R/S-PLUS Bioconductor NEWS

This is a maintenance release and fixes a number of mostly minor issues.

See the full list of changes below.

You can get it from

http://cran.r-project.org/src/base/R-2/R-2.9.1.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.

For the R Core Team

Peter Dalgaard


These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:


70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
11a746c387c5a94f172a27939b96dd4c NEWS
7abcbbc7480df75a11a00bb09783db90 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
8ea34a9306ef5cf5dc03b45883586129 FAQ
54a79eebdf0cec3fd2c489fc94d99b00 R-2.9.1.tar.gz
54a79eebdf0cec3fd2c489fc94d99b00 R-latest.tar.gz

Here is the relevant part of the NEWS file:

CHANGES IN R VERSION 2.9.1

NEW FEATURES

o New function anyDuplicated(x) returns 0 (= FALSE) or the index
of the first duplicated entry of x.

o matplot(), matlines() and matpoints() now also obey a 'lend'
argument, determining line end styles. (Wish of PR#13619).

o bw.SJ(), bw.bcv() and bw.ucv() now gain an optional 'tol'
argument allowing more accurate estimates.

o new.packages() no longer regards packages with the same name
as a member of an installed bundle as 'new' (this is now
consistent with the dependency checks in install.packages()).

It no longer reports on partially installed bundles (since
members can be updated individually if a bundle is unbundled).

o old.packages() and hence updates.packages() will look for
updates to members of package bundles before updates to the
whole bundle: this allow bundles to be split and installations
updated.

o nlminb() gives better non-convergence messages in some cases.

o S3 method dispatch will support S4 class inheritance for S3
methods, for primitives and via UseMethod(), if the argument
S3methods=TRUE is given to setClass(). S4 method dispatch
will use S3 per-object inheritance if S3Class() is set on the
object. See ?Methods and the paper referenced there.

o R CMD INSTALL is more tolerant of (malformed) packages with a
'man' directory but no validly named .Rd files.

o R CMD check now reports where options are used that cause some
of the checks to be skipped.

o RSiteSearch has been updated to be consistent with the new
layout of the search site itself, which now includes separate
options for vignettes, views, and r-sig-mixed-models, as well
as changed names for r-help. (Contributed by Jonathan Baron.)

o That R CMD check makes use of a
/tests/Examples/-Ex.Rout.save file as a reference
result is now documented in 'Writing R Extensions'.

DEPRECATED & DEFUNCT

o print.atomic() (defunct since 1.9.0) has been removed since it
caused confusion for an S4 class union "atomic".

o png(type="cairo1") is deprecated -- it was only needed for
platforms with 1.0 <= cairo < 1.2.

BUG FIXES

o The ... argument was not handled properly when ... was found
in the enclosure of the current function, rather than in the
function header itself. (This caused integrate() to fail in
certain cases.)

o col2rgb("#00000080", TRUE) would return the background colour.
(Reported by Hadley Wickham.)

o interaction() now ensures that the levels of the result are unique.

o packageDescription() and hence sessionInfo() now report the correct
package version also for a non-attached loaded namespace of
a version different from the default lib.loc.

o smoothScatter() now also works when e.g. xlim[2] < xlim[1].

o Invalid use of sprintf() such as sprintf("%S%") now give an error
instead of a segmentation fault, as do very unusual cases such as
sprintf("%s", tryCatch(stop(), error=identity)). (It was
always documented that misuse could crash R in
platform-dependent ways.)

o parse_Rd() would mishandle braces when they occurred at
the start of a line within an R string in an Rd file (reported
by Alex Couture-Beil) or when they occurred in an R comment
(reported by Mark Bravington).

o readNEWS() missed version numbers with more than one digit.

o building R --without-x no longer fails (PR#13665)

o printCoefmat(cbind(0,1)) now works too (PR#13677)

o bw.SJ(c(1:99, 1e6)) now works too.

o Rd2txt() could not handle empty descriptions of items in an Rd
file (reported by Mark Bravington), and did not wrap long lists
of arguments if they were given in a single item.

o stars() would do a partial plot when called with plot = FALSE;
it now consistently returns the locations of the stars.

o Rd2latex() could not handle empty sections.

o old.packages() and hence update.packages() would fail on a
repository which contained only one package but with multiple
versions of that package.

o as.character.Rd() added extra braces when displaying two-argument
macros. (Report and fix by Manuel Eugster.)

o unsplit() was misbehaving in the case of single-column data
frames. (Reported by Will Gray.)

o as(I(1), "vector") and similar coercions from objects of
"unregistered" S3 classes now work.

o srcref records produced by parse() and parse_Rd() did not record
the encoding of the source file. (Reported by Romain Francois.)

o The X11 version of View() was misbehaving in MBCS locales, and
PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama.

o R CMD check looked at the environment variable PDFLATEX, but
as from R 2.8.1 R CMD Rd2dvi used R_PDFLATEXCMD in
preference, and that was set by R CMD (and not PDFLATEX). Now
R CMD check looks at R_PDFLATEXCMD.

o sprintf() now signals an error when the result of single format
specification would be longer than the limit (8192 bytes); it would
return "somewhat random" results or segfault previously. (PR#13667)
Further, arguments of type "language" or "symbol" are no longer
allowed, as these, e.g., sprintf("%s", quote(list())), typically
lead to unexpected results or hard to understand error messages.

o The new (in 2.9.0) 'stringsAsFactors' argument to expand.grid()
was not working: it now does work but has default TRUE for
backwards compatibility.

o tcrossprod(<1d-array>, ) now does work when the arguments
are of compatible dimensions.

o qbinom() now is accurate also in (large size, small prob)
cases. (PR#13711)

o The calculation of the Spearman p-value in cor.test() is
slightly more accurate in some cases. (PR#13574)

o The digamma(), trigamma() and psigamma() functions could be
inaccurate for values of x around 1e-15 due to cancellation.
(PR#13714).

o median.default() was altered in 2.8.1 to use sum() rather
than mean(), although it was still documented to use mean().
This caused problems for POSIXt objects, for which mean() but
not sum() makes sense, so the change has been reverted.

o Assigning an extra 0-length column to a data frame by
DF$foo <- value gave a corrupt data frame rather than failing.
(PR#13724) This also happened for DF[["foo"]] <- value.

o R CMD INSTALL no longer gives a spurious warning about old R
versions ignoring multiple dependencies, if the conditions are
known to be satisfied.

o The test for setting dim() allowed a value with two or more
NAs to be set on a 0-length object. (PR#13729) Also, it
allowed an even number of negative values.

o xtfrm(), rank(), sort() and order() did not always make use of
custom comparison methods specific to the class of elements
being sorted.

o Increase NAMED value on 'seq' value in for() loop so loop code
cannot modify 'seq' value.

o Prevent rectangles of size < 0.5 pixel from disappearing in
Quartz when using rastered backend. (PR#13744)

o Printing _NA_complex_ had a low-level thinko; patch thanks to
Bill Dunlap.

o CP1257 encoding for postscript/PDF has been corrected. (PR#13736)

o aov() with an error term was evaluating the ... arguments in
2.9.0 whilst checking their names, so could fail by evaluating
them in the wrong place. (PR#13733)

o The print() method for arima() failed if all coefs were fixed.

o R CMD INSTALL --no-latex was not implemented in 2.9.0 (only).

o Added a needed PROTECT call in RunFinalizers to handle cases where
the routine is called recursively from a GC in a finalizer.

o Constructing error messages about unused arguments in calls to
closures no longer evaluates the arguments.

o qr(x, LAPACK=TRUE) did not coerce integer x to numeric.

o qr.coef() misbehaved in the LAPACK case with a matrix RHS, so
that solve(qr(x, LAPACK=TRUE)) gave wrong results. (Found by
Avraham Adler, PR#13762 by Ravi Varadhan.)

