"R Extension problems on MAC OS"

Dear All,

I am trying to no avail to install R Extension for Rapid-I. First, info of my system :

MAC OS : 10.6.4

Java : 1.6.0_22

R version: 2.12

I have added the following information to my .bash_profile

export R_HOME=/Library/Frameworks/R.framework/Versions/2.12/Resources

PATH=$PATH:/Library/Frameworks/R.framework/Versions/2.12/Resources/bin:/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rJava/jri

export PATH
export R_HOME

I have also added the following file to R tab in Preferences of RapidMiner :

/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rJava/jri/libjri.jnilib

When i start RapidMiner i get the following exception :

Process: java [804]
Path: /usr/bin/java
Identifier: com.apple.javajdk16.cmd
Version: 1.0 (1.0)
Code Type: X86-64 (Native)
Parent Process: sh [801]

PlugIn Path: /Library/Frameworks/R.framework/Versions/2.12/Resources/library/tcltk/libs/x86_64/tcltk.so
PlugIn Identifier: tcltk.so
PlugIn Version: ??? (???)

Date/Time: 2010-10-31 14:22:22.778 +0200
OS Version: Mac OS X 10.6.4 (10F569)
Report Version: 6

Interval Since Last Report: 2569235 sec
Crashes Since Last Report: 16
Per-App Interval Since Last Report: 1490860 sec
Per-App Crashes Since Last Report: 14
Anonymous UUID: C3422C24-3844-4E38-9F6F-950AFD494D79

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 1

Application Specific Information:
*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[NSApplicationAWT _setup:]: unrecognized selector sent to instance 0x100127f10'
*** Call stack at first throw:

Library tcltk.so is the problem. It seems to me that i have messed up x86_64 versions somehow. Any ideas? I am also trying to find the installation directions of R extension. Where could i find those?

Thank you in advance

Harry

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land

Hi Harry,
if I understood you correctly, you are assuming that you have messed up 32 and 64 bit versions of libraries, jvm, R and RapidMiner? Please verify this, otherwise we would have to investigate the problem further.

Does R start correctly itself?

Greetings,
Sebastian

hgwelec

Hi Sebastian,

Yes this is what i think (there seems to be some problem with these different 32-bit and 64-bit versions versions) but i am not sure. However I tested R and both versions (R32 and R64) work without any problems.

Please let me know if i can help in any other way

Harry

land

Hi Harry,
please do me the favor and deinstall R in the version you are not going to use. So if you start RM 64, please deinstall R 32 bit.
And try again.

Greetings,
Sebastian

hgwelec

Problem sorted Sebastian :-)

It is not necessary to de-install any version. It appears that i had to install a TclTk extension found here :

http://cran.cnr.berkeley.edu/

The required dmg is tcltk-8.5.5.dmg. After i installed this everything works fine!

Thanks again,

Harry

hgwelec

Hi again Sebastian,

One more thing. It appears that whenever i start Rapid-I there is an X-11 pop up to select a CRAN Mirror. I tried :

1) selecting a mirror and pressing OK
2) canceling the window

However every time i start Rapid_i the pop up keeps coming back. Any ideas how i can stop this? I have updated to the latest version of R extension just now but i believe the problem existed before too.

Thanks again

land

Hi,
this window opens, because the R Extension tries to install all necessary packages. it's the window to select a mirror for that. These downloaded libraries are stored in <home>/.RapidMiner5/rLibPath . If this isn't accessible or only temporary, these have to be downloaded again and again. Please check if the directory exists and if there are files in it before and after starting RapidMiner.
You can also type ".libPaths()" in the R console to check if it had been prepended on the list of these paths correctly.

Thanks for the hint with the TclTk. I will add this to the installation hints.

Greetings,
Sebastian

hgwelec

Hi again Sebastian,

Unfortunately the window keeps popping up. The directory RLibPaths exists under .RapidMiner5 and contains two directories named klaR and mlr which also have files in it.

Running .Libpaths() within Rapid-I i am getting the following information which looks fine to me :

"/Users/<home>/.RapidMiner5/RLibPath"
"/Library/Frameworks/R.framework/Versions/2.12/Resources/Library"

Should i erase RLibPath directory and try again?

Thanks for your help!

zozette

Hi,
It seems that R extension on Mac OS X is at pain.

1) loading RapidMiner by double-clicking on rapidminer.jar fails to "load" R extension. There is no R icon in the toolbar. It seems that R_HOME is not recognize. In fact, RapidMiner can't connect to R.
But,
2) loading RapidMiner with the script "RapidMinerGUI" does the job if
RAPIDMINER_HOME and R_HOME are provided the good information.
For example: at the top of the script, I have added
R_HOME="/Library/Frameworks/R.framework/Resources"
RAPIDMINER_HOME="/Applications/my_subfolder/rapidminer"
I have made the script executable.

