[Sciviews-commits] r229 - in komodo/SciViews-K: . content/js defaults templates
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 17 12:18:17 CET 2009
Author: phgrosjean
Date: 2009-11-17 12:18:16 +0100 (Tue, 17 Nov 2009)
New Revision: 229
Added:
komodo/SciViews-K/defaults/
komodo/SciViews-K/defaults/.DS_Store
komodo/SciViews-K/defaults/.Rprofile
komodo/SciViews-K/defaults/ANNOUNCE
komodo/SciViews-K/defaults/NEWS
komodo/SciViews-K/defaults/R reference.kpz
komodo/SciViews-K/defaults/R.bat
komodo/SciViews-K/defaults/README
komodo/SciViews-K/defaults/Rgui.bat
komodo/SciViews-K/defaults/SciViews-K.kpz
komodo/SciViews-K/defaults/print.help_files_with_topic.R
komodo/SciViews-K/defaults/svGUI_0.9-46.tar.gz
komodo/SciViews-K/defaults/svGUI_0.9-46.zip
komodo/SciViews-K/defaults/svMisc_0.9-56.tar.gz
komodo/SciViews-K/defaults/svMisc_0.9-56.zip
komodo/SciViews-K/defaults/svSocket_0.9-48.tar.gz
komodo/SciViews-K/defaults/svSocket_0.9-48.zip
komodo/SciViews-K/defaults/svStart.R
komodo/SciViews-K/sciviewsk-0.9.8-ko.xpi
Removed:
komodo/SciViews-K/R/
komodo/SciViews-K/koextlib_R.py
komodo/SciViews-K/koextlib_include_R_dir.patch
komodo/SciViews-K/templates/ANNOUNCE
komodo/SciViews-K/templates/NEWS
komodo/SciViews-K/templates/R reference.kpz
komodo/SciViews-K/templates/R.bat
komodo/SciViews-K/templates/README
komodo/SciViews-K/templates/Rgui.bat
komodo/SciViews-K/templates/SciViews-K.kpz
komodo/SciViews-K/templates/print.help_files_with_topic.R
komodo/SciViews-K/templates/svGUI_0.9-46.tar.gz
komodo/SciViews-K/templates/svGUI_0.9-46.tgz
komodo/SciViews-K/templates/svGUI_0.9-46.zip
komodo/SciViews-K/templates/svIDE_0.9-47.tar.gz
komodo/SciViews-K/templates/svIDE_0.9-47.tgz
komodo/SciViews-K/templates/svIDE_0.9-47.zip
komodo/SciViews-K/templates/svMisc_0.9-56.tar.gz
komodo/SciViews-K/templates/svMisc_0.9-56.tgz
komodo/SciViews-K/templates/svMisc_0.9-56.zip
komodo/SciViews-K/templates/svSocket_0.9-48.tar.gz
komodo/SciViews-K/templates/svSocket_0.9-48.tgz
komodo/SciViews-K/templates/svSocket_0.9-48.zip
komodo/SciViews-K/templates/svStart.R
Modified:
komodo/SciViews-K/content/js/commands.js
komodo/SciViews-K/content/js/r.js
komodo/SciViews-K/templates/.DS_Store
Log:
All R starting files moved to /defaults subdirectory instead of /R (do not want to have to patch Komodo), plus some reworking of svStart()
Modified: komodo/SciViews-K/content/js/commands.js
===================================================================
--- komodo/SciViews-K/content/js/commands.js 2009-11-13 21:47:01 UTC (rev 228)
+++ komodo/SciViews-K/content/js/commands.js 2009-11-17 11:18:16 UTC (rev 229)
@@ -90,26 +90,11 @@
"Rinitdir=" + sv.prefs.getString("sciviews.session.dir", "~"),
"koServe=" + sv.prefs.getString("sciviews.client.socket", "8888"),
"koPort=" + sv.prefs.getString("sciviews.server.socket", "7052"),
+ "koDebug=" + String(sv.socket.debug).toUpperCase(),
"koAppFile=" + sv.tools.file.path("binDir", "komodo" + (isWin? ".exe" : ""))
- ];
-
- // Apply patch (koext_include_R_dir.patch) to <komodoInstallDir>/lib/sdk/pylib/koextlib.py,
- // to make it include R directory in the .xpi
- // otherwise the directory can be added manually.