------------------------------------------------------------------------
製造業向け Spotfire & S-PLUS 活用セミナー
6/12（金） 西新宿 日本Tibcoにて
------------------------------------------------------------------------

※関係の皆様にご回覧ください。
※なお本セミナーは製造業関係業務に従事する方に向けた内容です。

Spotfire(http://spotfire.tibco.jp/)は、企業マネジメント層が他社との
競争に打ち勝つための第一線の分析ソリューションです。使いやすいGUIで、
インタラクティブかつ軽快にデータの可視化を実行でき、既に製造業の現場で
広く使われております。また有効な分析ワークフローや活用事例を再利用
できる分析アプリケーションを迅速に作成、共有することができます。
ロールベースのアーキテクチャにより、各部門の分析を幅広く採用することが
でき、分析フローを全社的に展開し、ビジネスの高速化を実現できます。

SpotfireとS-PLUSは補完する製品です。海外においては、SpotfireとS-PLUSの
両製品をご活用いただき、ビジネスの効率化を実現した事例も見受けられる
ようになりました。しかし、日本においては、まだまだ両製品を使用する
メリットをご理解いだけていないのが現状です。 本セミナーにおいて、
SpotfireとS-PLUSを活用することで、シームレスに強力なデータ解析を行い、
またその結果を共有することがいかに有効な分析であるかをご紹介させて
頂きます。

【日時】 2009年6月12日(金） 13:30〜 (受付開始13:00)

【場所】 日本ティブコソフトウェア株式会社 セミナールーム
（東京都新宿区西新宿6−5−1　新宿アイランドタワー22F、
メトロ西新宿駅0分またはJR新宿駅8分）

【参加費】 無料

【内容】
13:30〜14:00 ご挨拶&会社説明
14:00〜14:30 S-PLUS製品説明（田澤 司/数理システム）
14:30〜15:00 Spotfire製品説明（川端 英貴/TIBCO）
15:10〜15:50 製造業ユーザ様発表
（澤田 静雄氏/東芝エンジニアリング株式会社）
16:00〜16:50 Spotfire+S-PLUS紹介（Dan White/TIBCO）
17:00〜19:00 懇親会

【申込方法】 下記のページから申込書をダウンロードしてお申込頂けます。
http://www.msi.co.jp/splus/events/2009/spot09a.html

または、下記の内容を splus-info@msi.co.jp 宛にご送付ください。
------------------------------------------------------------------------
（製造業向けSpotfire&S-PLUS活用セミナ 6/12 申込書）
・お名前:
・会社名および部署名:
・メールアドレス:
・TEL:
・FAX:
・ご住所
・懇親会に（参加する/参加しない）
------------------------------------------------------------------------

折り返し、地図入りの受講票を送付致します。

available at http://ess.r-project.org/ from the "Download" tab.

After the long 5.3.x series, with the last previous release 5.3.11,
we have decided to simplify the numbering scheme from an x.y.z
to an x.y one.
The documentation has been re-organized partly, aiming for
improved clarity.

Also, several buglets have been fixed, for R and S, as well as
SAS and BUGS, see the *New Features* below.

For the ESS core team,
Martin Maechler, ETH Zurich


The rest of the 'ANNOUNCE' file :
------------------------------------------------------------------------

Emacs Speaks Statistics (ESS) provides an intelligent, consistent
interface between the user and the software. ESS interfaces with
S-PLUS, R, SAS, BUGS and other statistical analysis packages under the
Unix, Microsoft Windows, and Apple Mac OS operating systems. ESS is a
package for the GNU Emacs and XEmacs text editors whose features ESS
uses to streamline the creation and use of statistical software. ESS
knows the syntax and grammar of statistical analysis packages and
provides consistent display and editing features based on that
knowledge. ESS assists in interactive and batch execution of
statements written in these statistical analysis languages.

ESS is freely available under the GNU General Public License (GPL).
Please read the file COPYING which comes with the distribution, for
more information about the license. For more detailed information,
please read the README files that come with ESS.

1.1 Getting the Latest Version
==============================

The latest released version of ESS is always available on the web at:
ESS web page (http://ess.r-project.org) or StatLib
(http://lib.stat.cmu.edu/general/ESS/)

The latest development version of ESS is available via
`https://svn.R-project.org/ESS/', the ESS Subversion repository. If
you have a Subversion client (see `http://subversion.tigris.org/'), you
can download the sources using:
% svn checkout https://svn.r-project.org/ESS/trunk PATH
which will put the ESS files into directory PATH. Later, within
that directory, `svn update' will bring that directory up to date.
Windows-based tools such as TortoiseSVN are also available for
downloading the files. Alternatively, you can browse the sources with a
web browser at: ESS SVN site (https://svn.r-project.org/ESS/trunk).
However, please use a subversion client instead to minimize the load
when retrieving.

If you remove other versions of ESS from your emacs load-path, you
can then use the development version by adding the following to .emacs:

(load "/path/to/ess-svn/lisp/ess-site.el")

Note that https is required, and that the SSL certificate for the
Subversion server of the R project is

Certificate information:
- Hostname: svn.r-project.org
- Valid: from Jul 16 08:10:01 2004 GMT until Jul 14 08:10:01 2014 GMT
- Issuer: Department of Mathematics, ETH Zurich, Zurich, Switzerland, CH
- Fingerprint: c9:5d:eb:f9:f2:56:d1:04:ba:44:61:f8:64:6b:d9:33:3f:93:6e:ad

(currently, there is no "trusted certificate"). You can accept this
certificate permanently and will not be asked about it anymore.

1.2 Current Features
====================

* Languages Supported:
* S family (S 3/4, S-PLUS 3.x/4.x/5.x/6.x/7.x/8.x, and R)

* SAS

* BUGS/JAGS

* Stata

* XLispStat including Arc and ViSta

* Editing source code (S family, SAS, BUGS/JAGS, XLispStat)
* Syntactic indentation and highlighting of source code

* Partial evaluation of code

* Loading and error-checking of code

* Source code revision maintenance

* Batch execution (SAS, BUGS/JAGS)

* Use of imenu to provide links to appropriate functions

* Interacting with the process (S family, SAS, XLispStat)
* Command-line editing

* Searchable Command history

* Command-line completion of S family object names and file
names

* Quick access to object lists and search lists

* Transcript recording

* Interface to the help system

* Transcript manipulation (S family, XLispStat)
* Recording and saving transcript files

* Manipulating and editing saved transcripts

* Re-evaluating commands from transcript files

* Help File Editing (R)
* Syntactic indentation and highlighting of source code.

* Sending Examples to running ESS process.

* Previewing

1.3 Requirements
================

ESS is most likely to work with current/recent versions of the following
statistical packages: R/S-PLUS, SAS, Stata and JAGS. The one exception
is BUGS which is quite old, but should still work.

ESS supports current/recent versions of GNU Emacs and XEmacs. Most
notably, the GNU Emacs 22 series and XEmacs 21.4.14 or higher
(beta/pre-release versions are NOT SUPPORTED).

1.4 Stability
=============

Versions 5.3.x are meant to be release-quality versions. While some
new features are being introduced, we are cleaning up and improving the
interface. We know about some remaining documentation inconsistencies.
Patches or suggested fixes with bug reports are much appreciated!

