
o The Tcl console code didn't work with Tcl/TK 8.0, and has been
#ifdef'd out. (PR#2090)
o format.AsIs() was not handling matrices.
o sd() was not passing na.rm to var() for matrices and data frames.
o dist() {mva} silently treated +/-Inf as NA.
o setwd() now returns NULL invisibly.
o basename() and dirname() did not check the length of their
input and ignored elements after the first. This affected
undoc {tools}.
o If A had dimnames, eigen(A) had inappropriate dimnames. (PR#2116)
o as.POSIXct.dates had a sign error for the origin (PR#2222)
o The claim that pie charts should be avoiden (in pie.Rd) is now
supported by a quote from Cleveland (1985).
o The vsnprintf() functions supplied for systems that don't
supply their own had a bug in the output of fractional parts,
corrupting data if using save() with ascii=TRUE. (PR#2144)
o pretty() values close to 0 in some cases which are now 0 (PR#1032
and D.Brahm's mails).
BUILD ISSUES
o Toplevel Makefile was missing dependency of "docs" on "R" (causing
parallel makes to go wrong)
o When building with recommended packages those were installed
into the first path in R_LIBS, if the environment variable was
present.
--
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-1.6.1 is released
|
Peter Dalgaard BSA
| 87 |
|
From p.murrell at auckland.ac.nz Fri Aug 25 00:17:16 2006
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Fri, 25 Aug 2006 10:17:16 +1200
Subject: R News, volume 6, issue 3 is now available
Message-ID: <[email protected]>
Hi
The August 2006 issue of R News is now available on CRAN under the
Documentation/Newsletter link.
Many thanks to Ron Wehrens, our guest editor for this special issue.
Paul
(on behalf of the R News EditorialBoard)
--
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 3 is now available
|
Paul Murrell
| 458 |
|
From mikalzet at libero.it Thu Oct 5 22:20:32 2000
From: mikalzet at libero.it (mikalzet at libero.it)
Date: Thu, 5 Oct 2000 22:20:32 +0200 (CEST)
Subject: installing R-1.1.1 on Mandrake 7.1
Message-ID: <[email protected]>
The R-base-1.1.1-1.i586.rpm packaged for Mandrake 7.1 is now available on
CRAN.
I've installed it on my system and it seems to work all right so far !
Please let me know if there are any problems.
--
Dr. Michele Alzetta
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|
installing R-1.1.1 on Mandrake 7.1
|
mikalzet at libero.it
| 330 |
|
From p.dalgaard at biostat.ku.dk Mon Jan 15 12:04:06 2001
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 15 Jan 2001 12:04:06 +0100
Subject: R 1.2.1 is released
Message-ID: <[email protected]>
I've rolled up R-1.2.1.tgz a moment ago. This is mainly a bugfix
and minor tweaks release, although some new features (notably factor
analysis) has sneaked in.
You can get it from
ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.2.1.tgz
or
http://cvs.r-project.org/pub/CRAN/src/base/R-1.2.1.tgz
or wait for it to be mirrored at a CRAN site near you within a day or two.
There's also a version split in three for floppies and a patch file
against 1.2.0.
For the R Core Team,
Peter D.
Here's the relevant part of the NEWS file:
CHANGES IN R VERSION 1.2.1
NEW FEATURES
o New functions factanal(), varimax(), promax() and examples in
package mva.
o New functions readBin() and writeBin() to transfer binary data
to and from connections.
o merge() is partially moved to C to reduce its memory usage.
o library(help = PKG) now displays the contents of the package's
DESCRIPTION file in addition to its INDEX.
o Sd2Rd can handle S4-style documentation too: see `Writing R
Extensions'.
o prompt() now also works with a character argument (useful for
producing many *.Rd files in a loop).
o The Unix front-end shell script now ignores a value for R_HOME
found in the environment.
o Connections functions such as file() now accept a description of
length > 1, with a warning.
o All text-mode connections now accept input with LF, CR or CRLF
line endings. This means that readLines() can be used on DOS
files and source() on Mac files, for example.