-
- //Until we decide to keep R files in "R" or "templates"
- if (sv.tools.file.exists(sv.tools.file.path(
- "ProfD/extensions/sciviewsk at sciviews.org/R/.Rprofile"))) {
- var cwd = sv.tools.file.path("ProfD", "extensions",
- "sciviewsk at sciviews.org", "R");
- } else {
- var cwd = sv.tools.file.path("ProfD", "extensions",
- "sciviewsk at sciviews.org", "templates");
- }
-
- // with:
- //var cwd = sv.tools.file.path("ProfD", "extensions", "sciviewsk at sciviews.org", "R");
-
+ ];
+ var cwd = sv.tools.file.path("ProfD", "extensions",
+ "sciviewsk at sciviews.org", "defaults");
var command, runIn = "no-console";
sv.cmdout.message(sv.translate("Starting R... please wait"), 10000, true);
Modified: komodo/SciViews-K/content/js/r.js
===================================================================
--- komodo/SciViews-K/content/js/r.js 2009-11-13 21:47:01 UTC (rev 228)
+++ komodo/SciViews-K/content/js/r.js 2009-11-17 11:18:16 UTC (rev 229)
@@ -1228,10 +1228,10 @@
// if R is running
if (saveOld) {
// Save .RData & .Rhistory in the the session directory and clean WS
- // We need also to restore .required and .SciViewsReady variables
+ // We need also to restore .required variable
cmd = 'assignTemp(".required", .required)\nTempEnv()$.Last.sys()\n' +
'save.image()\nsavehistory()\nrm(list = ls())\n' +
- '.required <- getTemp(".required")\n.SciViewsReady <- TRUE\n';
+ '.required <- getTemp(".required")\n';
} else {
// Clear workspace (hint, we don't clear hidden objects!)
Added: komodo/SciViews-K/defaults/.DS_Store
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/.DS_Store
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: komodo/SciViews-K/defaults/.Rprofile
===================================================================
--- komodo/SciViews-K/defaults/.Rprofile (rev 0)
+++ komodo/SciViews-K/defaults/.Rprofile 2009-11-17 11:18:16 UTC (rev 229)
@@ -0,0 +1,6 @@
+# Avoid running this function recursively (R restarts sometimes in Linux)
+if (!exists("svStart", envir = .GlobalEnv, mode = "function")) {
+ source("svStart.R")
+ svStart()
+ rm(svStart)
+}
\ No newline at end of file
Added: komodo/SciViews-K/defaults/ANNOUNCE
===================================================================
--- komodo/SciViews-K/defaults/ANNOUNCE (rev 0)
+++ komodo/SciViews-K/defaults/ANNOUNCE 2009-11-17 11:18:16 UTC (rev 229)
@@ -0,0 +1,93 @@
+
+Windows Batchfiles 0.5-0
+
+This is a set of Windows batch and javascript
+utilities for use with R.
+
+They run R and perform associated tasks involving
+R by finding R in the registry and then calling
+the appropraite utility so that no paths need be
+set -- an otherwise significant source of
+potential error when using R. Also the R
+installer inserts a key into the registry each
+each time R is upgraded and these utilities detect
+that and run accordingly simplifying upgrades
+by eliminating the need to reset paths.
+
+The following utilities are provided. They are
+each mutually independent so any can be used
+without the others. Installation consists only of
+copying whichever file or files is desired to any
+folder in the Windows PATH.
+
+Legend:
+h = no args gives help
+0 = common usage is to enter command name without arguments
+
+#Rscript.bat - put at top of R file to make it a batch file (h)
+copydir.bat - copy a library from one version of R to another (h)
+el.js - run elevated - Vista and up, e.g. el Rgui runs R elevated
+find-miktex.hta - GUI to find MiKTeX (0)
+jgr.bat - like jgr.exe but finds R from registry as well as JGR library (0)
+kopy.bat - copy Rcmd to other batch files (h)
+movedir.bat - move library from one version of R to another (h)
+R.bat - like R.exe but finds R from registry (0)
+Rcmd.bat - like Rcmd.exe but finds R from registry (h)
+RExcelVersion.hta - like Rversions.hta but also sets .RData association (0)
+Rgui.bat - like Rgui.exe but finds R from registry (0)
+RguiStart.bat - like Rgui.bat but arg1 defines folder to start R in
+Rscript.bat - run .R script (h)
+Rterm.bat - like rterm.exe but finds R from registry (h)
+Rtidy.bat - reformat a .R file, e.g. Rtidy myfile.R > outfile.R
+Rtools.bat - place Rtools on path for remainder of console session (0)
+Rversions.bat - list which versions of R are in registry (0)
+Rversions.hta - GUI interface to RSetReg. List and set R version (0)
+show-svn-info.hta - show svn info if current folder is an svn checkout (0)
+Stangle.bat - run arg1 through Stangle (h)
+Sweave.bat - run arg1 through Sweave (h)
+
+Note that #Rscript.bat, R.bat, Rcmd.bat, Rgui.bat,
+RguiStart.bat, Rscript.bat, Rterm.bat, Rtools.bat
+and jgr.bat are all the same file but with
+different names. The program checks what name it
+was called by and acts accordingly. Similarly
+Sweave.bat and Stangle.bat are the same file with
+different names.