1.5 Mailing List
================

There is a mailing list for discussions and announcements relating to
ESS. Join the list by sending an e-mail with "subscribe ess-help" (or
"help") in the body to ;
contributions to the list may be mailed to
. Rest assured, this is a fairly
low-volume mailing list.

The purposes of the mailing list include

* helping users of ESS to get along with it.

* discussing aspects of using ESS on Emacs and XEmacs.

* suggestions for improvements.

* announcements of new releases of ESS.

* posting small patches to ESS.

1.6 Reporting Bugs
==================

Please send bug reports, suggestions etc. to


The easiest way to do this is within Emacs by typing

`M-x ess-submit-bug-report'

This also gives the maintainers valuable information about your
installation which may help us to identify or even fix the bug.

If Emacs reports an error, backtraces can help us debug the problem.
Type "M-x set-variable RET debug-on-error RET t RET". Then run the
command that causes the error and you should see a *Backtrace* buffer
containing debug information; send us that buffer.

Note that comments, suggestions, words of praise and large cash
donations are also more than welcome.

1.7 Authors
===========

* A.J. Rossini (mailto:blindglobe@gmail.com)

* Richard M. Heiberger (mailto:rmh@temple.edu)

* Kurt Hornik (mailto:Kurt.Hornik@R-project.org)

* Martin Maechler (mailto:maechler@stat.math.ethz.ch)

* Rodney A. Sparapani (mailto:rsparapa@mcw.edu)

* Stephen Eglen (mailto:stephen@gnu.org)

1.8 License
===========

ESS is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2, or (at your option) any later
version.

ESS is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
in the file COPYING in the same directory as this file for more details.

1.9 New Features
================

Changes/New Features in 5.4:
* ESS[SAS]: The long overdue change from `make-regexp' to
`regexp-opt' for font-locking is complete. The new
`regexp-opt' is now the default since it is better than the
old code in many ways (and especially more maintainable).
However, there are certainly some special cases missed (bug
reports and patches welcome!). Setting
`ess-sas-run-regexp-opt' to `nil' will result in the old code
being used.

* ESS[BUGS] and ESS[JAGS]: typing `=' now results in `<-'.

* ESS[R] function arguments "show" `(ess-r-args-show)' now
uses the new `(tooltip-show-at-point)' contributed by Erik
Iverson.

* Toolbar icons now also work in (beta) Emacs 23.

* ESS[S]: New function `ess-change-directory' for setting both
emacs' current directory and the directory of an *R* or *S*
buffer.

* ESS[S] when transient-mark-mode is true, the mark is now kept,
rather than deactivated, thanks to a patch from David Reitter.

Changes/New Features in 5.3.11:
* ESS[SAS]: work around bug in Emacs 22.2 & 22.3 which fails to
set case-fold fontification automatically.

* Rd mode: support new keyword 'Rdversion'

* ESS[R]: now again works with Emacs 21.x

Changes/New Features in 5.3.10:
* Fixed noweb-mode bug accidentally introduced into 5.3.9

* In noweb-mode, e.g., Rnw-mode, electric "<" also inserts
closing "@". Further, the code chunk boundaries are better
kept up-to-date, such that code[R] <-> text[LaTeX] minor
mode switching should happen more reliably.

* In noweb-mode, fix a buglet in rare [Enter] or [Tab]
behavior; further, by default disable the former `[[' ..
`]]' code-protection-when-filling behavior which has been
found to be buggy.

Changes/New Features in 5.3.9:
* ESS[SAS]: evince PDF viewer now supported as well; search
order: evince, Xpdf, Adobe/Acrobat Reader

* ESS[R]: added support for Roxygen, potentially to be extended.

* ESS[S] (and R): inferior (`*R*') and transcript modes no
longer fontify language keywords (such as `for', `in', etc).

* iESS[Stata]: Customize the `ess-sta-delimiter-friendly'
setting to `t' to convert embedded semi-colons to newlines
for Stata processing.

* Sweave fix for embedded blanks in PDF reader and PDF files

* Several fixes for Major Mode Convention violations in
`ess-mode' and `noweb-mode'.

* ESS[JAGS]: `M-x comment-region' now available!

* ESS[S] The `ess-swv-*' commands (and keybindings) are now in
a submenu of the "Noweb" menu, when editing Sweave files.

Changes/New Features in 5.3.8:
* ESS[JAGS]: more separation from ESS[BUGS] (as much as is
currently planned); now `C-c C-c' on an empty `.jmd' creates
a template as it should; symbolic links are created for CODA
output so BOA is happy: from `index.txt' to `.ind' and
`chain#.txt' to `#.out'

* ESS[SAS]: buffer-local `ess-sas-submit-command' and
`ess-sas-submit-command-options' now recognized by
`ess-sas-submit-region'

* ESS[S]: When trying to evaluate code in an S language buffer
and there is no associated process, now start R
automatically instead of signalling an error. Also, restart
R if there is an associated process which is not running.
However, do not start R just via the "electric" `('
(`ess-r-args-auto-show').

* ESS[S]: For (one-line) functions withOUT '{ .. }' bodys, the
end of function is now correctly found more often. This
notably improves `C-c C-c'
(`ess-eval-function-or-paragraph-and-step').

* ESS[JAGS]: cleanup/re-organization of elisp code; symbolic
links for CODA output are now only created by the new JAGS
`system' command in version 1.0.3; specify whether this
command is available via `ess-jags-system'; if not present,
then no links are created so that the `*shell*' buffer does
not become unresponsive during the batch run

Changes/New Features in 5.3.7:
* ESS: `ess-default-style' now *is* customizable, i.e.,
changing its value in `~/.emacs' now does have the desired
effect.

* ESS: `ess-font-lock-mode' is a new variable (default: t)
which controls whether font-locking is enabled in ESS buffers.

* ESS[R]: for XEmacs on Windows; another tweak to find R
versions

* ESS[SAS]: font-locking updated for ODS and SAS Bayesian
Procedures; a more consistent handling of SAS options by
`ess-sas-submit-command-options' which is buffer-local;
portable snooze for MS Windows via customize-able
`ess-sleep-for' (floats welcome); Xpdf now supported as a PDF
viewer

* ESS[Rnw]: now also works with "emacs -nw" and Emacs 22.

* ESS[JAGS]: now requires JAGS 1.0 (see the new ESS for JAGS
help section for more information): both need work;
suggestions welcome

* ESS[R]: [TAB] completion now uses the R-internal completion
mechanism (for R >= 2.5.0).

* ESS[R] ([S]): interpretation of "_" as assignment has been
removed in `ess-continued-statement-p' for R and S.

* several internal code cleanups.

* ESS[R]: An experimental version of a new command `Rgui' on MS
Windows to send lines directly from emacs to `Rgui' is
available in file `lisp/essd-rgui.el'. Preliminary
documentation is in file `doc/rgui-doc.txt'.

Changes/New Features in 5.3.6:
* ESS: for XEmacs, using "gnuclient" (without a "-q") works for
things like fix() after M-x gnuserv-start has been done.

* ESS[R]: M-x R-newest should now work in more situations on MS
Windows, e.g., when R has been installed in a non-default
"ProgramFiles" directory tree. In these cases, there's no
need to specify the name (and full path) of the R program
anymore.

* ESS[R]: For XEmacs, startup (with new tooltip code) works
again.

Changes/New Features in 5.3.5:
* ESS[R] a new defun is available, `M-x R-newest', which will
start the newest version of R that it can find on your system.