Also, CRLF-terminated files can be used as stdin on Unix, and
files with last lines without an EOL mark can be used as stdin
and source()-ed on Unix and Windows.
o DESCRIPTION file has a new recommended `Maintainer:' field.
o stars() now uses a larger "cex" for the labels, and cex and lwd
are now arguments. Further, the argument names (xlim, ylim,
axes) are now consistent with other plot functions. The key symbol
is not clipped anymore into the plot region by default.
o Date-time quantities are now printed with the timezone, if known.
o R CMD build now ignores all files specified (via Perl regexps)
in file `.Rbuildignore' in the top-level source directory of a
package.
o Horizontal boxplots are possible with horizontal = TRUE.
o all.equal() on lists now compares them as generic vectors, that
is they are equal if have identical names attributes and
all components are equal.
o Invalid lines in .Renviron now give warnings when R is started.
o Argument `na.last' implemented for rank().
BUG FIXES
o There have been many small improvements/corrections in the
documentation. In particular:
The help pages for lm and glm now describe the fitted objects.
is.vector() is now correctly documented: complex vectors and
lists return TRUE.
o The default sortedXyData constructor in the nls package now
handles missing values in the response.
o On startup, file .RData is now restored *after* the site and
user profiles are loaded (if at all). This is as previously
documented.
o as.POSIXlt (and *ct) operating on a character string
only extracted the date (and not the time) in some cases.
o as.POSIXct() on character objects was ignoring `tz'.
o codoc(ignore.generic.functions = TRUE) works again.
o Explicitly close files opened by sink() for OSes (such as
Windows) that benefit from it.
o Prevent closing the sink connection (which would be a silly
thing to do).
o showConnections(all = TRUE) was sometimes counting connections
incorrectly, and so not showing some closed ones.
o ts(1:10, start= c(1999,6), end = c(2000,3), frequency = 12)
now prints both years (as it should).
o Monthly multivariate time series now print proper month names
in all cases.
o print.stl(), print.princomp() and print.prcomp() now pass on
`digits =' etc.
o prompt() now produces a \usage{} line for data frames and
other datasets, as documented in `Writing R Extensions'.
o glm() now returns correct linear predictor and fitted values
for zero-weight cases.
o scan(strip.white=TRUE) and readline() could give incorrect
answers when an input field was empty or blank.
o dchisq() now behaves better for large values of its ncp parameter.
o besselJ(*, nu) is now ok for nu < 1; fix improves accuracy of
other values by a few bits as well.
o The convergence criterion in the Fortran SVD code has been
changed to circumvent spurious convergence errors when
comparing extended-precision quantities on ix86 Linux (and
some compilers and options).
o Rdindex now handles multi-line \title{}'s correctly.
o Add weights.glm() so that plot.lm() gets the correct weights from
glm objects (the ones that go with deviance residuals not the
working residuals).
o Printing a language object (e.g. a formula) in a list was
clobbering the buffer holding the tag labels which then were
lost in subsequent lines of printout (PR#746).
o aic in family() objects is now computed more precisely using
dxxxx(log=TRUE). For binomial fits the value was wrong for
models specified via proportions and weights (PR#796).
Avoid NaN values in aic where n = 0 occurs.
o Using non-integer numbers of successes in a binomial glm (as
formerly in demo(lm.glm)) now gives a warning, as the theory and
in particular the AIC value is not applicable.
o demo(is.things) works again {is.ALL() doesn't call methods
anymore}.
o persp(*, nticks = nn) now works (better) for too small nn.
persp(*, main = t1, sub= t2) now work (as always documented).
o Printing of attributes of a list element no longer precedes
`attr' by the tag (PR#715).
o It is no longer possible to use df[foo] to select non-existent
columns in df and so create an invalid object of class
"data.frame" (PR#698).
o edit.data.frame() was trying to set row.names on a list, which
is no longer allowed.
o In the \link[pkg]{topic}, `pkg' was not being used if `topic'
was found in a package in .lib.loc. Now `pkg' is always used.