+
+The main new features in version 0.5-0 are:
+
+ o testing on XP32, XPx64, Vista32, Win7x64.
+ Thanks to Nicholas Hirschey.
+
+ o added defensive code to batch files to work
+ even in the presence of certain bad components
+ in pre-existing PATH variables.
+
+ o new command show-svn-info.hta which when run
+ from a Tortoise SVN checkout folder shows some
+ info about it. Requires Tortoise SVN version
+ 1.5 or higher.
+
+ o new command find-miktex.hta can be run without
+ arguments from the Windows command line (or
+ double clicked from Windows Explorer). It
+ will show the path to the MiKTeX bin folder.
+
+ o Rversions.hta now also changes the .RData
+ association and has been verified to work on
+ both XP and Vista.
+
+ o new RExcelversion.hta (also distributed with
+ RExcel) that is like Rversions.hta but also sets
+ the version for Rexcel at the same time. Thanks
+ to Erich Neumann.
+
+ o jgr.bat now passes the Windows library
+ directory name and R home directory name to
+ jgr.exe automatically
+
+More info and pointers to download site on CRAN
+can be found on the home page:
+
+ http://batchfiles.googlecode.com
+
Property changes on: komodo/SciViews-K/defaults/ANNOUNCE
___________________________________________________________________
Name: svn:executable
+ *
Added: komodo/SciViews-K/defaults/NEWS
===================================================================
--- komodo/SciViews-K/defaults/NEWS (rev 0)
+++ komodo/SciViews-K/defaults/NEWS 2009-11-17 11:18:16 UTC (rev 229)
@@ -0,0 +1,254 @@
+Changes in version 0.5-0
+
+ o new command show-svn-info.hta when run from a Tortoise SVN checkout
+ folder shows some info about it. Requires Tortoise SVN version 1.5
+ or higher.
+
+ o new command find-miktex.hta can be run without arguments from the
+ Windows command line or double clicked it from Windows Explorer
+ and it will show the path to the MiKTeX bin directory.
+
+ o Rversions.hta now also changes the .RData association and has
+ been verified to work on both XP and Vista.
+
+ o new RExcelversion.hta (also distributed with RExcel) that is like
+ Rversions.hta but also sets the version for Rexcel at the same time
+ and has been verified to work on both XP and Vista.
+
+ o jgr.bat now passes the Windows library and R home to jgr.exe automatically
+
+ o added defensive code to allow code to work even in the presence of
+ certain bad PATH variables
+
+ o testing on XP32, XPx64, Vista32, Win7x64 (thanks to Nicholas Hirschey)
+
+Changes in version 0.4-3
+
+ o Sweave.bat and Stangle.bat were not automatically finding MiKTeX.
+ Fixed.
+
+Changes in version 0.4-2
+
+ o can optionally work off initialization files in place of registry.
+ Place rbatchfilesrc.bat in current directory or %userprofile% (so
+ different directories can work off different versions of R, say)
+ or same directory as the other batchfiles and it will run it first.
+ Typically rbatchfiles.bat would constain these two lines or similar:
+ set R_HOME=C:\Program Files\R\R-2.7.0
+ set R_TOOLS=C:\Rtools
+
+ o added Stangle.bat
+
+Changes in version 0.4-1
+
+ o it is no longer necessary to set any paths to build R packages
+ provided Rtools 2.7 or later is used. Rcmd.bat and the other
+ scripts automatically find Rtools from the registry (including perl)
+ and if MikTeX is at %ProgramFiles%\MiKTeX* or %SystemDrive%:\MiKTex
+ then it will find MiKTeX too. New optional environment variables
+ R_TOOLS and R_MIKTEX are available to force specified paths to be used.
+
+ o new Rtools.bat command that sets the path for the current cmd instance
+ to the one that R*.bat files use internally. That is, rtools/bin,
+ rtools/perl/bin, rtools/MinGW/bin and MiKTeX .../miktex/bin are added
+ to the path. This is not needed to run or install R programs but only
+ if you want to access the rtools for other purposes.
+
+ o new el.js command which runs the command given as its argument elevated.
+ e.g. el cmd
+
+Changes in version 0.4-0
+
+ o as of 0.4-0 batchfiles is being developed and tested on Vista.
+ It may still work on XP but if any of the commands do not then use
+ version 0.3-2 instead since that was exclusively tested on XP.
+
+ o added RguiStart.bat which is like Rgui.bat but takes a single argument
+ which is a directory and starts up there
+
+ o the dependency of sweave.bat on Rterm.bat was eliminated so all
+ batch and javascript programs in this collection are now independent
+ of each other and have no dependencies aside form R. (The perl
+ program, toggleDoc.pl, is does depend on perl and toggleDoc.js.)