* ESS[R] add Sven Hartenstein's "R function arguments tips"
functionality, via new file `../lisp/essd-r-args.el'. Note
that this includes an "electric "("" behavior inside `R-mode'
which is _active by default_ and can be customized via
`ess-r-args-electric-paren'; i.e., use `(setq
ess-r-args-electric-paren nil)' to turn it off. Further,
`ess-r-args-show-as' allows to switch to the "tooltip" mode.

* ESS: functions `ess-get-pdf-viewer' and *-ps-viewer; built on
new customizable variables `ess-pdf-viewer-pref' and
`ess-ps-viewer-pref'; currently used in `ess-swv-PDF' and
`*-PS'.

* ESS[R] Improved `ess-swv-PDF' to run pdf viewer only if
pdflatex was ok

* ESS[R] Improved `ess-swv-weave' to start R automatically if
none is running.

* ESS: Do no longer ask _which_ ESS process to use if there is
only one.

Changes/New Features in 5.3.4:
* ESS[R] now better work with options(error=recover); and the
new default of CHM help files on windows.

* ESS[R] some more cleanup in the "sweave" functions

* miscellaneous fixes

Changes/New Features in 5.3.3:
* ESS[S] fix buglet (5.3.2 only) which left command prompt in
"execute buffer" and hence help files.

* new customizable variable `ess-display-buffer-reuse-frames'
set to true (which changes default behavior) such that
execution or help *frames* are reused.

Changes/New Features in 5.3.2:
* Classic BUGS now supported by `(require 'essd-bugs)' with
ESS[BUGS] and JAGS by `(require 'essd-jags)' with
ESS[JAGS]. But, only one of them can be used at a time
since they don't play nice together. Also, `C-c C-c'
is now bound to the function `ess-bugs-next-action'
(`F12' has been retired). And finally, note that
`essl-bug.el' is deprecated and the replacement is
`essl-bugs.el'.

* ESS[R] Improved some of the "Sweave-make" functions (yet
scarcely documented) in `ess-swv.el'.

* ESS[S] No longer mess with .Last.value (nor in other
"languages").

Changes/New Features in 5.3.1:
* See the docs for 2 ways to install ESS for XEmacs
1. by uncommenting the XEmacs part of Section 1
of `Makeconf' and performing `make install'

2. by unpacking either `ess-5.3.1.tgz' or
`ess-5.3.1.zip' into
`PREFIX/lib/xemacs/site-packages' on unix or
`PREFIX\XEmacs\site-packages' on windows

* ESS[R]: fixed bugs so that Rterm.exe can be found by XEmacs

* ESS[S]: `ess-toggle-S-assign-key' is slightly changed; in
particular, the default `ess-assign-key' is now `C-x ='.

* ESS[R]: `M-x R-site-search' is a new (slightly experimental)
utility similar to R's `RSiteSearch(..)' but with the
advantage of using Emacs' preferred browser, see
`browse-url-browser-function'

Changes/New Features in 5.3.0:
* ESS[BUGS]: sanely re-format statistical output, `.bog', from
scientific notation to numbers rounded with 4 decimal places
with `M-x ess-bugs-sci-round-to-4-dp'.

* The keys for navigating among section headings in help buffers
worked, but only for one language per session; they should
now work for multiple languages. (They were also broken on
Windows machines.)

* ESS[S] long standing buglets in the internal logic for loading
lisp code on Windows. Particularly fixed behavior in help
mode with S-plus GUI.

* New variable, `ess-use-inferior-program-name-in-buffer-name',
which enables using the executable name instead of the
dialect name for R. Feature request.

* ESS[S] `ess-execute-screen-options' now also works correctly
when there is more than one window *side-by-side* in the same
frame and runs in the correct buffer also when there is more
than one S buffer.

* iESS[S] new functions `ess-eval-paragraph-and-step' and
`ess-eval-function-or-paragraph-and-step' are bound to keys
`C-c C-p' and `C-c C-c' respectively and to the menu in
ESS-mode; also bound in the help mode (for evaluating
examples).

* ESS[S] new function `ess-toggle-S-assign-key' allows to
assign the " <- " insertion to an arbitrary key.

------------------------------------------------------------------------
≫ S-PLUS トレーニングコースのご案内 ≪
------------------------------------------------------------------------
※ 6/5（金） 大阪でも開催！

数理システムでは、S-PLUSをこれからご利用になる方のためのトレーニング
コースを月例で開催しています。いずれも、一人 1 台のパソコンを用いた
実践的なコースです。どうぞご利用ください。

（料金）
◎ 年間メンテナンスサポート加入の方 いずれも無料
◎ 年間メンテナンスサポート未加入の方 10,500円（税別）

（申込み方法）
http://www.msi.co.jp/splus/support/training.html より申込書を入手して
FAX頂くか、直接 splus-info@msi.co.jp 宛のメールもしくはお電話でお問合せ
ください。

==================================================
★ S-PLUS for Windows入門トレーニングコース
6/15（月）、 7/8（水）
数理システムセミナールームにて（新宿）

主にGUIによるマウスでの「ポイント&クリック」方式の操作に重点を置いて
学びます。本コースを受講された後「S-PLUS for Window応用コース」を受講
されることをお勧めいたします。

==================================================
★ S-PLUS for Windows応用トレーニングコース
6/16（火）、 7/9（木）
数理システムセミナールームにて（新宿）

「S-PLUS for Window入門コース」を受講された方に向けたコースです。もう
少し進んだデータの編集やグラフ作成、統計解析を取り上げます。

==================================================
★ S言語入門トレーニングコース
5/21（木）、 6/17（水）、 7/13（月）
数理システムセミナールームにて（新宿）

いままでS言語を利用したことのない方がこれから利用するにあたって、最も
必要になる事項に絞り込んだ内容になっております。（全てのUNIX版および
Windows版でもコマンド利用を覚えたい方向き）

==================================================
★ S-PLUSプログラミング基礎
5/22（金）、 6/18（木）、 7/14（火）
数理システムセミナールームにて（新宿）

S言語のプログラミング技法の基礎（文法など）に関して学び、独力で必要な
処理をプログラミングできることを目指します。S-PLUSの利用にあたって、
しばしば利用される便利な関数のいくつか、デバッグ方法を紹介します。なお、
本コースのレベルは「S言語入門コース」を受講された方を対象としております。
Ｓ言語の利用経験のない方は「S言語入門コース」とセットで受講される事を
お勧めいたします。S 言語によるコースです。

==================================================
★ Windows版システム開発者コース
5/25（月）、7/15（水）
数理システムセミナールームにて（新宿）

S-PLUSを利用してシステムを構築する方のためのセミナです。OLEを用いた、
S-PLUSと(ExcelやVBなど)各種アプリケーションとのリンケージ、S-PLUSから
コールする方法などに関する技術解説を行います。なお、実例に関しては比較的
基本的な例を取り上げますが、本コースのレベルは「S言語入門コース」を受講
された方を対象としております。

==================================================
★ 大阪S-PLUS入門コース 6/5（金） 梅田 ax-netsにて

「S言語入門」および「S-PLUS for Windows入門」を要約した上で1日で実施
します。午前中にWindowsのGUIの使い方、午後はS言語によるコマンド・関数
操作の解説になります。

==================================================

※当日、終了後に直接の個別のご相談も承ります。

------------------------------------------------------------------------

データ解析ソフトS-PLUS 無料紹介セミナのご案内
【操作実習により、利用方法も習得！】
--- 6月4日（木） 大阪でも開催します ---

------------------------------------------------------------------------
※既にお申込の方にお届きの場合はご容赦ください。

