|
@@ -1,367 +1,367 @@
|
|
|
-
|
|
|
-batchfiles contains GPL-2 batch files for installing and maintaining R.
|
|
|
-
|
|
|
-Each is self contained, independent of the others and need no installation.
|
|
|
-Just place it anywhere on your path.
|
|
|
-
|
|
|
----
|
|
|
-
|
|
|
-PROGRAM LIST
|
|
|
-
|
|
|
-Legend:
|
|
|
-h = no args gives help
|
|
|
-0 = common usage is to enter command name without arguments
|
|
|
-d = in development
|
|
|
-2.11 = only works with R 2.11
|
|
|
-* = all files marked with one star are the same. Program checks name by which its called to determine action.
|
|
|
-** = all files marked with two stars are the same. Program checks name by which its called to determine action.
|
|
|
-
|
|
|
-#Rscript.bat - put at top of R file to make it a batch file (h) (*)
|
|
|
-clip2r.js - pastes clipboard into Rgui. See comments in file for use from vim. (0)(d)
|
|
|
-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)
|
|
|
-kopy.bat - copy Rcmd to other batch files (h)(d)
|
|
|
-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) (*)
|
|
|
-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 (d)
|
|
|
-Rtools.bat - place Rtools on path for remainder of console session (0) (*)
|
|
|
-Rversions.bat - list R and set R version in registry, e.g. on Vista: el cmd/c Rversions R-2.10.1 (0)
|
|
|
-Rversions.hta - GUI interface to RSetReg. List and set R version, e.g. on Vista: el cmd /c Rversions.hta (0)(2.11)
|
|
|
-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) (**)
|
|
|
-
|
|
|
----
|
|
|
-
|
|
|
-DESCRIPTIONS
|
|
|
-
|
|
|
-R.bat, Rcmd.bat, Rscript.bat, Rgui.bat, and RguiStart.bat are all the same
|
|
|
-file. They query the name by which they were called to determine what they do.
|
|
|
-Similarly Sweave.bat and Stangle.bat are the same file.
|
|
|
-
|
|
|
-The home page and NEWS file provide more info.
|
|
|
-
|
|
|
-BATCH PROGRAMS
|
|
|
-
|
|
|
-0. Rtools.bat
|
|
|
-1. R.bat, Rcmd.bat, Rscript.bat, Rgui.bat
|
|
|
-2. #Rscript.bat
|
|
|
-3. RguiStart.bat
|
|
|
-4. Sweave.bat and Stangle.bat
|
|
|
-5. copydir.bat
|
|
|
-6. movedir.bat
|
|
|
-7. 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 - 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
|
|
|
-
|
|
|
-(or to locate locate the SendTo folder in Windows Explorer on Vista
|
|
|
-enter shell:sendto into the Windows Explorer address bar and copy
|
|
|
-your RguiStart.bat file there.)
|
|
|
-
|
|
|
-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.bat - similar to Rversions.hta but
|
|
|
- the listed versions to set that as the new version
|
|
|
- e.g. el cmd /c Rversions.bat R-2.10.0
|
|
|
-
|
|
|
-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-2.11.0
|
|
|
- :: now perform the next two commands at the Windows console
|
|
|
-
|
|
|
- cd %userprofile%\Documents\R\win-library
|
|
|
- :: you can use movedir instead of copydir if you prefer to move them
|
|
|
- copydir 2.10\library 2.11\library
|
|
|
-
|
|
|
- :: ... now startup new version of R (R 2.11.0 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:
|
|
|
- # remove.packages(dp)
|
|
|
-
|
|
|
- :: ... exit R and start it up again ...
|
|
|
-
|
|
|
-Note that the checkBuilt=TRUE argument will potentially
|
|
|
-cause all your packages to be downloaded again so you could
|
|
|
-try leaving it off and then reissue the command with
|
|
|
-checkBuilt=TRUE later only if you run into problems. I
|
|
|
-normally do it without the checkBuilt=TRUE.