+
+ o added info on how to use RguiStart.bat and sweave.bat with SendTo
+ folder
+
+ o misc improvements to README file
+
+ o improved help message given by sweave.bat when issued with no arguments
+
+ o removed only tested on XP messages since they work on Vista
+
+ o changed algorithm in Rversions.bat. Now it checks current directory,
+ R_HOME and all keys in R's portion of the registry plus all sibling
+ folders of those mentioned. Also it runs RSetReg.exe elevated
+ on Vista. New version has not been tested on XP; however, older
+ versions are still available and were tested on XP.
+
+ o updated copydir.bat portion of README to discuss additional alternatives
+
+ o removed find-miktex.bat, Rfind.bat and makepkg.bat (they are still
+ available in batchfiles version 0.3-2)
+
+ o added toggleDoc.pl/toggleDoc.js which adds a toggle box to each 00Index.html
+ which when checked collapses similar HTML help lines into one. Contributed
+ by Dieter Menne.
+
+Changes in version 0.3-2
+
+ o sweave.bat now uses Rterm.bat rather than Rcmd.bat which makes it usable
+ with a basic R installation (i.e. sh.exe not needed). Previously it
+ required Rcmd.bat but now it requires Rterm.bat instead.
+
+ o added Rterm.bat (just a copy of Rcmd.bat)
+
+Changes in Version 0.3-1
+
+ o new find-miktex.bat which lists the mixktex folders from the registry
+
+ o new Rscript.bat which allows one to use the Rscript facility in
+ R 2.5.0 and later without changing pathnames. Just place Rscript.bat
+ in any existing path and it will automatically find the
+ current version of R from the registry and run the Rscript.exe that
+ is there.
+
+ o runR.bat. If you have an R script such as myfile.R then you can create
+ a batch script for it by copying runR.bat to myfile.bat. Then when you
+ issue the command myfile or myfile.bat it will run the R script in
+ myfile.R . Just place myfile.bat and myfile.R anywhere in your path.
+ This uses Rscript.bat .
+
+ o #Rscript. If you have an Rscript called myfile.R, say, then if you
+ copy the script to myfile.bat and place
+ #Rscript %0 %*
+ as the first line with the remainder being the R commands then issuing
+ the command myfile or myfile.bat will run the R script. The advantage
+ over the runR.bat method is that there is only one file, myfile.bat.
+ You don't need myfile.R anymore. The disadvantage is that it will
+ echo the #Rscript line to stdout. This will be fixed if and when
+ Rscript ever gets the perl/python/ruby -x flag. (The runR approach will
+ not echo additional lines but does require two files.)
+
+ o new Rtidy.bat is a sample Rscript that uses the #Rscript facility
+ based on George Georgalis' UNIX code
+
+ o withgs.bat now checks for latest ghostscript version. (Previously
+ version was hard coded and it only worked for that version.)
+
+Changes in Version 0.3-0
+
+ o sweave now generates a second .pdf ending which is a copy of the first
+ but has a unique name and displays that. This works around a problem
+ with acrobat that it will not display two files with the same name
+ at the same time.
+
+ o new --tex, --pdf, --nobck.pdf switches are available on sweave. Also
+ expanded help when entering sweave without args.
+
+Changes in Version 0.2-9
+
+ o updated README and other documentation files and inline documentation
+
+ o added sweave.bat
+
+ o new google code home page and svn repository
+ http://code.google.com/p/batchfiles/
+
+Changes in Version 0.2-8
+
+ o bug fix in copydir.bat and movedir.bat
+
+Changes in Version 0.2-7
+
+ o removed extra popup from Rversions.hta
+
+ o Rfind.bat now looks in registry for MiKTeX, replacing
+ previous heuristic. [Thanks for help from Duncan
+ Murdoch]. Also RToolsDir typo fixed in Rfind.bat.
+
+Changes in Version 0.2-6
+
+ o batch files no longer use short names internally since this
+ triggers a bug in Windows batch in the case of the new R
+ folder naming conventions.
+
+ o Rversions.hta - fix for path names with spaces
+
+ o Rrefresh.bat has been removed (after having been deprecated in
+ in previous versions of batchfiles).
+
+ o tested movedir.bat by using it to upgrade R-2.2.0pat to R-2.2.1.
+ See instructions in README.
+
+Changes in Version 0.2-5
+
+ o added movedir.bat which moves libraries from one version of
+ R to another. This is like copydir.bat but is much faster and
+ can be used when the older version of R is no longer needed
+ (unlike copydir.bat which preserves the older version). See
+ README for usage.
+
+Changes in Version 0.2-3
+
+ o added copydir.bat which can copy libraries from one version of
+ R to another. (This is a temporary solution until R provides
+ facilities for upgrading the libraries, expected in R 2.3.0 .)
+ See README for usage.
