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1 General Information: README

This is the README file for the distribution of ESS version

5.3.9

ESS is a GNU Emacs and XEmacs mode for interactive statistical programming and data analysis. Languages supported: the S family (S 3/4, S-PLUS 3/4/5/6/7, and R), SAS, XLispStat, Stata and BUGS. Installation help can be found in sections for both Unix and Windows. ESS grew out of the desire for bug fixes and extensions to S-mode and SAS-mode as well as a consistent union of their features in one package.

The current development team is led by Martin Maechler since August 2004. Former project leader A.J. (Tony) Rossini (rossini@blindglobe.net) did the initial port to XEmacs and has been the primary coder. Martin Maechler (maechler@stat.math.ethz.ch) and Kurt Hornik (Kurt.Hornik@R-project.org) have assisted with S-PLUS, S4, R, and XLispStat. Stephen Eglen (stephen@gnu.org) has worked mostly on R support. Richard M. Heiberger (rmh@temple.edu) has assisted with S-PLUS and S4 development for Windows. Richard and Rodney A. Sparapani (rsparapa@mcw.edu) have done much of the work implementing interactive SAS (iESS[SAS]) and batch SAS (ESS[SAS]) support.

We are grateful to the previous developers of S-mode (Doug Bates, Ed Kademan, Frank Ritter, David M. Smith), SAS-mode (Tom Cook) and Stata-mode (Thomas Lumley).

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1.1 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.

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1.2 Starting an ESS process

To start an S session on Unix or on Windows when you use the Cygwin bash shell, simply type M-x S RET.

To start an S session on Windows when you use the MSDOS prompt shell, simply type M-x S+6-msdos RET.

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1.3 New Features

Changes/New Features in 5.3.9:

Changes/New Features in 5.3.8:

Changes/New Features in 5.3.7:

Changes/New Features in 5.3.6:

Changes/New Features in 5.3.5:

Changes/New Features in 5.3.4:

Changes/New Features in 5.3.3:

Changes/New Features in 5.3.2:

Changes/New Features in 5.3.1:

Changes/New Features in 5.3.0:

Changes/New Features in 5.2.12:

Changes/New Features in 5.2.11:

Changes/New Features in 5.2.10:

Changes/New Features in 5.2.9:

Changes/New Features in 5.2.8:

Changes/New Features in 5.2.7:

Changes/New Features in 5.2.6:

Changes/New Features in 5.2.5:

Changes/New Features in 5.2.4:

Changes/New Features in 5.2.3:

Changes/New Features in 5.2.2:

Changes/New Features in 5.2.1:

Changes/New Features in 5.2.0:

Changes/New Features in 5.1.24:

Changes/New Features in 5.1.23:

Changes/New Features in 5.1.22:

Changes/New Features in 5.1.21:

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Changes/New Features in 5.1.14:

Changes/New Features in 5.1.13:

Changes/New Features in 5.1.12:

Changes/New Features in 5.1.11:

Changes/New Features in 5.1.10:

Changes/New Features in 5.1.9:

Changes/New Features in 5.1.8:

Changes/New Features in 5.1.2:

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1.4 Current Features

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1.5 Stability

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

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1.6 Requirements

ESS has been tested with

on the following platforms

with the following versions of emacs

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1.7 Getting the Latest Version

The latest released version of ESS is always available on the web at: ESS web page or StatLib

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. 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.

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1.8 Installation (from tar file)

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1.9 Unix installation

  1. cd to a directory where you keep emacs lisp files, or create a new directory (for example, $HOME/emacs) to hold the distribution. This directory will be referred to below as "the ESS distribution directory".

    Note for XEmacs packages: ESS is no longer available as an XEmacs package. But, you can still install ESS into the XEmacs package system by choosing ESSDIR=PREFIX/lib/xemacs/site-packages. ESS requires that the XEmacs sumo tarball (all XEmacs packages combined) also be installed. For information on installing XEmacs packages, follow this link: Quickstart Package Guide.

  2. Retrieve the latest version from ESS downloads area to ESSDIR.
  3. Extract the files from the disribution. 
              If you are using GNU tar, tar zxf ess-VERSION.tgz.
          Otherwise, gunzip < ess-VERSION.tgz | tar xf -,

    The tar command will create the subdirectory ess-VERSION and install the files there.