|
|
|
-
|
|
|
-It is anticipated that this command will ultimately be
|
|
|
-superceded by functionality in the R setup procedure at
|
|
|
-which time this will be deprecated. Note that this method
|
|
|
-of just copying libraries may not work depending on the
|
|
|
-versions of R involved. If its necessary to re-install most
|
|
|
-packages it can be done by issuing the following R command
|
|
|
-after performing the copydir.bat:
|
|
|
-install.packages(installed.packages()[,1])
|
|
|
-
|
|
|
-(Note that 2.8 of the R Windows FAQ
|
|
|
-
|
|
|
-http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
|
|
|
-
|
|
|
-refers to copying any installed package to the library
|
|
|
-folder but does not address how to accomplish that. That
|
|
|
-omission is what copydir.bat addresses.)
|
|
|
-
|
|
|
-An alternative to copydir is to reinstall all packages
|
|
|
-
|
|
|
- # Alternative to copydir.bat #1
|
|
|
- # this example is for moving from 2.4.1 to 2.5.0
|
|
|
- # run this in R 2.5.0
|
|
|
- setwd(R.home())
|
|
|
- ip <- installed.packages(lib.loc = "../R-2.4.1/library")
|
|
|
- ip <- ip[ip[,1]!="base" ,1]
|
|
|
- install.packages(ip)
|
|
|
-
|
|
|
-The above is taken from:
|
|
|
-https://www.stat.math.ethz.ch/pipermail/r-help/2007-May/131806.html
|
|
|
-Note that you may still have to use movedir.bat or copydir.bat
|
|
|
-after the above if it fails to install everything. Since movedir.bat
|
|
|
-and copydir.bat won't overwrite anything this should be safe.
|
|
|
-
|
|
|
- # Alternative to copydir.bat #2
|
|
|
- #---run in previous version, e.g. R 2.4.1
|
|
|
- packages <- installed.packages()[,"Package"]
|
|
|
- save(packages, file = "~/Rpackages")
|
|
|
-
|
|
|
- #---run in new version, e.g. R 2.5.0
|
|
|
- load("~/Rpackages")
|
|
|
- install.packages(setdiff(packages, installed.packages()[,"Package"]))
|
|
|
-
|
|
|
- file.remove("~/Rpackages")
|
|
|
-
|
|
|
-This copydir alternative is based on:
|
|
|
-https://www.stat.math.ethz.ch/pipermail/r-help/2007-May/131131.html
|
|
|
-
|
|
|
-7. movedir - same arguments as copydir. Only difference is
|
|
|
-that it moves the directories rather than copying them. This
|
|
|
-can be used if you are no longer interested in using the
|
|
|
-packages with the old version of R other than by
|
|
|
-reinstalling them.) This has the advantage that its much
|
|
|
-faster than copydir. The example under copydir works with
|
|
|
-movedir too. Just replace copydir with movedir in that
|
|
|
-example. Comments under copydir.bat apply here too. I
|
|
|
-mostly use movedir.bat myself instead of copydir.bat since
|
|
|
-its so much faster.
|
|
|
-
|
|
|
-8. show-svn-info.hta - Just run this from any Tortoise SVN folder
|
|
|
-and it will display some information about it. Requires version 1.5
|
|
|
-or higher of Tortoise SVN.
|
|
|
-
|
|
|
-9. find-miktex.hta - displays the path to the MiKTeX bin directory.
|
|
|
-Just enter find-miktex.hta at the Windows command line (no arguments
|
|
|
-are needed) or double click it from Windows Explorer.
|
|
|
-
|
|
|
-ADDITIONAL FILES
|
|
|
-
|
|
|
-1. RESOURCES - additional information on writing Windows XP
|
|
|
-batch files.
|
|
|
-
|
|
|
-2. COPYRIGHT and COPYING - this is free software subject to
|
|
|
- the GPL license as described.
|
|
|
-
|
|
|
-3. THANKS - acknowledgments.
|
|
|
-
|
|
|
-DEPRECATED AND CHANGED
|
|
|
-
|
|
|
-- Rfind.bat
|
|
|
-- makepkg.bat
|
|
|
-- Rversions.hta
|
|
|
-- toggerDoc.pl
|
|
|
-
|
|
|
-These are no longer distributed but can be found in older distributions of this
|
|
|
-package. It is unknown whether they work with recent versions of R. (I found
|
|
|
-I was not using these so am no longer maintaining them.)