o plot() with small relative ranges gave an error, which e.g. broke
library(ts); plot(stl(ts(rep(1:7, 15), freq = 7), s.win = "per"))
o Using scan() with a 0-length `what' argument now gives an error
message rather than a segfault.
o Loading .Random.seed could extremely rarely and with some
generators reject a value as NA_INTEGER when it was valid.
o save(..., ascii=TRUE) created broken files when saving strings
containing special characters (ASCII code > 127).
o mean(c(1,NA,NA,NA)[-1], trim = .1, na.rm = TRUE) doesn't give an
error anymore.
o As the supplied afm files are not properly in the ISOLatin1
encoding, the font metric for "-" was wrong since 0.63 on a
postscript/xfig device, and randomly wrong in 1.2.0. It will
now be correct (but the files remain incorrect: C45 is "minus"
not "hyphen" and there are missing slots).
Metrics for the duplicated characters (acute, dieresis,
macron, space) in ISOLatin1 encoding are now correct for both
occurrences: previously only one was present.
o The data-time functions try harder to guess the DST setting
when the OS does not know, as some OSes were printing times
in DST if this was marked as unknown.
o Setting par(pty=) after par(pin=) or par(plt=) was having no
effect until the margins were set.
o Nested \describe sections in .Rd files have (again) nested
indentation when converted to text.
o Concatenation of C strings by ## is no longer used, to avoid
spurious warnings from some recent versions of gcc.
o dev.copy2eps() allows a `paper' argument to be passed to
postscript().
o file.show() handles the case of zero files better.
o formula.lm uses object$formula if it exists, in preference
to object$terms.
o strsplit() is corrected for an empty split pattern.
o kronecker() now does a better job when creating dimnames.
o Better handling of input dimnames in fourfoldplot().
--
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 1.2.1 is released
|
Peter Dalgaard BSA
| 214 |
|
From guido at hal.stat.unipd.it Wed Jan 20 08:37:00 1999
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Wed, 20 Jan 1999 08:37:00 +0100
Subject: R-0.63.2 for Windows
Message-ID: <[email protected]>
I have updated to R-0.63.2 the version of R for Windows available from CRAN
in directory binaries/windows/WindowsNT/base.
No new Windows specific features but:
(i) I hope to have fixed the NT copy to the clipboard bug;
(ii) help files use latin1 encoding (but, to see the difference,
you must use a latin1 capable font; for this reason, now, as packed,
the R console uses "Courier New"; if you don't like it, edit etc/Rconsole).
Pre-compiled packages for this version of R are provided by
Brian D. Ripley (who, BTW, is also responsable for (ii) before,
thanks Brian!) and available at CRAN/binaries/WindowsNT/contrib.
guido masarotto
(ps) Note that my e-mail address is changed. Please, use this not the
old one.
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|
R-0.63.2 for Windows
|
Guido Masarotto
| 466 |
|
From pd.mes at cbs.dk Sat Apr 2 17:58:20 2016
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Sat, 2 Apr 2016 15:58:20 +0000
Subject: Extending the beta period for R 3.3.0 till April 25, Final release
on May 3
Message-ID: <[email protected]>
Due to delays in implementing an updated Windows toolchain for CRAN, R Core has found it unsafe to go with our usual 1-week beta testing period. Combined with other scheduling issues, we have decided to postpone the transition to 3.3.0 RC until April 26, with the final release happening on May 3.
Apologies for any inconvenience, but it is really rather important to get this right before the release of 3.3.0. One cannot mix and match binaries from different toolchains - CRAN packages binaries for 3.3.x must be all of the same kind. Accordingly, if we have too little time to fix issues discovered in the beta period, we might have to back out and be stuck with the old tools for another year.
Web site updates will happen shortly.
For the 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
|
Extending the beta period for R 3.3.0 till April 25, Final release on May 3
|
Peter Dalgaard
| 121 |
|
From pd@me@ @end|ng |rom cb@@dk Thu Feb 6 16:58:13 2020
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Thu, 6 Feb 2020 15:58:13 +0000
Subject: [Rd] R 3.6.3 scheduled for February 29
Message-ID: <[email protected]>
Full schedule is available on developer.r-project.org.
