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  • JRI Fatal Error on Ubuntu

    - by Peter Jackson
    I have successfully installed JRI and rJava on Windows 7. I am now trying to get it to work on Ubuntu with 64bit OS. I can make rJava calls from within R but getting JRI to work is more difficult. I am running NetBeans 7.1.2 and I have followed various tricks in setting R_HOME and java.library.path to enable all the classes to be loaded. That is, I am past the error messages such as "jri library not found" and "R_HOME not set". From my java code,I can see that R_HOME = /usr/lib64/R. The error message I get now is Fatal error: you must specify '--save', '--no-save' or '--vanilla' This happens when Rengine is first called: Rengine r = new Rengine(args,false,null); This appears to be an error message from R; it seems to be expecting a command line argument. I haven't seen any posting with this error message. Any ideas? Thanks, Peter

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  • R from java with no graphics: is it worth moving to JRI

    - by LH
    I have a system set up that's been happily running R from a java servlet, spawning processed & hooking into the process's stdin, stdout, and stderr streams, as in the second andwer to this question. After a system upgrade (that included glibc), the input is no longer reaching the R process.* Until now, 'R --vanilla --slave -f [file] ...' was working fine for me. I also have no swing dependencies right now, so I'm somewhat reluctant to add them. (I may actually not be able to add swing dependencies; am I right that using REngine automatically brings swing in? The examples import all of swing.) Are there advantages to switching to JRI? What changes would I need to make to my R script? (It currently reads from stdin and writes to stdout). I'm not finding the provided examples terribly helpful for how to use JRI in this situation. Thanks for your help & comments. *I can't even tell if the problem is data being written too soon or too late, but that's a separate issue/question; if I move to JRI I'm hoping it all becomes moot.

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  • Using R in Processing through rJava/JRI?

    - by tommy-o-dell
    Hi guys, Is it possible to run R in Processing through rJava/JRI? If I deployed a Processing app on the web, would the client need R on their system? I'm looking to create an interactive information dashboard that I can deploy on the web. It seems that Processing is probably my best bet for the interactive/web part of things. Unfortunately, it doesn't look like there are many math/stats functions built-in. And there aren't any libraries for plotting data either. I've been using R and gpplot2 for a few months and am thrilled (amazed) at how easily it manipulates and plots data. So I'm wondering now if can get the best of both worlds and run R through a Processing applet. From the JRI website: JRI is a Java/R Interface, which allows to run R inside Java applications as a single thread. Basically it loads R dynamic library into Java and provides a Java API to R functionality. It supports both simple calls to R functions and a full running REPL. In a sense JRI is the inverse of rJava and both can be combined (i.e. you can run R code inside JRI that calls back to the JVM via rJava). The JGR project makes the full use of both JRI and rJava to provide a full Java GUI for R. JRI uses native code, but it supports all platforms where Sun's Java (or compatible) is available, including Windows, Mac OS X, Sun and Linux (both 32-bit and 64-bit). Thanks for the advice :)

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  • Problem with launching JAGUAR in R

    - by Gerry
    Windows XP, R 2.11.1, Java JRE6 I just installed the Jaguar package. From an R console, I can do this: > library(JGR) Loading required package: rJava Loading required package: JavaGD Loading required package: iplots Please use the corresponding JGR launcher to start JGR. Run JGR() for details. You can also use JGR(update=TRUE) to update JGR. and so JGR appears to be correctly installed. JGR() yields On Windows JGR must be started using the JGR.exe launcher. Please visit http://www.rosuda.org/JGR/ to download it. > I'm not sure how to run Jaguar - I know I have to run jgr.exe - but should R be already open? If so, should the JGR library be already loaded? I've tried all of these, and what seems to happen regardless is a console window opens briefly, then disappears. I've run jrg --debug, with no apparent error message: (same file regardless of choice made above). What should I be doing? Thanks! System: Version 5.1 (build 2600), platform 2 [Service Pack 3] JGR loader version 1.61 (build Jul 23 2008) parseParams> 1 parameters parsed. parseParams par 10> "--debug" > rhome="C:\Program Files\R\R-2.11.1" > srhome="C:\PROGRA~1\R\R-211~1.1" getPkgVersion(JGR): 010702 getPkgVersion(rJava): 000805 getPkgVersion(JavaGD): 000503 getPkgVersion(iplots): 010103 Loading preferences from "C:\Documents and Settings\gblais\.JGRprefsrc" > javakey="Software\JavaSoft\Java Runtime Environment\1.6" > javah="C:\Program Files\Java\jre6" > tp="C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\" Got RuntimeLib from registry, using "C:\Program Files\Java\jre6\bin\client;" PATH prefix. Java home: "C:\Program Files\Java\jre6" R home: "C:\Program Files\R\R-2.11.1" JAR files: "-Drjava.class.path=C:\PROGRA~1\R\R-211~1.1\library\rJava\jri\JRI.jar;C:\PROGRA~1\R\R-211~1.1\library\iplots\java\iplots.jar;C:\PROGRA~1\R\R-211~1.1\library\JGR\java\JGR.jar;C:\PROGRA~1\R\R-211~1.1\etc\classes;C:\PROGRA~1\R\R-211~1.1\etc\classes.jar" desired PATH: "C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin;C:\Program Files\R\R-2.11.1\bin;C:\PROGRA~1\R\R-211~1.1\library\rJava\jri;C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\" actual PATH: "C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin\client;C:\Program Files\Java\jre6\bin;C:\Program Files\R\R-2.11.1\bin;C:\PROGRA~1\R\R-211~1.1\library\rJava\jri;C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\" getenv PATH: "C:\Perl\site\bin;C:\Perl\bin;C:\PHP\;C:\Program Files\MiKTeX 2.8\miktex\bin;C:\Python26\Lib\site-packages\PyQt4;C:\Program Files\Tcl\bin;C:\oracle\product\10.2.0\client_2\BIN;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Support Tools\;c:\belfry;c:\belfry\usr\local\wbin;C:\WINDOWS;C:\WINDOWS\System32;C:\WINDOWS\System32\WBEM;c:\Program Files\QuickTime\QTSystem\;C:\Program Files\SlikSvn\bin\;c:\progra~1\Microsoft Visual Studio 9.0\VC\bin\" argv[0]:C:\PROGRA~1\Java\jre6\bin\java.exe argv[1]:-Drjava.class.path=C:\PROGRA~1\R\R-211~1.1\library\rJava\jri\JRI.jar;C:\PROGRA~1\R\R-211~1.1\library\iplots\java\iplots.jar;C:\PROGRA~1\R\R-211~1.1\library\JGR\java\JGR.jar;C:\PROGRA~1\R\R-211~1.1\etc\classes;C:\PROGRA~1\R\R-211~1.1\etc\classes.jar argv[2]:-Xmx512m argv[3]:-cp argv[4]:C:\PROGRA~1\R\R-211~1.1\library\rJava\java\boot argv[5]:-Drjava.path=C:\PROGRA~1\R\R-211~1.1\library\rJava argv[6]:-Dmain.class=org.rosuda.JGR.JGR argv[7]:-Djgr.load.pkgs=yes argv[8]:-Djgr.loader.ver=1.61 argv[9]:RJavaClassLoader argv[10]:--debug

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