|
|
|
+
|
|
|
+batchfiles contains GPL-2 batch files for installing and maintaining R.
|
|
|
+
|
|
|
+Each is self contained, independent of the others and need no installation.
|
|
|
+Just place it anywhere on your path.
|
|
|
+
|
|
|
+---
|
|
|
+
|
|
|
+PROGRAM LIST
|
|
|
+
|
|
|
+Legend:
|
|
|
+h = no args gives help
|
|
|
+0 = common usage is to enter command name without arguments
|
|
|
+d = in development
|
|
|
+2.11 = only works with R 2.11
|
|
|
+* = all files marked with one star are the same. Program checks name by which its called to determine action.
|
|
|
+** = all files marked with two stars are the same. Program checks name by which its called to determine action.
|
|
|
+
|
|
|
+#Rscript.bat - put at top of R file to make it a batch file (h) (*)
|
|
|
+clip2r.js - pastes clipboard into Rgui. See comments in file for use from vim. (0)(d)
|
|
|
+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)
|
|
|
+kopy.bat - copy Rcmd to other batch files (h)(d)
|
|
|
+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) (*)
|
|
|
+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 (d)
|
|
|
+Rtools.bat - place Rtools on path for remainder of console session (0) (*)
|
|
|
+Rversions.bat - list R and set R version in registry, e.g. on Vista: el cmd/c Rversions R-2.10.1 (0)
|
|
|
+Rversions.hta - GUI interface to RSetReg. List and set R version, e.g. on Vista: el cmd /c Rversions.hta (0)(2.11)
|
|
|
+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) (**)
|
|
|
+
|
|
|
+---
|
|
|
+
|
|
|
+DESCRIPTIONS
|
|
|
+
|
|
|
+R.bat, Rcmd.bat, Rscript.bat, Rgui.bat, and RguiStart.bat are all the same
|
|
|
+file. They query the name by which they were called to determine what they do.
|
|
|
+Similarly Sweave.bat and Stangle.bat are the same file.
|
|
|
+
|
|
|
+The home page and NEWS file provide more info.
|
|
|
+
|
|
|
+BATCH PROGRAMS
|
|
|
+
|
|
|
+0. Rtools.bat
|
|
|
+1. R.bat, Rcmd.bat, Rscript.bat, Rgui.bat
|
|
|
+2. #Rscript.bat
|
|
|
+3. RguiStart.bat
|
|
|
+4. Sweave.bat and Stangle.bat
|
|
|
+5. copydir.bat
|
|
|
+6. movedir.bat
|
|
|
+7. 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 - 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
|
|
|
+
|
|
|
+(or to locate locate the SendTo folder in Windows Explorer on Vista
|
|
|
+enter shell:sendto into the Windows Explorer address bar and copy
|
|
|
+your RguiStart.bat file there.)
|
|
|
+
|
|
|
+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.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
|
|
|
+ e.g. el cmd /c Rversions.bat R-2.10.0
|
|
|
+
|
|
|
+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-2.11.0
|
|
|
+ :: now perform the next two commands at the Windows console
|
|
|
+
|
|
|
+ cd %userprofile%\Documents\R\win-library
|
|
|
+ :: you can use movedir instead of copydir if you prefer to move them
|
|
|
+ copydir 2.10\library 2.11\library
|
|
|
+
|
|
|
+ :: ... now startup new version of R (R 2.11.0 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:
|
|
|
+ # remove.packages(dp)
|
|
|
+
|
|
|
+ :: ... exit R and start it up again ...
|
|
|
+
|
|
|
+Note that the checkBuilt=TRUE argument will potentially
|
|
|
+cause all your packages to be downloaded again so you could
|
|
|
+try leaving it off and then reissue the command with
|
|
|
+checkBuilt=TRUE later only if you run into problems. I
|
|
|
+normally do it without the checkBuilt=TRUE.