I get in terminal.app :
*************************************************************************************
Last login: Mon Nov 15 11:28:26 on ttys000
/Applications/math/rapidminer/scripts/RapidMinerGUI ; exit;
MacBook-Pro-15-de-myname:~ frederic$ /Applications/math/rapidminer/scripts/RapidMinerGUI ; exit;
No maximum Java memory defined, using 512 Mb...
Starting RapidMiner from '/Applications/math/rapidminer', using classes from '/Applications/math/rapidminer/lib/rapidminer.jar'...
15 nov. 2010 11:37:45 com.rapid_i.Launcher ensureRapidMinerHomeSet
INFO: rapidminer.home is '/Applications/math/rapidminer'.
15 nov. 2010 11:37:45 com.rapid_i.Launcher main
INFO: Launching RapidMiner, platform ANY
2010-11-15 11:37:46 CONFIG: Locale not specified explicitly. Set default locale to US. (RapidMiner.init())
2010-11-15 11:37:46 INFO: rapidminer.home is '/Applications/math/rapidminer'. (Launcher.ensureRapidMinerHomeSet())
2010-11-15 11:37:46 CONFIG: Reading configuration resource com/rapidminer/resources/rapidminerrc. (ParameterService.loadAllRCFiles())
2010-11-15 11:37:46 CONFIG: Neither system property 'rapidminer.config.dir' nor environment variable 'RAPIDMINER_CONFIG_DIR' not set. Ignored. (ParameterService.getGlobalConfigDir())
2010-11-15 11:37:46 CONFIG: Trying rcfile '/Users/frederic/.RapidMiner5/5_0_10_rapidminerrc'...skipped (ParameterService.loadRCFile())
2010-11-15 11:37:46 CONFIG: Read rcfile '/Users/frederic/.RapidMiner5/5_0_10_rapidminerrc.Mac OS X'. (ParameterService.loadRCFile())
2010-11-15 11:37:46 CONFIG: Trying rcfile '/Users/frederic/rapidminerrc'...skipped (ParameterService.loadRCFile())
2010-11-15 11:37:46 CONFIG: Trying rcfile '/Users/frederic/rapidminerrc.Mac OS X'...skipped (ParameterService.loadRCFile())
2010-11-15 11:37:46 CONFIG: Property rapidminer.rcfile not specified...skipped (ParameterService.loadAllRCFiles())
2010-11-15 11:37:46 CONFIG: Read extension state. (ManagedExtension.readConfiguration())
2010-11-15 11:37:46 CONFIG: Scanning plugins in /Applications/math/rapidminer/lib/plugins. (Plugin.findAndRegisterPlugins())
2010-11-15 11:37:46 CONFIG: Loading renderers from 'Text Processing'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_text-5.0.7.jar!/com/rapidminer/resources/parserulesTextProcessing.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'PMML'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_pmml-5.0.2.jar!/com/rapidminer/resources/parserulesPMML.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'Weka'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_weka-5.0.1.jar!/com/rapidminer/resources/parserulesWekaExtension.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'PaREn Wizard'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_paren-5.0.1.jar!/com/rapidminer/resources/parserulesParen.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'R Extension'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_r-5.0.2.jar!/com/rapidminer/resources/parserulesR.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'Web Mining'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_web-5.0.4.jar!/com/rapidminer/resources/parserulesWeb.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'Series'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_series-5.0.2.jar!/com/rapidminer/resources/parserulesValueSeries.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading renderers from 'Reporting'. (RendererService.init())
2010-11-15 11:37:47 CONFIG: Reading parse rules from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_reporting-5.0.2.jar!/com/rapidminer/resources/parserulesReporting.xml (XMLImporter.importParseRules())
2010-11-15 11:37:47 CONFIG: Loading operators from 'OperatorsCore.xml'. (OperatorService.registerOperators())
2010-11-15 11:37:48 CONFIG: Loading operator documentation from jar:file:/Applications/math/rapidminer/lib/rapidminer.jar!/com/rapidminer/resources/i18n/OperatorsCoreDocumentation.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:49 WARNING: Password in XML file looks like unencrypted plain text. (ParameterTypePassword.decryptPassword())
2010-11-15 11:37:51 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_text-5.0.7.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:51 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_text-5.0.7.jar!/com/rapidminer/resources/i18n/OperatorsDocTextProcessing.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:51 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_parallel-5.0.1.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:51 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_parallel-5.0.1.jar!/com/rapidminer/resources/i18n/OperatorsDocParallel.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:51 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_pmml-5.0.2.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:51 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_pmml-5.0.2.jar!/com/rapidminer/resources/i18n/OperatorsDocPMML.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:51 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_weka-5.0.1.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:51 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_weka-5.0.1.jar!/com/rapidminer/resources/i18n/OperatorsDocWekaExtension.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:51 CONFIG: Creating operators from factory com.rapidminer.tools.WekaOperatorFactory (OperatorService.parseOperators())
