ESS 5.7 released
Posted on 07/12 22:19
Dear ESS lovers,
The good news is that ESS 5.7 does provide a "new feature" for
Windows users, see below.
the bad news is that release 5.6 from last Friday unfortunately
contained a small blunder (C-c C-l "Load Source File" would no
longer work), and 5.7 corrects this.
*Additionally* ESS 5.7 makes C-c C-l working even before R is
started, also on Windows. Also there, it starts an R process
when needed.
This should fix the problem reported by Ross Boylan on '30 Nov 2009',
and subject "No ESS process is associated with this buffer now"
For the ESS core team,
Martin Maechler, ETH Zurich
Here's the (first part of the) ANNOUNCE file:
1 ANNOUNCING ESS
****************
The ESS Developers proudly announce the release of ESS
5.7
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
=============
All released versions (5.x, x >= 4) 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 5.7:
* ESS[R]: loading a source file (`C-c C-l') now works in
Windows, similarly to other platforms; (further; it had
accidentally been broken in ESS 5.6 on all platforms)
Changes/New Features in 5.6:
* ESS[R]: help() calls have to differ from old default, with
newer versions of R; currently via .help.ESS <-
function(...) hack.
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.
The good news is that ESS 5.7 does provide a "new feature" for
Windows users, see below.
the bad news is that release 5.6 from last Friday unfortunately
contained a small blunder (C-c C-l "Load Source File" would no
longer work), and 5.7 corrects this.
*Additionally* ESS 5.7 makes C-c C-l working even before R is
started, also on Windows. Also there, it starts an R process
when needed.
This should fix the problem reported by Ross Boylan on '30 Nov 2009',
and subject "No ESS process is associated with this buffer now"
For the ESS core team,
Martin Maechler, ETH Zurich
Here's the (first part of the) ANNOUNCE file:
1 ANNOUNCING ESS
****************
The ESS Developers proudly announce the release of ESS
5.7
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
=============
All released versions (5.x, x >= 4) 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
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 5.7:
* ESS[R]: loading a source file (`C-c C-l') now works in
Windows, similarly to other platforms; (further; it had
accidentally been broken in ESS 5.6 on all platforms)
Changes/New Features in 5.6:
* ESS[R]: help() calls have to differ from old default, with
newer versions of R; currently via .help.ESS <-
function(...) hack.
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.
ESS 5.6 released
Posted on 07/12 00:49
Dear ESS lovers,
we've decided to release ESS 5.6 as it contains
a small change to make it work seemlessly with 'R-devel' (the R
2.11.0 unstable development version).
Apart from that it contains some cleanup (fixes); also related
to using SAS.
Here's the (first part of the) ANNOUNCE file:
1 ANNOUNCING ESS
****************
The ESS Developers proudly announce the release of ESS
5.6
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)
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
=============
All released versions (5.x, x >= 4) 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 5.6:
* ESS[R]: help() calls have to differ from old default, with
newer versions of R; currently via .help.ESS <-
function(...) hack.
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.
we've decided to release ESS 5.6 as it contains
a small change to make it work seemlessly with 'R-devel' (the R
2.11.0 unstable development version).
Apart from that it contains some cleanup (fixes); also related
to using SAS.
Here's the (first part of the) ANNOUNCE file:
1 ANNOUNCING ESS
****************
The ESS Developers proudly announce the release of ESS
5.6
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)
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
=============
All released versions (5.x, x >= 4) 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
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 5.6:
* ESS[R]: help() calls have to differ from old default, with
newer versions of R; currently via .help.ESS <-
function(...) hack.
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.
Bioconductor 2.5 is released
Posted on 29/10 11:54
Bioconductors:
We are pleased to announce the release of Bioconductor 2.5. This release includes 34 new software packages, and many changes to existing packages. Bioconductor 2.5 is comprised of 352 software packages and is compatible with the recently released R 2.10.0.
Please visit http://bioconductor.org for details and downloads.
Contents
========
o Getting Started with Bioconductor 2.5
o New Software Packages
o Software Packages in 2.4 that didn't make it to 2.5
Getting Started with Bioconductor 2.5
=====================================
To install Bioconductor 2.5
1. Install R 2.10.0. Bioconductor 2.5 has been designed expressly for this version of R.
2. Follow the instructions here:
http://bioconductor.org/docs/install
Please visit http://bioconductor.org for details and downloads.