|
|
|
+
|
|
|
+It is anticipated that this command will ultimately be
|
|
|
+superceded by functionality in the R setup procedure at
|
|
|
+which time this will be deprecated. Note that this method
|
|
|
+of just copying libraries may not work depending on the
|
|
|
+versions of R involved. If its necessary to re-install most
|
|
|
+packages it can be done by issuing the following R command
|
|
|
+after performing the copydir.bat:
|
|
|
+install.packages(installed.packages()[,1])
|
|
|
+
|
|
|
+(Note that 2.8 of the R Windows FAQ
|
|
|
+
|
|
|
+http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
|
|
|
+
|
|
|
+refers to copying any installed package to the library
|
|
|
+folder but does not address how to accomplish that. That
|
|
|
+omission is what copydir.bat addresses.)
|
|
|
+
|
|
|
+An alternative to copydir is to reinstall all packages
|
|
|
+
|
|
|
+ # Alternative to copydir.bat #1
|
|
|
+ # this example is for moving from 2.4.1 to 2.5.0
|
|
|
+ # run this in R 2.5.0
|
|
|
+ setwd(R.home())
|
|
|
+ ip <- installed.packages(lib.loc = "../R-2.4.1/library")
|
|
|
+ ip <- ip[ip[,1]!="base" ,1]
|
|
|
+ install.packages(ip)
|
|
|
+
|
|
|
+The above is taken from:
|
|
|
+https://www.stat.math.ethz.ch/pipermail/r-help/2007-May/131806.html
|
|
|
+Note that you may still have to use movedir.bat or copydir.bat
|
|
|
+after the above if it fails to install everything. Since movedir.bat
|
|
|
+and copydir.bat won't overwrite anything this should be safe.
|
|
|
+
|
|
|
+ # Alternative to copydir.bat #2
|
|
|
+ #---run in previous version, e.g. R 2.4.1
|
|
|
+ packages <- installed.packages()[,"Package"]
|
|
|
+ save(packages, file = "~/Rpackages")
|
|
|
+
|
|
|
+ #---run in new version, e.g. R 2.5.0
|
|
|
+ load("~/Rpackages")
|
|
|
+ install.packages(setdiff(packages, installed.packages()[,"Package"]))
|
|
|
+
|
|
|
+ file.remove("~/Rpackages")
|
|
|
+
|
|
|
+This copydir alternative is based on:
|
|
|
+https://www.stat.math.ethz.ch/pipermail/r-help/2007-May/131131.html
|
|
|
+
|
|
|
+7. movedir - same arguments as copydir. Only difference is
|
|
|
+that it moves the directories rather than copying them. This
|
|
|
+can be used if you are no longer interested in using the
|
|
|
+packages with the old version of R other than by
|
|
|
+reinstalling them.) This has the advantage that its much
|
|
|
+faster than copydir. The example under copydir works with
|
|
|
+movedir too. Just replace copydir with movedir in that
|
|
|
+example. Comments under copydir.bat apply here too. I
|
|
|
+mostly use movedir.bat myself instead of copydir.bat since
|
|
|
+its so much faster.
|
|
|
+
|
|
|
+8. show-svn-info.hta - Just run this from any Tortoise SVN folder
|
|
|
+and it will display some information about it. Requires version 1.5
|
|
|
+or higher of Tortoise SVN.
|
|
|
+
|
|
|
+9. find-miktex.hta - displays the path to the MiKTeX bin directory.
|
|
|
+Just enter find-miktex.hta at the Windows command line (no arguments
|
|
|
+are needed) or double click it from Windows Explorer.
|
|
|
+
|
|
|
+ADDITIONAL FILES
|
|
|
+
|
|
|
+1. RESOURCES - additional information on writing Windows XP
|
|
|
+batch files.
|
|
|
+
|
|
|
+2. COPYRIGHT and COPYING - this is free software subject to
|
|
|
+ the GPL license as described.
|
|
|
+
|
|
|
+3. THANKS - acknowledgments.
|
|
|
+
|
|
|
+DEPRECATED AND CHANGED
|
|
|
+
|
|
|
+- Rfind.bat
|
|
|
+- makepkg.bat
|
|
|
+- Rversions.hta
|
|
|
+- toggerDoc.pl
|
|
|
+
|
|
|
+These are no longer distributed but can be found in older distributions of this
|
|
|
+package. It is unknown whether they work with recent versions of R. (I found
|
|
|
+I was not using these so am no longer maintaining them.)
|