(The date is chosen to celebrate the 5th anniversary of R 1.0.0. Some irregularity may occur on the release day, since this happens to be a Saturday and the release manager is speaking at the CelebRation2020 event...)
--
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 3.6.3 scheduled for February 29
|
Peter Dalgaard
| 614 |
|
From andy_liaw at merck.com Tue Apr 2 17:22:41 2002
From: andy_liaw at merck.com (Liaw, Andy)
Date: Tue, 02 Apr 2002 10:22:41 -0500
Subject: random forests for R
Message-ID: <[email protected]>
Hi all,
There is now a package available on CRAN that provides an R interface to Leo
Breiman's random forest classifier.
Basically, random forest does the following:
1. Select ntree, the number of trees to grow, and mtry, a number no larger
than number of variables.
2. For i = 1 to ntree:
3. Draw a bootstrap sample from the data. Call those not in the bootstrap
sample the "out-of-bag" data.
4. Grow a "random" tree, where at each node, the best split is chosen among
mtry randomly selected variables. The tree is grown to maximum size and not
pruned back.
5. Use the tree to predict out-of-bag data.
6. In the end, use the predictions on out-of-bag data to form majority
votes.
7. Prediction of test data is done by majority votes from predictions from
the ensemble of trees.
In the tech report
http://oz.berkeley.edu/users/breiman/randomforest2001.pdf, Breiman showed
that this technique is very competitive to boosting classification trees.
In our own experience, it is competitive with nonlinear classifiers such as
artificial neural nets and support vector machines. Two of the significant
advantages of random forests over other methods (IMHO) are: a) there is only
one parameter (mtry) to adjust, and the result usually not sensititve to it;
and b) the built-in cross-validation via the use of out-of-bag data gives
quite accurate estimate of test set error, and offers quite effective
protection against overfitting.
The code is based on version 3.1 of the original Fortran code written by
Breiman and Cutler (http://www.stat.berkeley.edu/users/breiman/). The User
Guide for the Fortran code on Breiman's web site explains some of the
facilities provided in the code (such as assessing variable importance, and
proximity measures). Some facilities provided in the original Fortran code
have be taken out: transforming data to principal components, and
multidimensional scaling of the "proximity" matrix. These can easily be
done in R before and after calls to the random forest functions. Random
numbers are generated by R's RNG, rather than the one supplied in the
original Fortran code.
I'd like to thank Profs. B. D. Ripley, J. Lindsey, and others on R-help that
answered many of my questions when I was working on this package. The
formula interface and part of the code in the predict method are out-right
"stolen" from svm() in the e1071 package and nnet() in the VR bundle.
Questions/comments/bugs/patches welcomed!
Regards,
Andy
Andy I. Liaw, PhD
Biometrics Research Phone: (732) 594-0820
Merck & Co., Inc. Fax: (732) 594-1565
P.O. Box 2000, RY70-38 Rahway, NJ 07065
mailto:andy_liaw at merck.com
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|
random forests for R
|
Liaw, Andy
| 20 |
|
From Detlef.Steuer at unibw-hamburg.de Wed Oct 2 09:37:28 2002
From: Detlef.Steuer at unibw-hamburg.de (Detlef Steuer)
Date: Wed, 02 Oct 2002 09:37:28 +0200 (CEST)
Subject: SuSE rpms for R-1.6.0 available
In-Reply-To: <[email protected]>
Message-ID: <[email protected]>
["CC: R-announce" made this message bounce;
I'm not sure if it should be "R-announced", MM]
RPMs for R-1.6.0 for SuSE Linux Versions 7.3/8.0
have been built and uploaded to CRAN.
They should be found on the website within the next 24 hours.
The contrib RPMs will need a day or two to be rebuild for R-1.6.0.
SuSE 8.1 RPMS will be uploaded as soon as I have updated one of my machines.
(Or got user mode linux running, whatever happens first.)
Thank you, R Core Team!