2010-11-15 11:37:54 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_paren-5.0.1.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:54 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_paren-5.0.1.jar!/com/rapidminer/resources/i18n/OperatorsDocParen.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:54 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_r-5.0.2.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:54 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_r-5.0.2.jar!/com/rapidminer/resources/i18n/OperatorsDocR.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:54 CONFIG: Creating operators from factory com.rapidminer.operator.r.ROperatorFactory (OperatorService.parseOperators())
2010-11-15 11:37:54 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_web-5.0.4.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:54 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_web-5.0.4.jar!/com/rapidminer/resources/i18n/OperatorsDocWeb.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:54 INFO: No operator descriptor specified for plugin Community. Trying plugin initializtation class com.rapidminer.community.CommunityPluginInit. (Plugin.registerOperators())
2010-11-15 11:37:54 WARNING: No operator descriptor defined for: Community (Plugin.registerOperators())
2010-11-15 11:37:54 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_series-5.0.2.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:54 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_series-5.0.2.jar!/com/rapidminer/resources/i18n/OperatorsDocValueSeries.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:54 CONFIG: Loading operators from '/Users/frederic/.RapidMiner5/managed/rmx_reporting-5.0.2.jar'. (OperatorService.registerOperators())
2010-11-15 11:37:54 CONFIG: Loading operator documentation from jar:file:/Users/frederic/.RapidMiner5/managed/rmx_reporting-5.0.2.jar!/com/rapidminer/resources/i18n/OperatorsDocReporting.xml. (OperatorDocBundle$XMLControl.newBundle())
2010-11-15 11:37:54 CONFIG: Number of registered operator classes: 581; number of registered operator descriptions: 721; number of replacements: 533 (OperatorService.init())
2010-11-15 11:37:54 CONFIG: Loading operator usage statistics. (UsageStatistics.load())
2010-11-15 11:37:54 CONFIG: Reading parse rules from jar:file:/Applications/math/rapidminer/lib/rapidminer.jar!/com/rapidminer/resources/parserules.xml (XMLImporter.importParseRules())
2010-11-15 11:37:55 CONFIG: Loading JDBC driver information from 'resource jdbc_properties.xml'. (DatabaseService.loadJDBCProperties())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver com.mysql.jdbc.Driver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver org.postgresql.Driver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver net.sourceforge.jtds.jdbc.Driver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver org.hsqldb.jdbcDriver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 WARNING: Missing database driver class name for 'ODBC Bridge (e.g. Access)' (JDBCProperties.<init>())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver net.sourceforge.jtds.jdbc.Driver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver com.ingres.jdbc.IngresDriver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 CONFIG: Loaded JDBC driver ca.ingres.jdbc.IngresDriver (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 INFO: JDBC driver oracle.jdbc.driver.OracleDriver not found. Probably the driver is not installed. (JDBCProperties.registerDrivers())
2010-11-15 11:37:55 CONFIG: Neither system property 'rapidminer.config.dir' nor environment variable 'RAPIDMINER_CONFIG_DIR' not set. Ignored. (ParameterService.getGlobalConfigDir())
2010-11-15 11:37:55 CONFIG: Loading repositories from /Users/frederic/.RapidMiner5/repositories.xml (RepositoryManager.load())
2010-11-15 11:37:55 CONFIG: Adding repository fredrepository (RepositoryManager.addRepository())
2010-11-15 11:37:55 CONFIG: Loading renderers from 'file:/Applications/math/rapidminer/lib/rapidminer.jar!/com/rapidminer/resources/ioobjects.xml'. (RendererService.init())
2010-11-15 11:37:55 CONFIG: Loading renderers from 'ioobjects.xml'. (RendererService.init())
2010-11-15 11:37:58 CONFIG: Loading perspectives. (ApplicationPerspectives.loadAll())
initGui(MainFrame mainFrame)
ARGUMENT 'LANGUAGE=en' __ignoré__