汎用データ解析ソフトウエアS-PLUSは、プロユースの本格的な機能を持った
解析ソフトとして、研究開発におけるデータ解析やデータの可視化、アンケ
ートなどの調査データの加工および統計処理、顧客の分析などマーケティン
グ分野、将来の需要予測、金融工学、製造における品質管理・歩留まり解析、
教育など、幅広い分野で活躍しているソフトウエアです。
(URL) http://www.msi.co.jp/splus/

このS-PLUSの無料紹介セミナを東京・新宿にて開催致しております。上記の
ような問題解決にご関心のある方は、この機会に是非御参加頂ければ幸いです。
実際に一人1台のPCでの操作実習を伴いますので、S-PLUSの大まかな使い方も
習得できます。会場にて無料試用版を配布していますので、その後、職場等で
ご自分のデータに対して解析を行うこともできるようになります。

・期日（各回同一内容で、時間は 13:30-16:30 です）

2009年 5月11日（月） 東京新宿
2009年 6月 4日（木） 大阪梅田※
2009年 6月11日（木） 東京新宿
2009年 6月26日（金） 東京新宿

・場所
【東京会場】 株式会社 数理システム セミナールーム（新宿）
（東京都新宿区新宿2-3-10 新宿御苑ビル4F
JR新宿駅 徒歩8分、東京メトロ&都営 新宿三丁目 徒歩4分
東京メトロ 新宿御苑駅 徒歩2分）

【大阪会場】 西梅田 ax-nets
（大阪市北区曽根崎新地2-3-21 axビル4F Tel. 06-346-3001
JR大阪駅桜橋口より徒歩5分、地下鉄四つ橋線西梅田駅9番出口よりすぐ）

・参加無料

（内容）
・データ解析、統計解析、データマイニングについて
・S-PLUSの生立ち
・S-PLUSの機能
・S-PLUSの応用例、実績
・S-PLUSご購入について
・S-PLUSアドオンモジュール
・S-PLUS Enterprise Server（データ解析WEBサーバ）
・体験S-PLUS（デモンストレーションと実習）
※一人1台のPC利用を伴います
・質疑応答

なお、終了後、個別のご相談にお答えすることも可能です。
会場では、S-PLUSの30日間トライアル版（フル機能）、S-PLUSユーザカンファ
レンスの過去の論文等の無料配布を行います。

受講希望の方は、受講希望日、氏名、会社名（学校名）、住所、TEL番号、
FAX番号、e-mailアドレスを明記の上、弊社S-PLUSグループ宛にお申込み頂くか、
http://www.msi.co.jp/splus/events/seminar.html
から申込書をダウンロードしてFAXでご送付ください。おり返し受講票をお送
りいたします。
詳細のお問合せは splus-info@msi.co.jp 宛でも承ります。

Dear members of the R user community,

I am pleased to inform you that the program of the useR! 2009 conference (Rennes, France, July 8 to 10, 2009) is available online:
http://www.agrocampus-ouest.fr/math/useR-2009/program.html

You can register from the link below:
http://www.agrocampus-ouest.fr/math/useR-2009/formulaires/registration.php

The conference web page:
http://www.agrocampus-ouest.fr/math/useR-2009/accomodation.html
gives a list of hotels and some student rooms (200) are also available
on the campus (Rennes will be very busy at the conference time because
the cultural event `Festival Les tombées de la nuit' will take place at
the same time, so we recommend to book as soon as possible).

We hope to meet you in Rennes!

I've rolled up R-2.9.0.tar.gz a short while ago. This is a development
release which contains a number of new features.

Also, a number of mostly minor bugs have been fixed. See the full list
of changes below.

You can get it (later today) from

http://cran.r-project.org/src/base/R-2/R-2.9.0.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you. In case of
impatience, try http://www.biostat.ku.dk/~pd/R-release

Binaries for various platforms will appear in due course.

For the R Core Team

Peter Dalgaard



These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:


70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
7861f511a3f8e8598c9b84d65e93c389 NEWS
7abcbbc7480df75a11a00bb09783db90 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
b96e9596f947794c5628712f8016aa90 FAQ
a5b79a2bc1372136cda4674b5f46d146 R-2.9.0.tar.gz
a5b79a2bc1372136cda4674b5f46d146 R-latest.tar.gz



This is the relevant part of the NEWS file:

CHANGES IN R VERSION 2.9.0


SIGNIFICANT USER-VISIBLE CHANGES

o expand.grid() by default no longer coerces strings into factors.


NEW FEATURES

o Package 'Matrix' is now a recommended package contained in the
basic R distribution. It provides S4 classes and methods for
dense and sparse matrices, often by using the numerical
libraries Lapack and from the SuiteSparse collection CHOLMOD,
CSparse, and SPQR among others.

o pdf() and postscript() gain a 'useKerning' argument to place
strings using kerning (which had previously been ignored in
display but not in strwidth), based in part on an idea and
code from Ei-ji Nakama. The default is TRUE.

Kerning involving spaces is now ignored (it was previously
only used in the computation of string widths).

o seq.default() and seq.int() ensure that the result is within the
interval [from, to] even when the last value would previously
have been slightly out of range because of the allowance for
rounding error in computing the number of elements.

o boxplot() gains a simple 'matrix' method, enabling boxplot(mat)
instead of boxplot(data.frame(mat)).

o zip.file.extract() gains an optional 'dir' argument (but use
unzip() instead).

o source() with 'encoding' specified (and not as "unknown") marks
the encoding of character strings in Latin-1 and UTF-8
locales.

o parse(text=z) now marks the encoding of character strings in
Latin-1 and UTF-8 locales if 'z' is of known encoding (that is
all elements are either ASCII or marked as Latin-1 or UTF-8).

o sprintf() does stricter error checking on input formats to
avoid passing invalid formats to the OS (which have a tendency
to crash under such inputs).

o expand.grid() gains a 'stringsAsFactor' argument to ask for
automatic conversion of character vectors to factors (which
happened for many years but was not previously documented, and
is no longer the default).

o bxp() now coputes the 'ylim' including the outliers only if
'outline = TRUE'. (Wish of PR#13196)

o barplot() gains a 'args.legend' argument. (Wish of PR#13265).

o RweaveLatexSetup() now accepts all (and not just some) options
passed through from Sweave()

o cumsum(x) and cumprod(x) for double precision x now use a long
double accumulator where available and so more closely match
sum() and prod() in potentially being more accurate.

o plot() methods for "stepfun" (and hence "ecdf") gain an 'col'
argument, allowing to set all three colors simultaneously.

o Iterating over a factor in a for loop now coerces to a character
vector (rather than using the integer codes).

o data.frame() now recycles columns of list arguments, not just
vectors and factors.

o plot.ts(plot.type="multiple") now makes use of *.lab and
*.axis graphical parameters (wish of PR#13134 and 13135).

o Classes can be exported from a name space using the NAMESPACE
file directive 'exportClassPattern' which has the same syntax
as 'exportPattern'.

o strftime() now converts its first argument with as.POSIXlt()
and so is no longer an alias for format.POSIXLt.

o body<-() now treats list values consistently with other
types: they no longer need to be wrapped in a list() call.

o option("pdfbrowser") is now set on Windows as well as on
Unix-alikes.

o object.size() now returns an object of class "object_size" and
has a print() method.

o [col/row]Sums(), *Means() now have an additional '...' argument,
so that they can more easily be turned into generic functions.

o Package 'tools' contains dependsOnPkgs() to compute reverse
dependencies.

o Strict type checking is now turned on: this catches more
internal corruptions, and some badly written contributed code.