New Packages
============
The following 34 packages are new in this release of Bioconductor:
1. AgiMicroRna:
Processing and Differential Expression Analysis of Agilent microRNA chips
http://bioconductor.org/packages/2.5/bioc/html/AgiMicroRna.html
2. baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
http://bioconductor.org/packages/2.5/bioc/html/baySeq.html
3. BioSeqClass
Classification for Biological Sequences
http://bioconductor.org/packages/2.5/bioc/html/BioSeqClass.html
4. BUS
Gene network reconstruction
http://bioconductor.org/packages/2.5/bioc/html/BUS.html
5. CGHnormaliter
Normalization of array CGH data with imbalanced aberrations
http://bioconductor.org/packages/2.5/bioc/html/CGHnormaliter.html
6. ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments
http://bioconductor.org/packages/2.5/bioc/html/ChIPpeakAnno.html
7. chipseq
A package for analyzing ChIP-seq data
http://bioconductor.org/packages/2.5/bioc/html/chipseq.html
8. ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
http://bioconductor.org/packages/2.5/bioc/html/ChIPseqR.html
9. ChIPsim
Simulation of ChIP-seq experiments
http://bioconductor.org/packages/2.5/bioc/html/ChIPsim.html
10. ChromHeatMap
Heat map plotting by genome coordinate
http://bioconductor.org/packages/2.5/bioc/html/ChromHeatMap.html
11. clippda
A package for the clinical proteomic profiling data analysis
http://bioconductor.org/packages/2.5/bioc/html/clippda.html
12. CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses
http://bioconductor.org/packages/2.5/bioc/html/CNTools.html
13. CNVtools
A package to test genetic association with CNV data
http://bioconductor.org/packages/2.5/bioc/html/CNVtools.html
14. cycle
Significance of periodic expression pattern in time-series data
http://bioconductor.org/packages/2.5/bioc/html/cycle.html
15. ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
http://bioconductor.org/packages/2.5/bioc/html/ddCt.html
16. DEGseq
Identify Differentially Expressed Genes from RNA-seq data
http://bioconductor.org/packages/2.5/bioc/html/DEGseq.html
17. flowFP
Fingerprinting for Flow Cytometry
http://bioconductor.org/packages/2.5/bioc/html/flowFP.html
18. flowMerge
Cluster Merging for Flow Cytometry Data
http://bioconductor.org/packages/2.5/bioc/html/flowMerge.html
19. GeneAnswers
Integrated Interpretation of Genes
http://bioconductor.org/packages/2.5/bioc/html/GeneAnswers.html
20. GenomicFeatures
Support package for genomic annotations
http://bioconductor.org/packages/2.5/bioc/html/GenomicFeatures.html
21. HTqPCR
Automated analysis of qPCR data
http://bioconductor.org/packages/2.5/bioc/html/HTqPCR.html
22. LiquidAssociation
Calculates direct and model-based estimators for liquid association
http://bioconductor.org/packages/2.5/bioc/html/LiquidAssociation.html
23. mBPCR
Bayesian Piecewise Constant Regression for DNA copy number estimation
http://bioconductor.org/packages/2.5/bioc/html/mBPCR.html
24. methylumi
Handle Illumina methylation data
http://bioconductor.org/packages/2.5/bioc/html/methylumi.html
25. MiChip
MiChip Parsing and Summarizing Functions
http://bioconductor.org/packages/2.5/bioc/html/MiChip.html
26. plateCore
Statistical tools and data structures for plate-based flow cytometry
http://bioconductor.org/packages/2.5/bioc/html/plateCore.html
27. RmiR
Package to work with miRNAs and miRNA targets with R
http://bioconductor.org/packages/2.5/bioc/html/RmiR.html
28. Rolexa
Statistical analysis of Solexa sequencing data
http://bioconductor.org/packages/2.5/bioc/html/Rolexa.html
29. RPA
Probe reliability and differential gene expression analysis
http://bioconductor.org/packages/2.5/bioc/html/RPA.html
30. RTCA
Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche
http://bioconductor.org/packages/2.5/bioc/html/RTCA.html
31. RTools4TB
Data mining of public microarray data through connections to the TranscriptomeBrowser database
http://bioconductor.org/packages/2.5/bioc/html/RTools4TB.html
32. SJava
The Omegahat interface for R and Java
http://bioconductor.org/packages/2.5/bioc/html/SJava.html
33. SpeCond
Condition specific detection from expression data
http://bioconductor.org/packages/2.5/bioc/html/SpeCond.html
34. Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
http://bioconductor.org/packages/2.5/bioc/html/Starr.html
For a complete listing of all the packages in 2.5, visit
http://bioconductor.org/packages/release/Software.html
Software Packages in 2.4 that didn't make it to 2.5
===================================================
Two packages from BioC 2.4 aren't included in BioC 2.5:
1. Rintact - reached its end of life
2. stam - is anticipated to return in BioC 2.6
Thanks to all who contributed to this release and made it a reality!