+
+ o eliminated all code associated with reading and manipulation of
+ R_ENVIRON, R_PROFILE and R_LIBS simplifying the batch files. Use
+ copydir.bat instead.
+
+ o Rversions.hta is a javascript GUI version of Rversions.bat
+
+Changes in Version 0.2-2
+
+ o added jgr.bat which starts up the JGR GUI.
+
+ o added Rversions.bat which can list the directories of all R versions
+ available and can set one to become the current R version.
+
+ o all batch scripts which used the environment variable name Rrw now
+ use the environment variable name R_HOME instead.
+
+ o Rcmd.bat, Rgui.bat, R.bat, jgr.bat files will now read R_ENVIRON,
+ if present, and set the R_LIBS definition in it, if present (unless
+ R_LIBS is already defined as an environment variable). All R_ENVIRON
+ file syntax accepted by R is supported including comments (#),
+ var=value, var=${foo-bar} and recursions, var=${A-${B-C}}.
+
+ o makepkg.bat internals were simplified due to previous point.
+
+ o updated WISHLIST.
+
+ o updated THANKS.
+
+ o updated README. More introductory information. Also instructions
+ for Rgui shortcut will disable screen flash on startup. Corrections.
+
+Changes in Version 0.2-1
+
+ o improvements to README
+
+Changes in Version 0.2-0
+
+ o can now support configurations without *.site files (as well as
+ configurations with *.site files) thereby reducing the minimum
+ configuration even further.
+
+ o Rcmd.bat, Rgui.bat and R.bat now temporarily set R_ENVIRON,
+ R_PROFILE and R_LIBS as needed so that it is no longer necessary to
+ copy the *.site files into the etc directory eliminating all
+ reconfiguration when upgrading to a new version of R (except for
+ refreshing MiKTeX).
+
+ o new command miktex-refresh.bat is used to refresh MiKTeX after a
+ new version of R is installed. Previously this was done in
+ Rrefresh.bat which is now deprecated. Rrefresh.bat is no longer
+ needed (unless you want each R version to have its own *.site files).
+
+ o new NEWS, WISHLIST and RESOURCES files.
+
+ o README provides additional details.
+
Property changes on: komodo/SciViews-K/defaults/NEWS
___________________________________________________________________
Name: svn:executable
+ *
Added: komodo/SciViews-K/defaults/R reference.kpz
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/R reference.kpz
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: komodo/SciViews-K/defaults/R.bat
===================================================================
--- komodo/SciViews-K/defaults/R.bat (rev 0)
+++ komodo/SciViews-K/defaults/R.bat 2009-11-17 11:18:16 UTC (rev 229)
@@ -0,0 +1,148 @@
+
+ at echo off
+if /i "%1"==path (path %2) && goto:eof
+
+setlocal
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: Placing this file in your path will allow rcmd to be run anywhere
+:: without changing your path environment variable. See comments
+:: below on how it finds where R is. Your path can be listed by
+:: the Windows console command: path
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+rem at one tine this script had only been tested on XP
+rem recent tests have only been on Vista
+rem ver | findstr XP >NUL
+rem if errorlevel 1 echo Warning: This script has only been tested on Windows XP.
+
+set scriptdir_=%~dp0
+set lookin=.;%userprofile%;%scriptdir_%
+if not defined R_BATCHFILES_RC (
+ for %%f in ("rbatchfilesrc.bat") do set "R_BATCHFILES_RC=%%~$lookin:f"
+)
+if defined R_BATCHFILES_RC (
+ if exist "%R_BATCHFILES_RC%" call %R_BATCHFILES_RC%
+)
+
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: use environment variable R_HOME if defined
+:: else current folder if bin\rcmd.exe exists
+:: else most current R as determined by registry entry
+:: else error
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+if not defined R_HOME if exist bin\rcmd.exe set R_HOME=%CD%
+if not defined R_HOME for /f "tokens=2*" %%a in (
+ 'reg query hklm\software\R-core\R /v InstallPath 2^>NUL ^| findstr InstallPath'
+ ) do set R_HOME=%%~b
+if not defined R_HOME for /f "tokens=2*" %%a in (
+ 'reg query hklm\software\wow6432Node\r-core\r /v InstallPath 2^>NUL ^| findstr InstallPath'
+ ) do set R_HOME=%%~b
+if not defined R_HOME echo "Error: R not found" & goto:eof
+
+:: add R_MIKTEX to PATH if defined. Otherwise if its not
+:: in the PATH already then check \Program Files\miktex* or \miktex*
+:: and if found add that to PATH.