Detlef Steuer
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|
SuSE rpms for R-1.6.0 available
|
Detlef Steuer
| 71 |
|
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
| 106 |
|
From jago at mclink.it Mon Sep 3 14:41:31 2001
From: jago at mclink.it (Stefano Iacus)
Date: Mon, 3 Sep 2001 14:41:31 +0200
Subject: R-1.3.1 for both MacOS version released (correct URLs)
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/
and for the Darwin/X11 version refer to
http://cran.r-project.org/bin/macosx/
(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.
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|
R-1.3.1 for both MacOS version released (correct URLs)
|
Stefano Iacus
| 270 |
|
From pd.mes at cbs.dk Wed Sep 25 13:16:24 2013
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Wed, 25 Sep 2013 13:16:24 +0200
Subject: R 3.0.2 is released
Message-ID: <[email protected]>
The build system rolled up R-3.0.2.tar.gz (codename "Frisbee Sailing") 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-3.0.2.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) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 77da68a9d0abfa9121d54f6ff0bced33
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = e01b5a01aade71ccef967d39f3738e0a
MD5 (NEWS.html) = 1925b57c75bd51373adb33a04e2c18f8
MD5 (R-latest.tar.gz) = f9a8374736e7650e4848f33e2e3bbee3
MD5 (README) = e259ae5dd943b8547f0b7719664e815b
MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4
MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649
MD5 (R-3/R-3.0.2.tar.gz) = f9a8374736e7650e4848f33e2e3bbee3
This is the relevant part of the NEWS file
CHANGES IN R 3.0.2:
NEW FEATURES:
* The NEWS files have been re-organized.
This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The
latter files are now installed when R is installed. An HTML
version of news from 2.10.0 to 2.15.3 is available as
doc/html/NEWS.2.html.
* sum() for integer arguments now uses an integer accumulator of at
least 64 bits and so will be more accurate in the very rare case
that a cumulative sum exceeds 2^53 (necessarily summing more than
4 million elements).
* The example() and tools::Rd2ex() functions now have parameters to
allow them to ignore \dontrun markup in examples. (Suggested by
Peter Solymos.)
* str(x) is considerably faster for very large lists, or factors
with 100,000 levels, the latter as in PR#15337.
* col2rgb() now converts factors to character strings not integer
codes (suggested by Bryan Hanson).
* tail(warnings()) now works, via the new `[` method.
* There is now support for the LaTeX style file zi4.sty which has
in some distributions replaced inconsolata.sty.
* unlist(x) now typically returns all non-list xs unchanged, not
just the "vector" ones. Consequently, format(lst) now also works
when the list lst has non-vector elements.
* The tools::getVignetteInfo() function has been added to give
information about installed vignettes.
* New assertCondition(), etc. utilities in tools, useful for
testing.
* Profiling now records non-inlined calls from byte-compiled code
to BUILTIN functions.
* Various functions in stats and elsewhere that use non-standard
evaluation are now more careful to follow the namespace scoping
rules. E.g. stats::lm() can now find stats::model.frame() even
if stats is not on the search path or if some package defines a
function of that name.
* If an invalid/corrupt .Random.seed object is encountered in the
workspace it is ignored with a warning rather than giving an
error. (This allows R itself to rely on a working RNG, e.g. to
choose a random port.)
* seq() and seq.int() give more explicit error messages if called
with invalid (e.g. NaN) inputs.
* When parse() finds a syntax error, it now makes partial parse
information available up to the location of the error. (Request
of Reijo Sund.)
* Methods invoked by NextMethod() had a different dynamic parent to
the generic. This was causing trouble where S3 methods invoked
via lazy evaluation could lose track of their generic.
(PR#15267)
* Code for the negative binomial distribution now treats the case
size == 0 as a one-point distribution at zero.
* abbreviate() handles without warning non-ASCII input strings
which require no abbreviation.
* read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
PR#15250.)
* formatC(x) no longer copies the class of x to the result, to
avoid misuse creating invalid objects as in PR#15303. A warning
is given if a class is discarded.
* Dataset npk has been copied from MASS to allow more tests to be
run without recommended packages being installed.