The Biocore Team
We are pleased to announce the release of Bioconductor 2.5. This release includes 34 new software packages, and many changes to existing packages. Bioconductor 2.5 is comprised of 352 software packages and is compatible with the recently released R 2.10.0.
Please visit http://bioconductor.org for details and downloads.
Contents
========
o Getting Started with Bioconductor 2.5
o New Software Packages
o Software Packages in 2.4 that didn't make it to 2.5
Getting Started with Bioconductor 2.5
=====================================
To install Bioconductor 2.5
1. Install R 2.10.0. Bioconductor 2.5 has been designed expressly for this version of R.
2. Follow the instructions here:
http://bioconductor.org/docs/install
Please visit http://bioconductor.org for details and downloads.
New Packages
============
The following 34 packages are new in this release of Bioconductor:
1. AgiMicroRna:
Processing and Differential Expression Analysis of Agilent microRNA chips
http://bioconductor.org/packages/2.5/bioc/html/AgiMicroRna.html
2. baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
http://bioconductor.org/packages/2.5/bioc/html/baySeq.html
3. BioSeqClass
Classification for Biological Sequences
http://bioconductor.org/packages/2.5/bioc/html/BioSeqClass.html
4. BUS
Gene network reconstruction
http://bioconductor.org/packages/2.5/bioc/html/BUS.html
5. CGHnormaliter
Normalization of array CGH data with imbalanced aberrations
http://bioconductor.org/packages/2.5/bioc/html/CGHnormaliter.html
6. ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments
http://bioconductor.org/packages/2.5/bioc/html/ChIPpeakAnno.html
7. chipseq
A package for analyzing ChIP-seq data
http://bioconductor.org/packages/2.5/bioc/html/chipseq.html
8. ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
http://bioconductor.org/packages/2.5/bioc/html/ChIPseqR.html
9. ChIPsim
Simulation of ChIP-seq experiments
http://bioconductor.org/packages/2.5/bioc/html/ChIPsim.html
10. ChromHeatMap
Heat map plotting by genome coordinate
http://bioconductor.org/packages/2.5/bioc/html/ChromHeatMap.html
11. clippda
A package for the clinical proteomic profiling data analysis
http://bioconductor.org/packages/2.5/bioc/html/clippda.html
12. CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses
http://bioconductor.org/packages/2.5/bioc/html/CNTools.html
13. CNVtools
A package to test genetic association with CNV data
http://bioconductor.org/packages/2.5/bioc/html/CNVtools.html
14. cycle
Significance of periodic expression pattern in time-series data
http://bioconductor.org/packages/2.5/bioc/html/cycle.html
15. ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
http://bioconductor.org/packages/2.5/bioc/html/ddCt.html
16. DEGseq
Identify Differentially Expressed Genes from RNA-seq data
http://bioconductor.org/packages/2.5/bioc/html/DEGseq.html
17. flowFP
Fingerprinting for Flow Cytometry
http://bioconductor.org/packages/2.5/bioc/html/flowFP.html
18. flowMerge
Cluster Merging for Flow Cytometry Data
http://bioconductor.org/packages/2.5/bioc/html/flowMerge.html
19. GeneAnswers
Integrated Interpretation of Genes
http://bioconductor.org/packages/2.5/bioc/html/GeneAnswers.html
20. GenomicFeatures
Support package for genomic annotations
http://bioconductor.org/packages/2.5/bioc/html/GenomicFeatures.html
21. HTqPCR
Automated analysis of qPCR data
http://bioconductor.org/packages/2.5/bioc/html/HTqPCR.html
22. LiquidAssociation
Calculates direct and model-based estimators for liquid association
http://bioconductor.org/packages/2.5/bioc/html/LiquidAssociation.html
23. mBPCR
Bayesian Piecewise Constant Regression for DNA copy number estimation
http://bioconductor.org/packages/2.5/bioc/html/mBPCR.html
24. methylumi
Handle Illumina methylation data
http://bioconductor.org/packages/2.5/bioc/html/methylumi.html
25. MiChip
MiChip Parsing and Summarizing Functions
http://bioconductor.org/packages/2.5/bioc/html/MiChip.html