+
+:: if miktex found in PATH skip searching for it
+PATH | findstr /i miktex > nul
+if not errorlevel 1 goto:end_miktex
+
+:: check for presence of %ProgramFiles%\miktex* or \miktex*
+
+if not defined R_MIKTEX for /f "delims=" %%a in (
+ 'dir /b /on "%ProgramFiles%"\miktex* 2^>NUL'
+) do set R_MIKTEX=%ProgramFiles%\%%a
+
+if not defined R_MIKTEX for /f "delims=" %%a in (
+ 'dir /b /on %SystemDrive%:\miktex* 2^>NUL'
+) do set R_MIKTEX=%SystemDrive%:\miktex\%%a
+
+:end_miktex
+if defined R_MIKTEX PATH %R_MIKTEX%\miktex\bin;%PATH%
+
+if not defined R_TOOLS for /f "tokens=2*" %%a in (
+ 'reg query hklm\software\R-core\Rtools /v InstallPath 2^>NUL ^| findstr InstallPath'
+ ) do set R_TOOLS=%%~b
+if not defined R_TOOLS for /f "tokens=2*" %%a in (
+ 'reg query hklm\software\wow6432Node\Rtools /v InstallPath 2^>NUL ^| findstr InstallPath'
+ ) do set R_TOOLS=%%~b
+
+set PATHQ=%PATH%
+:WHILE
+ if "%PATHQ%"=="" goto WEND
+ for /F "delims=;" %%i in ("%PATHQ%") do if exist "%%~sfi" set PATH2=%PATH2%;%%~sfi
+ for /F "delims=; tokens=1,*" %%i in ("%PATHQ%") do set PATHQ=%%j
+ goto WHILE
+:WEND
+
+set path2=%path2:~1%
+
+if defined R_TOOLS (
+ set path2=%R_TOOLS%\bin;%R_TOOLS%\perl\bin;%R_TOOLS%\MinGW\bin;%PATH2%
+)
+
+path %path2%
+
+set here=%CD%
+set args=%*
+
+:: get name by which this command was called
+:: this allows same file to be used for Rgui, Rterm, etc. by just renaming it
+for %%i in (%0) do set cmd=%%~ni.exe
+
+if /i %cmd%==rtools.exe (endlocal & set path=%path2%) && goto:eof
+
+cd %R_HOME%\bin
+if /i not %cmd%==rguistart.exe goto:notRguiStart
+ set cmd=rgui.exe
+ set firstArgument=%1
+ if defined firstArgument (
+ dir %1 | findstr "<DIR>" > nul
+ if errorlevel 1 goto:notRguiStart
+ set here=%~1
+ set firstArgument=
+ )
+ set args=
+ shift
+ :startloop
+ set firstArgument=%1
+ if defined firstArgument (
+ set args=%args% "%~1"
+ shift
+ goto:startloop
+ )
+:notRguiStart
+
+set st=
+if /i %cmd%==rgui.exe set st=start
+if /i %cmd%==#rscript.exe set cmd=rscript.exe
+cd %here%
+set cmdpath=%R_HOME%\bin\%cmd%
+
+:: if called as jgr.bat locate the JGR package to find jgr.exe
+if /i not %cmd%==jgr.exe goto:notJGR
+ set st=start
+ set st
+ set cmdpath=jgr.exe
+ set cmdpath
+ if not defined JGR_LIBS set JGR_LIBS=%R_LIBS%
+ for %%a in ("%R_HOME%\bin\Rscript.exe") do set RSCRIPT=%%~sfa
+ if not defined JGR_LIBS for /f "usebackq delims=" %%a in (
+ `%RSCRIPT% -e "cat(.libPaths(),sep=';')"`
+ ) do set JGR_LIBS=%%~a
+ if not defined JGR_LIBS (
+ echo "Error: JGR package not found in R library" & goto:eof
+ )
+ for %%f in ("JGR") do set "jgrpkg=%%~$JGR_LIBS:f"
+ set JGR_LIB=%jgrpkg:~0,-4%
+ for %%a in ("%JGR_LIB%") do set JGR_LIB_SHORT=%%~sfa
+ for %%a in ("%R_HOME%") do set R_HOME_SHORT=%%~sfa
+ set args=--libpath=%JGR_LIB_SHORT% --rhome=%R_HOME_SHORT%
+
+:notJGR
+
+if defined st (start "" "%cmdpath%" %args%) else "%cmdpath%" %args%
+goto:eof
+
+
+endlocal
Property changes on: komodo/SciViews-K/defaults/R.bat
___________________________________________________________________
Name: svn:executable
+ *
Added: komodo/SciViews-K/defaults/README
===================================================================
--- komodo/SciViews-K/defaults/README (rev 0)
+++ komodo/SciViews-K/defaults/README 2009-11-17 11:18:16 UTC (rev 229)
@@ -0,0 +1,361 @@
+batchfiles contains batch and GUI files for installing and maintaing R.
+
+License. GPL-2. See COPYING file.
+
+NEWS. See NEWS file.