* The initialization of the regression coefficients for
non-degenerate differenced models in arima() has been changed and
in some examples avoids a local maximum. (PR#15396)
* termplot() now has an argument transform.x to control the display
of individual terms in the plot. (PR#15329)
* format() now supports digits = 0, to display nsmall decimal
places.
* There is a new read-only par() parameter called "page", which
returns a logical value indicating whether the next plot.new()
call will start a new page.
* Processing Sweave and Rd documents to PDF now renders backticks
and single quotes better in several instances, including in \code
and \samp expressions.
* utils::modifyList() gets a new argument keep.null allowing NULL
components in the replacement to be retained, instead of causing
corresponding components to be deleted.
* tools::pkgVignettes() gains argument check; if set to TRUE, it
will warn when it appears a vignette requests a non-existent
vignette engine.
UTILITIES:
* R CMD check --as-cran checks the line widths in usage and
examples sections of the package Rd files.
* R CMD check --as-cran now implies --timings.
* R CMD check looks for command gfile if a suitable file is not
found. (Although file is not from GNU, OpenCSW on Solaris
installs it as gfile.)
* R CMD build (with the internal tar) checks the permissions of
configure and cleanup files and adds execute permission to the
recorded permissions for these files if needed, with a warning.
This is useful on OSes and file systems which do not support
execute permissions (notably, on Windows).
* R CMD build now weaves and tangles all vignettes, so suggested
packages are not required during package installation if the
source tarball was prepared with current R CMD build.
* checkFF() (used by R CMD check) does a better job of detecting
calls from other packages, including not reporting those where a
function has been copied from another namespace (e.g. as a
default method). It now reports calls where .NAME is a symbol
registered in another package.
* On Unix-alike systems, R CMD INSTALL now installs packages group
writably whenever the library (lib.loc) is group writable.
Hence, update.packages() works for other group members (suggested
originally and from a patch by Dirk Eddelbuettel).
* R CMD javareconf now supports the use of symbolic links for
JAVA_HOME on platforms which have realpath. So it is now
possible to use
R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0
on a Linux system and record that value rather than the
frequently-changing full path such as
/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64.
* (Windows only.) Rscript -e requires a non-empty argument for
consistency with Unix versions of R. (Also Rterm -e and R -e.)
* R CMD check does more thorough checking of declared packages and
namespaces. It reports
* packages declared in more than one of the Depends, Imports,
Suggests and Enhances fields of the DESCRIPTION file.
* namespaces declared in Imports but not imported from, neither
in the NAMESPACE file nor using the :: nor ::: operators.
* packages which are used in library() or requires() calls in
the R code but were already put on the search path _via_
Depends.
* packages declared in Depends not imported _via_ the NAMESPACE
file (except the standard packages). Objects used from
Depends packages should be imported to avoid conflicts and to
allow correct operation when the namespace is loaded but not
attached.
* objects imported _via_ ::: calls where :: would do.
* objects imported by :: which are not exported.
* objects imported by ::: calls which do not exist.
See 'Writing R Extensions' for good practice.
* R CMD check optionally checks for non-standard top-level files
and directories (which are often mistakes): this is enabled for
--as-cran.
* LaTeX style file upquote.sty is no longer included (the version
was several years old): it is no longer used in R. A much later
version is commonly included in LaTeX distributions but does not
play well with the ae fonts which are the default for Sweave
vignettes.
* R CMD build makes more use of the build sub-directory of package
sources, for example to record information about the vignettes.
INSTALLATION and INCLUDED SOFTWARE:
* The macros used for the texinfo manuals have been changed to work
better with the incompatible changes made in texinfo 5.x.
* The minimum version for a system xz library is now 5.0.3 (was
4.999). This is in part to avoid 5.0.2, which can compress in
ways other versions cannot decompress.
* The included version of PCRE has been updated to 8.33.
* The included version of zlib has been updated to 1.2.8, a bug-fix
release.
* The included version of xz utils's liblzma has been updated to
5.0.5.