26. plateCore
Statistical tools and data structures for plate-based flow cytometry
http://bioconductor.org/packages/2.5/bioc/html/plateCore.html
27. RmiR
Package to work with miRNAs and miRNA targets with R
http://bioconductor.org/packages/2.5/bioc/html/RmiR.html
28. Rolexa
Statistical analysis of Solexa sequencing data
http://bioconductor.org/packages/2.5/bioc/html/Rolexa.html
29. RPA
Probe reliability and differential gene expression analysis
http://bioconductor.org/packages/2.5/bioc/html/RPA.html
30. RTCA
Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche
http://bioconductor.org/packages/2.5/bioc/html/RTCA.html
31. RTools4TB
Data mining of public microarray data through connections to the TranscriptomeBrowser database
http://bioconductor.org/packages/2.5/bioc/html/RTools4TB.html
32. SJava
The Omegahat interface for R and Java
http://bioconductor.org/packages/2.5/bioc/html/SJava.html
33. SpeCond
Condition specific detection from expression data
http://bioconductor.org/packages/2.5/bioc/html/SpeCond.html
34. Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
http://bioconductor.org/packages/2.5/bioc/html/Starr.html
For a complete listing of all the packages in 2.5, visit
http://bioconductor.org/packages/release/Software.html
Software Packages in 2.4 that didn't make it to 2.5
===================================================
Two packages from BioC 2.4 aren't included in BioC 2.5:
1. Rintact - reached its end of life
2. stam - is anticipated to return in BioC 2.6
Thanks to all who contributed to this release and made it a reality!
The Biocore Team
R 2.10.0 is released
Posted on 27/10 01:15
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 François.
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' 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 Hervé Pagès.
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.
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 François.
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
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 Hervé Pagès.
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.
useR! 2010: submission & registration started!
Posted on 19/10 21:43
We are happy to inform you that abstract submission and registration for `useR! 2010' is now available online from
http://www.R-project.org/useR-2010/
This meeting of the R user community will take place at the Gaithersburg, Maryland, USA campus of the National Institute of Standards and Technology (NIST), July 21-23, 2010.
The conference schedule is comprised of invited lectures and user-contributed sessions as well as half-day tutorials presented by R experts on July 20, 2010, prior to the conference.
Invited speakers will include
Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer,
Richard Stallman, Luke Tierney, Diethelm Wuertz.
We invite you to submit abstracts on topics presenting innovations or exciting applications of R. The call for papers along with the link for abstract submission is available at
http://www.R-project.org/useR-2010/#Call
******************************************************************************
Reminder: tutorial proposals are due by November 1, 2009, as specified in the call for tutorials available at
http://www.R-project.org/useR-2010/tutorials/
******************************************************************************
http://www.R-project.org/useR-2010/
This meeting of the R user community will take place at the Gaithersburg, Maryland, USA campus of the National Institute of Standards and Technology (NIST), July 21-23, 2010.
The conference schedule is comprised of invited lectures and user-contributed sessions as well as half-day tutorials presented by R experts on July 20, 2010, prior to the conference.
Invited speakers will include
Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer,
Richard Stallman, Luke Tierney, Diethelm Wuertz.