o There are new functions in package 'tcltk', tk_choose.files(),
tk_choose.dir() and tk_messageBox(), analogues of functions
available on Windows (the last is an analogue of winDialog).

o Sys.glob() now does tilde expansion on all platforms.

o read.table() and friends gain a 'fileEncoding' argument to
make re-encoding of input just a little bit simpler.

o grep() gains an 'invert' argument mimicking 'grep -v/--invert'.

o strwrap() now allows a separate prefix for the first line.

o grep() has a more efficient sibling grepl() that returns a
logical vector.

o xfig() has new arguments 'defaultFont' and 'textSpecial'
contributed by Sebastian Fischmeister.

o parse() and parse_Rd() now point to syntax errors in the
reported error context, and include the filename and line and
column numbers so smart text editors can jump to the error
location.

o str(<1d-array>) now writes "[1:n(1d)]" instead of the previous
less clear "[, 1:n]".

o New function testInstalledPackage() in package 'tools' allows
the examples (and if they were installed) any package-specific
tests to be run on an installed package.

testInstalledPackages() can run all the examples and tests in
the standard and/or recommended packages. Also
testInstalledBasic() can run the basic tests (if installed).

o file.copy() now has a 'recursive' argument.

o Errors in setOldClass() will cause a previous definition to be
restored.

o Ambiguities in class inheritance and method selection resulting
from duplicates in superclasses are now resolved by requiring
(if possible) consistency with all the superclass inheritance. The
rules for method selection have been revised to take advantage of
the improved ordering.
See ?Methods and the reference there related to inheritance.

o New function unzip() in package 'utils' to expand or list zip
archives.

o Replacement functions for class() and oldClass() will unset
the S4 bit when the replacement can't be an S4 object;
oldClass() will return the S3 class for S4 objects with slot
.S3Class.

o clip() takes extra steps to avoid the next graphics call
resetting the clip region.

o New function sample.int() to provide documented access to the
internal part of sample() (sampling from seq_len(n)).

o New version of withVisible() for better handling of cases like
withVisible(eval.parent(....)). Moved to package 'base' with a
view to replace .Internal(eval.with.vis) in source() later.

o showClass() which is also used to auto-print class definitions, now
mentions the package where the class comes from, if there is one.

o simulate(obj) now also works for "glm" objects and for weighted
fits, thanks in part to contributions from Ben Bolker and
Heather Turner. There is now a means to extend the methods
available for "glm" objects, as glm families can have an
optional 'simulate' component.

o S4 classes that inherit from any of the "structure" classes or
from "vector" will turn on methods for all the "Ops" group of
functions when the package containing the classes is
loaded. See class?structure.

o A mechanism now allows S4 classes to inherit from object types
"environment", "externalptr" and symbol ("name"). See ?setClass.

o demo() gains 'echo' and 'ask' arguments, with defaults similar
to example().

o library() no longer checks for the packages merged during the
re-organization of 1.9.0.

o New function poisson.test() in package 'stats' for exact test
of rates and rate ratios.

o New function isdebugged() indicates whether its argument has the
debug flag set or not.

o ls.str() [via print method] now also works when some objects in
the environment are missing().

o Subsetting S4-objects (without an explicit "[" method) no longer
preserves the class in cases like setClass("C",
contains="list"); This reverts a "bug fix" activated in R 2.8.0.

o .packages() and .find.packages() no longer check the package
info for installed packages with dumped metadata, since this
was checked when the package was installed. .packages() only
considers such packages to be validly installed (any others
were installed in a long-obsolete version of R). Both changes
speed up searches in libraries of thousands of packages().

o boxplot() uses butt line endings for its median line
(suggestion of Uwe Ligges, PR#13553).

o S4 objects passed to a non-default S3 method will be converted
to a valid S3 object with the S3 class. See the section on
inheriting from non-S4 classes in ?Classes.

o A new class "nonStructure" has been defined; classes that extend
a vector class but that should lose their slots under Math or
Ops functions should extend this class. See class?nonStructure.

o axis.POSIXct() now plots in the timezone marked for its inputs
(if any) rather than in the local time. The latter was a
deliberate choice, but is easy to select by removing the
'tzone' attribute. (Suggestion of Dan Kelley.)

o A new function classesToAM() returns an adjacency matrix
representing the inheritance of the classes specified. Allows
better human examination of the patterns, e.g. by using the
matrix as input to one of the graph packages (see the
documentation).

o X11options(antialias = "none") now works, for consistency with
X11().

o sprintf() now allows zero-length arguments (with a zero-length
result). (Suggestion of Bill Dunlap.)

o unlink() is now able to remove broken symbolic links on
Unix-alikes.

o New selectSuperClasses() utility.

o HoltWinters() now allows parameters alpha and beta to be fixed
at 0 and hence beta = FALSE and gamma = FALSE are used to
specify restricted models.

o A new function smoothScatter has been added to package
'graphics'. It is appropriate for very dense scatter plots
and uses density estimation and color to reflect density of
plotting.


DEPRECATED & DEFUNCT

o allGenerics() is defunct.

o Use of allocVector(CHARSXP ...) is defunct and gives an error.

o The compatibility define for graphics structure NewDevDesc in
GraphicsDevice.h has been removed.

o Support for versioned installs (R CMD INSTALL
--with-package-versions
and install.packages(installWithVers = TRUE)) has been removed.
Packages installed with versioned names will be ignored.

o The numeric and power(0.5) forms of argument to make.link()
which were deprecated in 2.4.0 are now defunct: use power()
directly.

o Conversion to Sd and Ssgm by R CMD Rdconv is now defunct.

o Support for R --gui=gnome is now defunct (and package
gnomeGUI has been withdrwan as it used a long-obsolete version
of GNOME).

o R CMD SHLIB on Windows will call the first target (not 'all') in
Makevars[.win] in future versions: so make 'all' the first
target if you have any.


UTILITIES

o R CMD build now also uses a Makevars[.win] file for cleaning
up src/.

o R CMD Rd2dvi and R CMD check are now able to cope with Cyrillic
characters in UTF-8 if environment variable _R_CYRILLIC_TEX_
is set to a non-empty value and the latex system has suitable
fonts (thanks to a hint from Alexey Shipunov).

o New function rtags() in package 'utils' that provides etags-like
indexing capabilities for R code files.

New front-end script R CMD rtags provides an interface to the
rtags() function (see R CMD rtags --help for details).

o New environment variable R_TEXI2DVICMD to hold the path (if any)
to 'texi2dvi' found at configure time: this now provides the
default to option("texi2dvi").

o massage-Examples.pl has been replaced by the R function
tools:::massageExamples().

o R CMD REMOVE now uses remove.packages() and hence removes all
members of a bundle.

o R CMD SHLIB is now an R script and has a new option -n aka
--dry-run to show what commands would be run. The same code
is used on Unix and Windows.

o R CMD Rdconv has new options --package and --version to set the
corresponding fields in HTML conversion.

o R CMD check runs the package tests with a custom startup file,
currently containing 'options(useFancyQuotes = FALSE)'.

Those tests are run by an R script: using a tests/Makefile
(undocumented) no longer works.

o R CMD config now knows about DYLIB_EXT and SHLIB_EXT, for use
in configure files.

o R CMD BATCH has a new option --no-timing to suppress printing
out the session timing.

o R CMD Rd2dvi can now work on an installed package.

o R CMD check no longer loads package 'tcltk' when checking for
code problems, so more problems may be reported.

o For R CMD SHLIB on Windows the default 'all' target only makes
the DLL, and no longer call targets 'before' and 'after'.