* Since javareconf (see above) is used when R is installed, a
stable link for JAVA_HOME can be supplied then.
* Configuring with --disable-byte-compilation will override the
DESCRIPTION files of recommended packages, which typically
require byte-compilation.
* More of the installation and checking process will work even when
TMPDIR is set to a path containing spaces, but this is not
recommended and external software (such as texi2dvi) may fail.
PACKAGE INSTALLATION:
* Installation is aborted immediately if a LinkingTo package is not
installed.
* R CMD INSTALL has a new option --no-byte-compile which will
override a ByteCompile field in the package's DESCRIPTION file.
* License BSD is deprecated: use BSD_3_clause or BSD_2_clause
instead.
License X11 is deprecated: use MIT or BSD_2_clause instead.
* Version requirements for LinkingTo packages are now recognized:
they are checked at installation. (Fields with version
requirements were previously silently ignored.)
* The limit of 500 S3method entries in a NAMESPACE file has been
removed.
* The default 'version' of Bioconductor for its packages has been
changed to the upcoming 2.13, but this can be set by the
environment variable R_BIOC_VERSION, e.g. in file Renviron.site.
C-LEVEL FACILITIES:
* Rdefines.h has been tweaked so it can be included in C++ code
after R_ext/Boolean.h (which is included by R.h).
Note that Rdefines.h is not kept up-to-date, and Rinternals.h is
preferred for new code.
* eval and applyClosure are now protected against package code
supplying an invalid rho.
DEPRECATED AND DEFUNCT:
* The unused namespace argument to package.skeleton() is now
formally deprecated and will be removed in R 3.1.0.
* plclust() is deprecated: use the plot() method for class "hclust"
instead.
* Functions readNEWS() and checkNEWS() in package tools are
deprecated (and they have not worked with current NEWS files for
a long time).
DOCUMENTATION:
* 'An Introduction to R' has a new chapter on using R as a
scripting language including interacting with the OS.
BUG FIXES:
* help.request() could not determine the current version of R on
CRAN. (PR#15241)
* On Windows, file.info() failed on root directories unless the
path was terminated with an explicit ".". (PR#15302)
* The regmatches<-() replacement function mishandled results coming
from regexpr(). (PR#15311)
* The help for setClass() and representation() still suggested the
deprecated argument representation=. (PR#15312)
* R CMD config failed in an installed build of R 3.0.1 (only) when
a sub-architecture was used. (Reported by Berwin Turlach.)
* On Windows, the installer modified the etc/Rconsole and
etc/Rprofile.site files even when default options were chosen, so
the MD5 sums did not refer to the installed versions. (Reported
by Tal Galili.)
* plot(hclust(), cex =) respects cex again (and possibly others
similarly). (Reported by Peter Langfelder.)
* If multiple packages were checked by R CMD check, and one was
written for a different OS, it would set --no-install for all
following packages as well as itself.
* qr.coef() and related functions did not properly coerce real
vectors to complex when necessary. (PR#15332)
* ftable(a) now fixes up empty dimnames such that the result is
printable.
* package.skeleton() was not starting its search for function
objects in the correct place if environment was supplied.
(Reported by Karl Forner.)
* Parsing code was changing the length field of vectors and
confusing the memory manager. (PR#15345)
* The Fortran routine ZHER2K in the reference BLAS had a
comment-out bug in two places. This caused trouble with eigen()
for Hermitian matrices. (PR#15345 and report from Robin Hankin)
* vignette() and browseVignettes() did not display non-Sweave
vignettes properly.
* Two warning/error messages have been corrected: the (optional)
warning produced by a partial name match with a pairlist, the
error message from a zero-length argument to the : operator.
(Found by Radford Neal; PR#15358, PR#15356)
* svd() returned NULL rather than omitting components as
documented. (Found by Radford Neal; PR#15360)
* mclapply() and mcparallel() with silent = TRUE could break a
process that uses stdout output unguarded against broken pipes
(e.g., zip will fail silently). To work around such issues, they
now replace stdout with a descriptor pointed to /dev/null
instead. For this purpose, internal closeStdout and closeStderr
functions have gained the to.null flag.