We invite you to submit abstracts on topics presenting innovations or exciting applications of R. The call for papers along with the link for abstract submission is available at
http://www.R-project.org/useR-2010/#Call
******************************************************************************
Reminder: tutorial proposals are due by November 1, 2009, as specified in the call for tutorials available at
http://www.R-project.org/useR-2010/tutorials/
******************************************************************************
国際シンポジウム「育種の新パラダイム 高効率育種のためのゲノム情報・遺伝 資源の戦略的活用」
Posted on 14/10 12:09
国際シンポジウム「育種の新パラダイム 高効率育種のためのゲノム情報・遺伝
資源の戦略的活用」のお知らせ
来る12月2、3日、エポカルつくば国際会議場にて、下記の農研機構国際シンポジ
ウムを開催いたします。「育種の新パラダイム高効率育種のためのゲノム情報・
遺伝資源の戦略的活用」というタイトルのもとに、生物測定学者、育種家、ゲノ
ム研究者、作物学者など多様な研究者をお招きし、DNA多型、表現型、環境デー
タ等大量な情報を戦略的に活用した高効率育種の実現に向けて議論をいたしま
す。なお、参加費は無料で、同時通訳サービスも提供されます。育種関係者をは
じめ、多分野からの多くの方々のご参加を、心よりお待ちしております。
なお、会場の関係で「定員」があります。参加ご希望の方は、お早めに以下の情
報をipbs@ml.affrc.go.jpまでお送りください。
（締め切り11月15日、ただし定員に達し次第締め切ります）
----------------------------------------------------------------
メールの見出し（Subject）：農研機構シンポ参加申し込み
名前：
所属：
メールアドレス：
電話番号：
懇親会：参加・不参加（一方をお消しください）
----------------------------------------------------------------
※懇親会の場所は未定ですが予算5,000円程度を考えています．
----------------------------------------------
シンポジウムHP: http://narc.naro.affrc.go.jp/event/h21/ipbs/index.htm
農研機構国際シンポジウム
「育種の新パラダイム 高効率育種のためのゲノム情報・遺伝資源の戦略的活用」
現在、主要作物における育種による収量増は年1%程度と言われていますが、今後
の世界的な人口増を考えると、より速いペースでの遺伝的改良が必要です。その
ためには、従来のパラダイムにとらわれない新発想の育種法を思考し、その実用
化に向けて研究を進めることが重要です。近年、緻密で詳細なデータ解析に基づ
く遺伝資源の活用、ゲノムワイドマーカーを選抜育種に利用する全ゲノム選抜、
ロボティックスやインターネット技術を活用した効率的な育種など、新しい視点
からの育種研究が世界中で進められています。本シンポジウムでは、このような
研究の現状を、育種家、育種学研究者に紹介するとともに、今後の高効率育種の
ための戦略について議論します。
●講演タイトル（予定）：
「インフォマティクスによる遺伝資源の活用と育種への展開」
「植物育種における全ゲノム選抜」
「イネゲノムとその育種への応用」
「小麦育種の現場から見た全ゲノム選抜とその展望」
「作物の環境応答とその遺伝解析」
「ゲノム情報を現場育種に活かす技術」 他
●講演予定者：
Jose Crossa (CIMMYT), Jean-Luc Jannink (USDA-ARS), 矢野昌裕（生物研）,
Mark Sorrells (Cornell University), 長谷川利拡（農環研）, 岩田洋佳 (中央
農研) 他
なお、本シンポジウムでは同時通訳サービスが提供されます
●場所：エポカルつくば国際会議場中ホール （http://www.epochal.or.jp/）
●日時：平成21年12月2日13時〜12月3日12時30分
●主催：農業・食品産業技術総合研究機構 (中央農研・作物研)
●共催：農業生物資源研究所，筑波大学，日本育種学会
資源の戦略的活用」のお知らせ
来る12月2、3日、エポカルつくば国際会議場にて、下記の農研機構国際シンポジ
ウムを開催いたします。「育種の新パラダイム高効率育種のためのゲノム情報・
遺伝資源の戦略的活用」というタイトルのもとに、生物測定学者、育種家、ゲノ
ム研究者、作物学者など多様な研究者をお招きし、DNA多型、表現型、環境デー
タ等大量な情報を戦略的に活用した高効率育種の実現に向けて議論をいたしま
す。なお、参加費は無料で、同時通訳サービスも提供されます。育種関係者をは
じめ、多分野からの多くの方々のご参加を、心よりお待ちしております。
なお、会場の関係で「定員」があります。参加ご希望の方は、お早めに以下の情
報をipbs@ml.affrc.go.jpまでお送りください。
（締め切り11月15日、ただし定員に達し次第締め切ります）
----------------------------------------------------------------
メールの見出し（Subject）：農研機構シンポ参加申し込み
名前：
所属：
メールアドレス：
電話番号：
懇親会：参加・不参加（一方をお消しください）
----------------------------------------------------------------
※懇親会の場所は未定ですが予算5,000円程度を考えています．
----------------------------------------------
シンポジウムHP: http://narc.naro.affrc.go.jp/event/h21/ipbs/index.htm
農研機構国際シンポジウム
「育種の新パラダイム 高効率育種のためのゲノム情報・遺伝資源の戦略的活用」
現在、主要作物における育種による収量増は年1%程度と言われていますが、今後
の世界的な人口増を考えると、より速いペースでの遺伝的改良が必要です。その
ためには、従来のパラダイムにとらわれない新発想の育種法を思考し、その実用
化に向けて研究を進めることが重要です。近年、緻密で詳細なデータ解析に基づ
く遺伝資源の活用、ゲノムワイドマーカーを選抜育種に利用する全ゲノム選抜、
ロボティックスやインターネット技術を活用した効率的な育種など、新しい視点
からの育種研究が世界中で進められています。本シンポジウムでは、このような
研究の現状を、育種家、育種学研究者に紹介するとともに、今後の高効率育種の
ための戦略について議論します。
●講演タイトル（予定）：
「インフォマティクスによる遺伝資源の活用と育種への展開」
「植物育種における全ゲノム選抜」
「イネゲノムとその育種への応用」
「小麦育種の現場から見た全ゲノム選抜とその展望」
「作物の環境応答とその遺伝解析」
「ゲノム情報を現場育種に活かす技術」 他
●講演予定者：
Jose Crossa (CIMMYT), Jean-Luc Jannink (USDA-ARS), 矢野昌裕（生物研）,
Mark Sorrells (Cornell University), 長谷川利拡（農環研）, 岩田洋佳 (中央
農研) 他
なお、本シンポジウムでは同時通訳サービスが提供されます
●場所：エポカルつくば国際会議場中ホール （http://www.epochal.or.jp/）
●日時：平成21年12月2日13時〜12月3日12時30分
●主催：農業・食品産業技術総合研究機構 (中央農研・作物研)
●共催：農業生物資源研究所，筑波大学，日本育種学会