Rd CONVERSION

o Rd files have an optional \Rdversion{} section, which if
missing defaults to 1.0. There is support for version 1.1, a
slightly modified version with the following changes:

- The warnings for \code{} inside example are suppressed.

- Whitespace between arguments in \item and \section is
accepted without a warning (see below).

- $ is treated literally in text, even for latex conversions.

- \ is only an escape before % { } \ .

- \R, \dots and \ldots can be followed by {}, and it is
recommended that they when not followed by whitespace.

- The obsolete interpretation of \Alpha etc is no longer done.

o Rd conversion now handles ^ ~ < > | correctly in non-code
environments (such as \samp), and # and _ even in latex
conversion (but $ still needs to be escaped in version 1.0).

o Whitespace between first and second arguments is now accepted
for \item and \section, e.g. \item{foo} {some value}.
Previously arguments after whitespace were silently ignored,
and a warning is given for version 1.0 files.

o The Rd files created by prompt() and friends are declared to be
version 1.1.

o \alias now supports the escaping of { as well as of %, and this
is recommended.

o parse_Rd(), an experimental parser for Rd files, and Rd2txt(),
Rd2HTML(), Rd2latex() and Rd2ex(), even more experimental
converters, have been added to package 'tools'.

o R CMD check runs the package's Rd files through parse_Rd() for a
stricter syntax check. This can be suppressed by setting
_R_CHECK_RD_PARSE_ to FALSE.

o Added markup \verb, which displays like \code, but parses as
verbatim text. Currently only supported by parse_Rd() and
Rd2HTML().


INSTALLATION

o The shell used by the 'R' script and other shell scripts
intended to be run directly can be specified at installation
time by setting the (precious) configure variable R_SHELL.

o libtool has been updated to 2.2.6a.

o --with-ICU is now the default: this means that ICU will be
used for collation on Mac OS >= 10.4.

o make install-tests can be used to install the test files,
to allowed an installed version of R to be tested -- see the
R-admin manual. This is also supported by the function
testInstalledPackages() in package 'tools'.

o 'make install' using a parallel make should now work.

o 'make check' now always re-makes and re-runs the package
examples, which are now collated in the locale's order (and
not ASCII order).

o configure will now set the default optimization level for
gfortran on x86_64 Linux to -O as -O2 has caused problems with
gfortran 4.3.x.


PACKAGE INSTALLATION

o install.packages() is able to infer that repos=NULL was
intended from the extension on the file name specified as 'pkgs'.

On Mac OS X it now supports local binary packages with .tar.gz
extension. Nonetheless .tgz remains the preferred extension
and is expected in repositories.

It now checks >= version dependencies for dependent packages,
and so will install a newer version of a dependency if needed
and available on the repositories.

The library being installed into is considered when looking
for installed packages if it is not already part of
.libPaths() (as INSTALL already does).

It has a new argument 'Ncpus' to support parallel installs of
source packages.

o HTML links will be resolved first to the standard packages: this
avoids other installed packages diverting help on e.g. qr()
and plot() to themselves. The HTML files are only "touched" if
they have changed.

o A check is done that the R files can be parsed: this both
prevents a broken package without lazy-loading from being
installed and gives better diagnostics.

o install.packages() gains a 'configure.vars' argument, and both
this and 'configure.args' get their defaults from options().

o There is a unified R script for INSTALL on both Unix-alike and
Windows that takes option names used by either in the past.

It adds --no-multiarch to disable building other than the main
sub-architecture, and allows multiple instances of
--configure-args and --configure-vars (which will be
concatenated).

New option --install-tests will install any package-specific
tests.

o Times in the Packaged: and Built: fields are now recorded in
UTC, and in most cases in ISO 8601 format.


C-LEVEL FACILITIES

o A helper function, asCharacterFactor, converts from factors to
character vectors.


BUG FIXES

o The postscript() output for setting text is faster and smaller.

o Subsetting a data frame with duplicate column names without
selecting columns (e.g. z[i,]) no longer makes the column
names unique. This was never documented, but some packages
have assumed it.

o data.frame() no longer ignores row names on objects if the
first name is empty. (PR#13230: this has been the behaviour
for a long time, but apparently undocumented.)

o deparse(control="S_compatible") now never uses backticks.

o X-spline drawing is improved for cases where the control
points are located well off the edges of the device.

The symptom of this problem is the error "reached MAXNUMPTS".

o exists() with mode= "any" will no longer run an active binding's
function.

o format(c(1 + 2i, NA)) no longer has extraneous space in " NA".

o mood.test() could fail in 2.8.x on large samples because of
integer overflow.

o heatmap() without a dendrogram could fail. (PR#13512)

o Checks for missing values will no longer occasionally result in
an infinite loop or stack overflow error, depending on the
compiler. Active bindings are now always considered to be
non-missing.

o Rd conversion was not accepting \p (as in \pkg} or (when using
Perl 5.10.x) \k (as in \kbd) in any preamble text in a
\value{} section, since those are nowadays interpreted by
Perl. (PR#13575)

o if(as.raw(1)) TRUE now works as expected. (PR#13630)
Also, c(as.raw(12), TRUE) or c(raw(3), pi) do.

o duplicated(, incomparables = NA) now gives the
intended error message.

o name handling of as.data.frame() has been sanitized somewhat

o Evaluating an assignment expression with a string on the left
hand side no longer destructively changes the string to a symbol
in the expression.



**************************************************
* *
* 2.8 SERIES NEWS *
* *
**************************************************


CHANGES IN R VERSION 2.8.1 patched


NEW FEATURES

o R CMD check has a new argument '--install-args' to pass
command-line arguments to INSTALL.
E.g. --install-args="--docs=normal" on Windows if the HTML
Help Workshop is not installed.

o R-Forge has been added to R_HOME/etc/repositories, so it will
be available interactively in setRepositories().

o The compiled loess() code has been updated to the current
version of dloess from Netlib. This includes patches from Ben
Tyner which correct some errors when degree = 0 and hence
solve PR#13570.


INSTALLATION

o --with-ICU is now supported (and recommended) on Mac OS X using
Apple's supplied port. Note however that the locale category
LC_COLLATE cannot be changed whilst R is running on Apple's
version of ICU.

Configure supports a wider range of ICU versions on other
OSes: version 3.0 should suffice, and 3.2, 3.8 and 4.0 have
been tested.


BUG FIXES

o grid-based plots no longer reset the base text size to the
default 96dpi in cairo-based bitmap devices.

o Rd conversion was incorrectly parsing \\\* and \\\{ (and other
cases with an odd number of backslashes greater than one).

Text conversion of \code{\ etc} was incorrect (a single
backslash stands for itself inside \code).

\code{} inside \examples{} is now fixed up (but the warning
remains, since it will be handled incorrectly in earlier
versions of R).

o as.matrix.data.frame() could fail if coercion changed the
dimension of one of the columns (as e.g. the coercion of a "Surv"
object to a character vector does).

o When extracting part of a complex list structure using [[]]
with a vector index, the extracted part was not marked for
duplication on change. (PR#13411)

o Assigning an additional element to a pairlist/language element
by x[["foo"]] <- value did not name the additional element.

o .Call() and .External() were not accepting "NativeSymbolInfo"
and "NativeSymbol" objects as claimed. (Patch from Olaf
Mersmann.)

o codoc() was missing some default value mismatches with
unescaped backslashes, e.g. final="\\" needs to be written as
final="\\\\" in the Rd file.