  4. Edit the file ESSDIR/ess-VERSION/lisp/ess-site.el as explained in the comments section of that file.
  5. If you are using GNU Emacs add the line 
              (load "ESSDIR/ess-VERSION/lisp/ess-site")

    to $HOME/.emacs. For XEmacs, if you followed the XEmacs package system installation advice, add the line 

              (require 'ess-site)

    to $HOME/.xemacs/init.el. Otherwise, for XEmacs, add the line 

              (load "ESSDIR/ess-VERSION/lisp/ess-site")

    to $HOME/.xemacs/init.el.

  6. That's it! ESS is now ready to use. (The remaining step below is only for a custom installation.) To edit statistical programs, just open files with the requisite extensions (.R for R, .sas for SAS, .bug for BUGS, etc.). To start a statistical process within emacs, such as R, type M-x R.
  7. (OPTIONAL) READ THIS ITEM THOROUGHLY BEFORE STARTING:

    If you want to place the compiled files in other locations edit the LISPDIR, INFODIR and ETCDIR entries in Section 1 of Makeconf in the ESSDIR/ess-VERSION directory (if you are using XEmacs, then uncomment the XEmacs subsection in Section 1).

    You can compile those files by: 

              make all

    When that completes successfully, install the compiled files: 

              make install

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1.10 Microsoft Windows installation

For Microsoft Windows installation, please follow the next steps.

  1. cd to a directory where you keep emacs lisp files, or create a new directory (for example, c:\emacs\) to hold the distribution. This directory will be referred to below as "the ESS distribution directory".

    Note for XEmacs packages: ESS is no longer available as an XEmacs package. But, you can still install ESS into the XEmacs package system by choosing ESSDIR=PREFIX\XEmacs\site-packages. ESS requires that the XEmacs sumo tarball (all XEmacs packages combined) also be installed. For information on installing XEmacs packages, follow this link: Quickstart Package Guide.

  2. Retrieve the latest zip file (ess-VERSION.zip) from ESS downloads area and store it in the ESS distribution directory. Be aware that http browsers on Windows frequently change the "." and "-" characters in filenames to other punctuation. Please change the names back to their original form.
  3. Extract all the files from ess-VERSION.zip into the ESS distribution directory as c:\emacs\ess-VERSION\. (It is possible to unpack the zip archive in Windows Explorer by double clicking on the folder; you should then see a new folder called ess-VERSION. Drag that folder into your ESS distribution directory.)
  4. If you are using GNU Emacs add the line 
              (load "ESSDIR/ess-VERSION/lisp/ess-site")

    to %HOME%/.emacs. For XEmacs, if you followed the XEmacs package system installation advice, add the line 

              (require 'ess-site)

    to %HOME%/.xemacs/init.el. Otherwise, for XEmacs, add the line 

              (load "ESSDIR/ess-VERSION/lisp/ess-site")

    to %HOME%/.xemacs/init.el. Note: Both GNU Emacs and XEmacs require that the HOME environment variable be set on your system, otherwise, your initialization file will not be utilized, and therefore, ESS will not work.

    After saving your initialization file, ESS is now installed. Start a new emacs and you should be ready to use ESS. For example, to edit statistical programs, load the files with the requisite extensions (".sas" for SAS, ".S" or "s" or "q" or "Q" for S-PLUS, ".r" or ".R" for R, and ".lsp" for XLispStat). One further step is needed if you wish to run statistical processes, see below.

  5. To run statistical processes under ESS, Windows users will need to make sure that the directories for the software they will be using is in the PATH environment variable. On Windows 9x, add lines similar to the following to your c:\autoexec.bat file: 
              path=%PATH%;c:\progra~1\insightful\splus70\cmd

    On Windows NT/2000/XP, add the directories to the PATH using the My Computer/Control Panel/System/Advanced/Environment Variables menu. Note that the directory containing the program is added to the PATH, not the program itself. One such line is needed for each software program. Be sure to use the abbreviation progra~1 and not the long version with embedded blanks. Use backslashes "\".