+
+INSTALLATION
+
+To use any of these utilities just make sure that they are either
+in the current directory you are using or else are anywhere in your
+PATH. No installation is necessary. The utilities are all
+written in Windows batch or javascript as HTA files and have
+no dependencies.
+
+Note that R.bat, Rcmd.bat, Rscript.bat, Rgui.bat, JGR.bat and RguiStart.bat
+are actually all the same file. When any of them are run they check what
+name is was called by to determine what to do. Similarly Sweave.bat and
+Stangle.bat are the same file.
+
+BATCH & JAVASCRIPT PROGRAMS (also see separate section for perl programs)
+
+0. Rtools.bat
+1. R.bat, Rcmd.bat, Rscript.bat, Rgui.bat, JGR.bat
+2. #Rscript.bat
+3. RguiStart.bat
+4. Sweave.bat and Stangle.bat
+5. Rversions.hta
+6. copydir.bat
+7. movedir.bat
+8. find-miktex.hta
+
+
+0. Rtools.bat. Sets path to what Rcmd.bat and others use internally.
+This only sets the path for the current command shell instance.
+
+1. R.bat, Rcmd.bat, Rscript.bat, Rgui.bat, Rscript.bat, JGR.bat - are front
+ends to the corresponding .exe files. They locate R in the registry (and also
+look in a few other places if not found there). Then they look for Rtools and
+MiKTeX and if found they add them temporarily to the path. (Rtools and MiKTeX
+are needed when building R packages from source but are not needed for just
+running R nor are they need to download and install binary packages from CRAN.)
+Then they run R.exe, Rcmd.exe, Rscript.exe, Rgui.exe or JGR.exe with the same
+arguments. They are actually all the same file just renamed. (RguiStart.bat
+described separately is also the same file and all the code from this file is
+also at the end of Sweave.bat, also described separately.) The file checks
+what name it was called by and acts accordingly.
+
+Their main advantages are:
+- you don't have to modify your path just to run R.
+- you don't have to modify your path to build R packages from source.
+- when you upgrade R they automatically work without change
+ since they will pick up the new version of R from the registry
+ automatically.
+- Sweave.bat and Stangle.bat, unlike, Rcmd Sweave and Rcmd Stangle
+ do not depend on rtools.
+
+You can put Rgui.bat on your desktop and associate a Windows
+ShortCut key (http://support.microsoft.com/kb/310417) with
+it so that you can just press the Windows key and
+R, say, to activate R.
+
+Here are some examples of using them from the command line.
+It assumes you have placed el.js, Rcmd.bat and Rgui.bat in
+your path. el cmd spawns a command console with Administrator
+rights. This is needed to build HTML help but you can omit
+the el command if you don't need that.
+
+ el cmd
+ Rcmd check mypackage
+ Rcmd build mypackage
+ Rcmd build mypackage --binary
+ Rcmd INSTALL mypackage_1.0-0.tar.gz
+ Rcmd INSTALL mypackage_1.0-0.tar.gz -l library
+ Rscript myprog.R < mydata.dat
+ Rgui
+
+(When installing packages on Vista it is recommended that
+you do this from within a console session that has Administrator
+rights. It will typically work even without that; however, the
+HTML help will not be created.)
+
+Older version of the Rcmd BATCH command in R had problems
+with spaces in pathnames so be sure you use a sufficiently
+recent version of R. If you are using an old version of R
+that has problems use the short name corresponding to any
+long name with spaces:
+
+For example, suppose we have a file
+ C:\Documents and Settings\Administrator\myfile.R .
+Then try this:
+
+ cd \
+ dir/x doc*
+ Rcmd BATCH c:\docume~1\Administrator\myfile.R
+
+where the dir/x command showed us the short name corresponding to
+the longer space-embedded name: Documents and Settings.
+
+2. #Rscript.bat
+
+#Rscript.bat can be used as the first line of an R script to make
+it callable as a batch file. For example, if we have a myfile.R
+file then we can create a myfile.bat file that looks like this:
+
+#Rscript %0 %*
+...R code from myfile.R goes here...
+
+and now we can just issue the command myfile to run it. We
+no longer need myfile.R.
+
+See the Rtidy.bat file for an example. Note that it does have
+the disadvantage that the output of the R program starts off
+with the command itself. R needs to be able to handle the
+perl/python/ruby -x switch. In the meantime #Rscript.bat
+will mainly be useful for those scripts where the output does
+not go to the standard output or where the addition of this
+line is acceptable.
+
+3. RguiStart.bat
+
+This is like Rgui.bat except it intercepts the first argument
+and interprets it as the folder in which to start R (or if its
+an .Rdata file then it interprets it as the .Rdata file to start
+R with). The main reason for its existence is so that you can
+place it in your SendTo folder. On Vista do this:
+
+ copy RguiStart.bat %APPDATA%\Microsoft\Windows\SendTo
+
+Then, on Vista, when you are in Windows Explorer you can right click
+on any folder in your user area and choose SendTo. From the SendTo
+menu choose RGuiStart.bat to start up R in that folder. If you
+right click on an .Rdata file rather than a folder then R will
+start up with that file loaded (although in that case its probably
+easier to just double click the .Rdata file provided you have
+file type associations set up -- if you don't then the RguiStart.bat
+will provide an alternative).