The reports on values now give strings in the original quoted
format (with \ and " escaped).

o The $<- method for pairlists (including language objects)
failed to duplicate if NAMED was 2.

o read.table(blank.lines.skip = FALSE) gave a final empty row on
files with less than 5 lines (PR#13433).

o Workaround for a bug in some versions of iconv that was seen
with output lines of more than 10,000 bytes and with
re-encoding requested on an output connection.

o The fullrefman.{dvi,pdf} duplicated part I in part II (at
least on some systems).

o cbind() could crash with a zero-length input and a list result.

o pdf(colormodel = "gray") was setting the stroke colour for fills.

o file.show() with multiple files would only show multiple
copies of the first one. (PR#13469)

o formatC(mode = "character") was documented to work, but
did not. (PR#13474)

o besselI(x,.., expon.scaled=TRUE) now gives accurate results for
x < 1e5 whereas it previously underflowed for x >~= 1500.
Further, besselJ(x,..) also computes up to 1e5 (instead of 1e4).

o str() was incorrectly warning about its option component
'formatNum' set by strOptions().

o nls(algorithm = "port") did not accept the [factor] notation.
(PR#13650)

o The relational (aka "comparison") operators are now binary, also in
a lower level sense, and an expression as "<"(1) is now erronous.

o The 'offset' argument for lm() and glm() is not longer
documented to be allowed to be of length 1: this has not been
true for a long time.

o format.info(x) is now also correct when x has no finite content.

o predict.lm() now works correctly when the fit had more than
one offset (possibly specified both in the formula and as an
argument). This function is called by predict.glm(), so the
same isses are corrected there.

o besselI(x, nu) with nu a negative integer (a singular case) is now
correct. (PR#13556)

REMINDER: Abstract deadline for the 2009 Bioinformatics Open Source Conference (BOSC) 2009 is Monday, April 13.

An ISMB 2009 Special Interest Group (SIG)
Date: June 27-28, 2009
Location: Stockholm, Sweden
URL: http://www.open-bio.org/wiki/BOSC_2009
Abstract submission via EasyChair: https://www.easychair.org/login.cgi?conf=bosc2009

Important Dates
Monday, April 13: Abstract deadline
May 1, 2009: Notification of accepted abstracts
May 15, 2009: Early Registration Discount Cut-off date
June 27-28, 2009: BOSC 2009

Keynote Speakers

Alan Ruttenberg
Principal Scientist at Science Commons. He works with Semantic Web technologies in computational biology, with an emphasis on the creation and application of structured biological knowledge to interpret experimental results.

Robert S. Hanmer
Consulting Member of Technical Staff in the Technical Component Management area in Alcatel-Lucent’s Operations area, developing software-sourcing strategies for middleware and open source software, active in the software patterns community,and current President of The Hillside Group.

About BOSC
The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.

Sessions
This year’s conference will mark the 10th anniversary of BOSC. To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead: Open Source Solutions to Grand Challenges in Bioinformatics.” We are inviting abstracts for two different types of talks:

1. Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.

2. Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.

In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session. This year’s topics include:
Topics
Design Patterns in Bioinformatics
Regulatory Genomics
Multicore and GPGPU computing
Data & Analysis Management (shared session with DAM SIG)
Computational Grids
Visualization
There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.

BOSC Post-conference Proceedings
The BOSC 2009 Organizing Committee is currently working out an agreement with an Open Access bioinformatics journal to publish a Post-conference Proceedings based on this year's presenations. Details will be available on the BOSC web site as they become available.

Contact
To contact the organizing committee, e-mail bosc@open-bio.org.

To sign up for BOSC-related announcements, subscribe to the Bosc-announce list (http://lists.open-bio.org/mailman/listinfo/bosc-announce).

BOSC 2009 Organizing Committee
Kam D. Dahlquist (Chair)
Lonnie R. Welch (Co-chair)
Hilmar Lapp
Jens Lichtenberg
Frank Drews
Andrew Dalke
Jim Procter
Seán I. O' Donoghue
Anton Nekrutenko
Steffen Moeller

Registration for BioC2009, to be held 27-28 July 2009 at the FHCRC in Seattle WA USA, is now open. The conference is divided into two components: scientific talks and practical computer sessions:

https://secure.bioconductor.org/BioC2009/

The speakers for the scientific talks are listed as well as roughly half of the titles and abstracts for these talks. A list of some afternoon practicals is also available and content for both the talks and the practicals will be updated shortly.

There are some scholarships, travel funds etc. available, so follow the appropriate link and submit an application if you are interested.

Those wanting to present practicals, please e-mail biocworkshop AT fhcrc DOT org with the title and an abstract for your session. There is a nominal 30 April deadline for proposals and all applications will be assessed by the BioC2009 program committee to determine acceptance.

We would like to invite you to the Los Angeles area R user group's first
meeting. This group is aimed to bring together practitioners (from
industry and academia alike) in order to exchange knowledge and
experience in solving data analysis/statistical problems by using R.
More information about the group at:
http://www.meetup.com/LAarea-R-usergroup/

Meeting: Four case studies of using R

The goal of this first meeting is to bring together people of a wide
range of interests related to R and to open a forum for discussions and
further interaction.

Agenda:

- Introduction
- Using R in research (Jan de Leeuw, UCLA)
- Using R in applications related to credit card transactions (Szilard
Pafka, Epoch)
- Using R in teaching (Rob Gould, UCLA)
- Using R in consulting (Brigid Brett-Esborn, UCLA)
- Q&A, general discussions
- Discussions/networking

We plan 15 minutes for each speaker and for the general discussions.
Then participants are encouraged to initiate discussions with each other
(the place is reserved until 9pm). Bottled water and cookies will be
available free of charge.

Please RSVP on meetup.com (http://www.meetup.com/LAarea-R-usergroup/) as
places are limited.

Those who are unfamiliar with R but would like to get basic hands-on
knowledge (installation, working with data, plotting etc.) are welcome
to attend the “Basic R” course (free) of the UCLA Statistical Consulting
Center, 5-7pm (right before the meetup) in the same room. Please email
to susan@stat.ucla.edu as places are limited. You can also download the
notes, or attend the course at another time at your convenience (see
http://scc.stat.ucla.edu/mini-courses/ ).

Our speakers:
- Jan de Leeuw is Distinguished Professor and Chair at UCLA Department
of Statistics. He is also Editor in Chief of the Journal of Statistical
Software (the primary journal for publishing work related to R) and the
Journal of Multivariate Analysis.
- Szilard Pafka, PhD is Chief Scientist at Epoch, a credit card
transactions processor. He uses R for various data analysis, statistical
modeling and visualization projects. Previously, he worked on a variety
of research problems ranging from physics to financial prices.
- Rob Gould received his PhD from UC San Diego in 1994 and has been at
UCLA since. He is director of the UCLA Center for Statistics Education,
Associate Director of Professional Development of the Consortium of the
Advancement of Undergraduate Statistics Education, and former chair of
the ASA Advisory Committee on Teacher Enhancement.
- Brigid Brett-Esborn is a PhD student in the Department of Statistics
at UCLA. She also works as a consultant with the Department's
Statistical Consulting Center and the Statistical Computing group within
UCLA's Academic Technology Services department. She has contributed to
the Journal of Statistical Software.

Time and venue:
May 7, 2009, Thursday, 7-9pm
UCLA Boelter Hall Room 9413
(this room is next to the Statistical Consulting Center, Boelter Hall 9434)
The only way to access the venue is from the southeast corner of Boelter
Hall (southeast elevator/southeast stairwell). Directions here:
http://scc.stat.ucla.edu/contact-us/map/
To find Boelter Hall on campus: http://maps.ucla.edu/campus/
Information on how to get to UCLA: http://www.ucla.edu/map/