* log(), signif() and round() now raise an error if a single named
argument is not named x. (PR#15361)
* deparse() now deparses raw vectors in a form that is
syntactically correct. (PR#15369)
* The jpeg driver in Sweave created a JPEG file, but gave it a .png
extension. (PR#15370)
* Deparsing of infix operators with named arguments is improved.
(PR#15350)
* mget(), seq.int() and numericDeriv() did not duplicate arguments
properly. (PR#15352, PR#15353, PR#15354)
* kmeans(algorithm = "Hartigan-Wong") now always stops iterating in
the QTran stage. (PR#15364).
* read.dcf() re-allocated incorrectly and so could segfault when
called on a file with lines of more than 100 bytes.
* On systems where mktime() does not set errno, the last second
before the epoch could not be converted from POSIXlt to POSIXct.
(Reported by Bill Dunlap.)
* add1.glm() miscalculated F-statistics when df > 1. (Bill Dunlap,
PR#15386).
* stem() now discards infinite inputs rather than hanging.
(PR#15376)
* The parser now enforces C99 syntax for floating point hexadecimal
constants (e.g. 0x1.1p0), rather than returning unintended values
for malformed constants. (PR#15234)
* model.matrix() now works with very long LHS names (more than 500
bytes). (PR#15377)
* integrate() reverts to the pre-2.12.0 behaviour: from 2.12.0 to
3.0.1 it sometimes failed to achieve the requested tolerance and
reported error estimates that were exceeded. (PR#15219)
* strptime() now handles %W fields with value 0. (PR#15915)
* R is now better protected against people trying to interact with
the console in startup code. (PR#15325)
* Subsetting 1D arrays often lost dimnames (PR#15301).
* Unary + on a logical vector did not coerce to integer, although
unary - did.
* na.omit() and na.exclude() added a row to a zero-row data frame.
(PR#15399)
* All the (where necessary cut-down) vignettes are installed if R
was configured with --without-recommended-packages.
* source() did not display filenames when reporting syntax errors.
* Syntax error reports misplaced the caret pointing out the bad
token.
* (Windows only) Starting R with R (instead of Rterm or Rgui) would
lose any zero-length strings from the command line arguments.
(PR#15406)
* Errors in the encoding specified on the command line via
--encoding=foo were not handled properly. (PR#15405)
* If x is a symbol, is.vector(x, "name") now returns TRUE, since
"name" and "symbol" should be synonyms. (Reported by Herv'e
Pag`es.)
* R CMD rtags works on platforms (such as OS X) with a
XSI-conformant shell command echo. (PR#15231)
* is.unsorted(NA) returns false as documented (rather than NA).
* R CMD LINK did not know about sub-architectures.
* system() and system2() are better protected against users who
misguidedly have spaces in the temporary directory path.
* file.show() and edit() are now more likely to work on file paths
containing spaces. (Where external utilities are used, not the
norm on Windows nor in R.app which should previously have
worked.)
* Packages using the methods package are more likely to work when
they import it but it is not attached. (Several parts of its C
code were looking for its R functions on the search path rather
than in its namespace.)
* lgamma(-x) is no longer NaN for very small x.
* (Windows) system2() now respects specifying stdout and stderr as
files if called from Rgui. (PR#15393)
* Closing an x11() device whilst locator() or identify() is in
progress no longer hangs R. (PR#15253)
* list.dirs(full.names = FALSE) was not implemented. (PR#15170)
* format() sometimes added unnecessary spaces. (PR#15411)
* all.equal(check.names = FALSE) would ignore the request to ignore
the names and would check them as attributes.
* The symbol set by tools::Rd2txt_options(itemBullet=) was not
respected in some locales. (PR#15435)
* mcMap() was not exported by package parallel. (PR#15439)
* plot() for TukeyHSD objects did not balance dev.hold() and
dev.flush() calls on multi-page plots. (PR#15449)
--
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 3.0.2 is released
|
Peter Dalgaard
| 435 |
|
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
| 102 |
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