Free Introductory R Course Taught Over the Web
Posted on 14/10 12:00
Free Introductory R Course Taught Over the Web
The course is designed for natural resource managers and is open to all
who are interested without charge. Audio of the presentations is available
either using your computer speakers and optional microphone or headset or
by calling a phone bridge long distance. Live video of the presenter's
computer screen is available over the web. You can also share your
computer's screen with other participants when asking a question or making
a point. An audio and video recording of the presentations and discussion
will be available on our FTP site after the presentations. There are no
specific prerequisites but some knowledge of statistics would be helpful.
A basic knowledge of computers and the internet will be assumed.
Please forward this notice to those who may be interested.
The course will start Monday, November 9. There will be presentations on
Mondays and Wednesdays, and a lab on Tuesdays for two hours. The times
will be: Hawaii 9:00-11:00, Alaska 10:00-12:00, Pacific 11:00-1:00,
Mountain 12:00-2:00, Central 1:00-3:00, Eastern 2:00-4:00, UTC 7:00-9:00.
The course will continue until we finish the outline: 2-3 weeks if you
only continue through the GUI interface (menu) portion, perhaps 6-8 weeks
including more advanced statistical analyses.
Links:
You can register at
http://www.fort.usgs.gov/brdscience/courseRegister.aspx
The course website: http://www.fort.usgs.gov/brdscience/learnR.htm
Last year's course website:
http://www.fort.usgs.gov/brdscience/learnR08.htm
The course is designed for natural resource managers and is open to all
who are interested without charge. Audio of the presentations is available
either using your computer speakers and optional microphone or headset or
by calling a phone bridge long distance. Live video of the presenter's
computer screen is available over the web. You can also share your
computer's screen with other participants when asking a question or making
a point. An audio and video recording of the presentations and discussion
will be available on our FTP site after the presentations. There are no
specific prerequisites but some knowledge of statistics would be helpful.
A basic knowledge of computers and the internet will be assumed.
Please forward this notice to those who may be interested.
The course will start Monday, November 9. There will be presentations on
Mondays and Wednesdays, and a lab on Tuesdays for two hours. The times
will be: Hawaii 9:00-11:00, Alaska 10:00-12:00, Pacific 11:00-1:00,
Mountain 12:00-2:00, Central 1:00-3:00, Eastern 2:00-4:00, UTC 7:00-9:00.
The course will continue until we finish the outline: 2-3 weeks if you
only continue through the GUI interface (menu) portion, perhaps 6-8 weeks
including more advanced statistical analyses.
Links:
You can register at
http://www.fort.usgs.gov/brdscience/courseRegister.aspx
The course website: http://www.fort.usgs.gov/brdscience/learnR.htm
Last year's course website:
http://www.fort.usgs.gov/brdscience/learnR08.htm
R 2.10.0 is scheduled for October 26
Posted on 27/09 17:19
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.
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.
R 2.9.1 is released
Posted on 30/06 21:00
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
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>,
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
Posted on 09/06 13:57
------------------------------------------------------------------------
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。
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。
Since 2008-07-28