    An alternative, for R users, is that rather than adjusting the PATH variable, you can add the following to your emacs initialization file (and restart emacs): 

              (setq inferior-R-program-name "C:/progra~1/R/R-2.2.1/bin/Rterm.exe")

    This assumes that you have installed R-2.2.1 in the default location. Change the path otherwise to point to other locations.

    Windows users who place S-PLUS anywhere other than the default location will also need to add the following three lines (properly adjusted for their location) to their %HOME%/.emacs or %HOME%/.xemacs/init.el file: 

              (setq-default inferior-S+6-program-name
              "c:/progra~1/Insightful/SPLUS70/cmd/Splus")
          (setq-default inferior-Sqpe+6-SHOME-name
              "c:/progra~1/Insightful/SPLUS70")
          (setq-default inferior-Sqpe+6-program-name
              "c:/progra~1/Insightful/SPLUS70/cmd/Sqpe.exe")

    The above example uses the default location of S-PLUS in c:/progra~1/Insightful. Please note that ESS considers S-PLUS 6, 7, and 8 to be variants of S+6.

    These users may also need to modify the emacs variable ess-SHOME-versions to match their installation in order to get the full set of S-PLUS versions on their machine into the ESS menu.

    To start the S-PLUS [678].x GUI from ESS under emacs:

    1. If you use Cygwin bash as your primary shell, then 
                     M-x S
               (or M-x S+6).
    2. If you use the MSDOS prompt window as your primary shell, then 
                     M-x S+6-msdos
    You will then be asked for a pathname ("S starting data directory?"), from which to start the process. The prompt will propose your current directory as the default. ESS will start the S-PLUS GUI. There will be slight delay during which emacs is temporarily frozen. ESS will arrange for communication with the S-PLUS GUI using the DDE protocol. Send lines or regions from the emacs buffer containing your S program (for example, myfile.s) to the S-PLUS Commands Window with the C-c C-n or C-c C-r keys. (If you are still using S-PLUS 4.x or 2000,\ then use M-x S+4 or M-x S+4-msdos.)

    To start an S-PLUS [678].x session inside an emacs buffer—and without the S-PLUS GUI: 

              M-x Sqpe
          (or M-x Sqpe+6).

    This works with both the bash and msdos shells. You will then be asked for a pathname ("S starting data directory?"), from which to start the process. The prompt will propose your current directory as the default. You get Unix-like behavior, in particular the entire transcript is available for emacs-style search commands. Send lines or regions from the emacs buffer containing your S program (for example, myfile.s) to the *S+6* buffer with the C-c C-n or C-c C-r keys. Interactive graphics are available with Sqpe by using the java library supplied with S-PLUS 6.1 and newer releases. Enter the commands: 

              library(winjava)
          java.graph()

    Graphs can be saved from the java.graph device in several formats, but not PostScript. If you need a PostScript file you will need to open a separate postscript device. (If you are still using S-PLUS 4.x or 2000, then use M-x Sqpe+4.)

    To connect to an already running S-PLUS GUI (started, for example, from the S-PLUS icon): 

              M-x S+6-existing

    or 

              M-x S+6-msdos-existing

    You will then be asked for a pathname ("S starting data directory?"), from which to start the process. The prompt will propose your current directory as the default. ESS will arrange for communication with the already running S-PLUS GUI using the DDE protocol. Send lines or regions from the emacs buffer containing your S program (for example, myfile.s) to the S-PLUS Commands Window with the C-c C-n or C-c C-r keys. (If you are still using S-PLUS 4.x or 2000, then use M-x S+4-existing or M-x S+4-msdos-existing.)

    If you wish to run R, you can start it with: 

              M-x R

    XLispStat can not currently be run with 

              M-x XLS

    Hopefully, this will change. However, you can still edit with emacs, and cut and paste the results into the XLispStat *Listener* Window under Microsoft Windows.

  6. That's it!

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1.11 Reporting Bugs

Please send bug reports, suggestions etc. to ESS-bugs@stat.math.ethz.ch

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.

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1.12 Mailing Lists

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 ess-help-request@stat.math.ethz.ch; contributions to the list may be mailed to ess-help@stat.math.ethz.ch. Rest assured, this is a fairly low-volume mailing list.

The purposes of the mailing list include

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1.13 Authors

Footnotes

[1] require the files.el patch to revert-buffer for the Local Variables updating problem