2010-11-15 11:38:00 INFO: Connecting to: http://www.myexperiment.org/workflows.xml?num=100 (MyExperimentConnection.connectTo())
2010-11-15 11:38:00 CONFIG: Ignoring update check. Last update check was on Sun Nov 14 19:03:53 CET 2010 (UpdateManager.checkForUpdates())
*****************************************************************************************

Is there another way to provide to the "double-click-rapidminer.jar" the good information about R_HOME and RAPIDMINER_HOME?

zozette

land

Hi,
if you update your R installation, you will need to erase the .RapidMiner5/RLibPath directory and its content, because the stored binary files aren't compatible anymore. They will be downloaded with the next RapidMiner start.

Thanks for the hints on MacOS zozette. Unfortunately I'm not familiar with MacOS and don't know where you can set enviroment variables permanently.

Greetings,
Sebastian

zozette

Hi,
"Unfortunately I'm not familiar with MacOS and don't know where you can set enviroment variables permanently."
Me too ! Snip ! I'am far from being an UNIX-on-Mac guru... But maybe someone on another planet in another millennium may help us ;-)

In my previous post : caution ! When R_HOME is added in the path in the .profile file, do not add it in the script "RapidMinerGUI" (infinite loop of loading).

Dear Sebastian, I have a .RapidMiner5/rLibPath directory, but it is empty. What should I expect to find in it ? There may be there something to dig.

Sincerely,

Zozette

land

Hi,
usually there should be a few libraries that have been downloaded during start of RapidMiner. (Before the downloading the nasty window for selecting a mirror is shown) if you never got that far, it will be empty...

Greetings,
Sebastian

zozette

Hi,

I have found THE solution!

On mac OSX there is a little application called Automator.

1) Open Automator.app
2) choose to create an "Application"
3) on the left most column, choose "utilitaires" (utilities? Sorry my Mac speaks french)
4) On the second column, choose "Exécuter un script shell" (execute a shell script ?)
5) Double click on it
6) In the window that appears, choose (on the left) shell : /bin/bash and on the right "Données en entrée : comme arguments" (input data : as arguments?)
7) paste the following in the text area:
export R_HOME=/Library/Frameworks/R.framework/Resources
export RAPIDMINER_HOME=/Applications/subfolders_where_is_rapidminer/rapidminer
cd /Applications/subfolders_where_is_rapidminer/rapidminer/lib
java -jar rapidminer.jar
6) Save as: name_choosen_by_you
with, file format: application

Now, you have a double-clickable little application that launches RapidMiner without opening terminal.app.
When you quit RapidMiner, the little application quit as well. On my Mac, R extension is OK.

Sorry for my poor english,

Sincerely,

Zozette

land

Hi Zozette,
thanks for this hints. I will collect all of them and will try to combine them to a better way of deploying RapidMiner with R...

Just a little remark, because you might find that you won't have enough memory to do anything inside RapidMiner. If you add -Xmx512m to the java command "java -jar rapidminer.jar -Xmx512m" you can control the amount of memory RapidMiner is allowed to use. In this case it would be 512 mb.

Greetings,
Sebastian

pop

Hello,

the problem for installing the R extension on a MacOs platform lies in the setting of the environement variables. To do so you shloud download this small App on the apple web site that manage environemet variable.

http://www.apple.com/downloads/macosx/system_disk_utilities/environmentvariablepreferencepane.html

With this you can set:
PATH=$PATH:/Library/Frameworks/R.framework/Versions/2.12/Resources/bin:/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rJava/jri
R_HOME=/Library/Frameworks/R.framework/Versions/2.12/Resources

Restart the mac and launch Rapidminer.
When asked for R preferences, you have to point to:
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rJava/jri/libjri.jnilib

This is working for MacOs X 10.6.5, Rapidminer 5.0.10, R 2.12

Regards,
Pop

pleonard

pop wrote:

With this you can set:
PATH=$PATH:/Library/Frameworks/R.framework/Versions/2.12/Resources/bin:/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rJava/jri
R_HOME=/Library/Frameworks/R.framework/Versions/2.12/Resources

This technique is confirmed to work for me with 10.6.6 and R 2.11. BUT ---

It's important to note that variable expansion does NOT work in the ~/.MacOSX/environment.plist file (which is what this System Preference is modifying). So what you really want is:

/opt/local/bin:/usr/local/bin:/usr/bin:/usr/sbin:/bin:/Library/Frameworks/R.framework/Versions/2.11/Resources/bin:/Library/Frameworks/R.framework/Versions/2.11/Resources/library/rJava/jri

or something similar.

Thanks for the solution to a vexing problem!