+
+A second possibility is to place RguiStart.bat on your desktop and
+then drag a folder to it to start R in that folder.
+
+A third possibility is to just shift right click a folder in Windows
+Explorer and choose Open Command Window Here and then when the command
+window opens enter Rgui assuming you have placed Rgui.bat somewhere in
+your path.
+
+4. Sweave.bat and Stangle.bat - will run Sweave, then pdflatex and then
+display latex file. Stangle.bat will run Stangle producing an R file.
+Unlike Rcmd Sweave and Rcmd Stangle these do not depend on rtools.
+Sweave.bat and Stangle.bat are actually the same file. The file determines
+what to do by looking at the name by which it was called.
+
+ Sweave mydoc.Rnw
+ or
+ Sweave mydoc
+
+The script runs Sweave, pdflatex and then displays the pdf
+file (assuming the user has .pdf extension associated with a
+pdf viewer). If there is an error in Sweave or the .tex
+file is not newer than the Sweave'd file the script stops.
+Similarly if there is an error in pdflatex or the .pdf is
+not newer than the .tex file then the script stops. Note
+that _two_ .pdf files are generated. They are identical
+except one has a unique name created by suffixing the base
+with the date and time and .bck.pdf. The one with the unique name
+is the one viewed. This overcomes problems of not being able to
+view the .pdf if the .pdf from a prior run is current being
+viewed (which would happen since by default the Acrobat viewer
+won't allow you to view two files of the same name concurrently).
+Every so often the user should delete all *.bck.pdf files.
+
+Try:
+
+sweave
+
+without arguments to see options and get more info.
+
+Aside from using sweave from the command line, if you place
+sweave.bat in your SendTo folder as discussed under
+RguiStart.bat you can right click .Rnw files and choose
+SendTo > sweave to sweave them.
+
+You may need to copy Sweave.sty to the directory containing
+your .Rnw sweave file to use sweave.bat .
+
+5. Rversions.hta - This displays a GUI that lists all
+versions of R on your system and allows you to choose one
+as your default, setting the registry appropriately. Just
+run without arguments, .e.g.
+
+ Rversions.hta
+
+For example, suppose we want to check a package using two
+different versions of R. Then run
+
+ Rcmd check mypkg
+
+ :: in next command set different version of R
+ Rversions.hta
+ Rcmd check mypkg
+
+ :: in next command reset to original version of R
+ Rversions.hta
+
+5. Rversions.bat - similar to Rversions.hta but
+-- its batch whereas Rversions.hta is GUI
+-- uses slightly different heuristic to find R versions
+-- run without args to list versions available; run with any of
+ the listed versions to set that as the new version
+-- both forms work on XP; to run arg form on Vista run it elevated
+
+Examples:
+
+ :: list R versions
+ rversions.bat
+
+ :: check mypkg using R current version, 2.4.0, say
+ Rcmd check mypkg
+
+ :: switch to version R-2.5.0 and recheck
+ rversions R-2.5.0
+ Rcmd check mypkg
+
+ :: reset back to version 2.4.0
+ rversions.bat R-2.4.0
+
+6. copydir.bat - can be used to copy the libraries from an
+old version of R to your new one. It will not overwrite any
+libraries already there so it should be safe to use. e.g. to
+upgrade R to a new version
+
+ :: Example is for upgrading from R-2.4.1 to R-2.5.0
+
+ :: first, download and install R-2.5.0, say
+ :: now perform the next two commands at the Windows console
+ cd \Program Files\R
+ copydir R-2.4.1\library R-2.5.0\library
+
+ :: next command only needed if you have *.site files
+ copy R-2.4.0\etc\*.site R-2.5.0\etc
+
+ :: ... now startup new version of R (R 2.5.0 in this example)
+ # issue this command in R 2.5.0
+ update.packages(checkBuilt = TRUE, ask = "graphics")
+ # or (see note below)
+ update.packages(ask = "graphics")
+
+ :: press OK and it will update those packages as necessary
+
+ # ... optionally check for deprecated packages
+ # 1. first select all repositories that you use with menu:
+ # Packages | Repositories
+ # 2. second check if there are any deprecated packages that
+ # were copied over but are not longer on CRAN or other repository
+ dp <- setdiff(installed.packages()[,1], available.packages()[,1])
+ # look at what we have
+ dp
+ # if you wish to remove them issue the remove.packages command:
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/sciviews -r 229
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