Strange error from R interactive nodes

KNIME Extensions Scripting
#1

Hi Folks,

I am running knime on a linux (redhat) workstation and each time I try to do anything with an iterative R node I get this message

Error in unique.default(unlist(lapply(x, length))) : 
  3 arguments passed to .Internal(unique) which requires 4
Error in unique.default(unlist(lapply(x, length))) : 
  3 arguments passed to .Internal(unique) which requires 4
Error in unique.default(unlist(lapply(x, length))) : 
  3 arguments passed to .Internal(unique) which requires 4

this happen even before I edit the R script window and also for all the nodes in the category: snippet, table to R, source etc.

have you seen something like this before?

thanks a lot

Giovanni

 

#2

Hi Giovanni,

I am trying to find out the reason for the warning message. Could you please tell me the version of your R installation? Is it a 32bit auch a 64bit system?

Heiko

#3

Hi Hofer,

the R version is 2.13.2 (2011-09-30) and it's a 64 bit system

thanks for looking into this

 

Giovanni

#4

This problem has been addressed and fixed in KNIME 2.9

#5

Hi Gabriel,

I upgraded to 2.9.1 but I still get the same error. is there any other upgrade or change I need to do?

thanks a lot

 

Giovanni

#6

Sorry for that. Can you please check the steps as described in our faq entry: http://tech.knime.org/faq#q25

#7

Gabriel,

it looks like my problem is intalling rJava on my Centos system: I've tried every suggestion found on different forums and I still can't make it work.

very frustrating!

I guess I'll stick with the non-interactive nodes untill I find a way to install rJava

thanks

Giovanni

#8

Hello Giovanni,

What is your problem to install rJava. I also have a CentOS system and it was a little bit difficult but I finally found a way.

However, I still cannot use Knime with my R installation. In the faq you say:

3. Add a system property to your knime.ini:

-Djava.library.path=C:\...library\3.0\rJava\jri\x64

pointing to the jri.dll (make sure you point to x64 when using 64bit)

But on Linux, I think there is no dll file. Anyway, in my local installation /opt/R-2.15.2/library/rJava/jri/, there are 2 archives JRIEngine.jar and REngine.jar.

Is there a change to make it work in a different way or did I do something wrong?

By the way, on windows it works perfectly!

Nicolas
 

#9

I believe on linux it is either a .jnilib, or a .so (I can't recall which, but on mac it is a .jnilib). Have you tried to use "/opt/R-2.15.2/library/rJava/jri/" as your path?  I think that should work. 

Regards,

Aaron

 

 

#10

Unfortunately, I cannot find any jri.so or jri.jnilib.

I also tried -Djava.library.path=/opt/R-2.15.2/library/rJava/jri/ in my knime.ini but it does not change anything.

By the way, the R snippet console displays:

R cannot be intialized.
Cannot load JRI native library

#11

From inside R, you should be able to find the path to rJava with: path.package("rJava")

also, the path to your executable should be accessible in R with: R.home() 

Keep us posted on your progress. 

Regards,

Aaron

#12

Hello Aaron,

> library(rJava)
> path.package("rJava")
[1] "/opt/R-2.15.2/library/rJava"
> R.home()
[1] "/opt/R-2.15.2"

R home is correctly set in Knime preferences for "R (labs)" and I add -Djava.library.path=/opt/R-2.15.2/library/rJava to knime.ini, but R still cannot be initialized is Knime.

Is there an environment variable I should add to my .bashrc? Currently I have:

export R_HOME=/opt/R-2.15.2/
export JAVA_HOME=/usr/java/jdk1.7.0_25/jre/
export PATH=$PATH:$JAVA_HOME/bin

Thanks

Nicolas

#13

I found a CentOS installation, and the path, as adapted for your system would be:

/opt/R-2.15.2/library/rJava/jri

Note the lack of a trailing slash.  Maybe try that?

Also, make sure that org.knime.features.rengine.r2.feature.group is uninstalled as per the FAQ.

 

 

#14

Unfortunately, with ou without slash, it does not change the result.

org.knime.features.rengine.r2.feature.group is uninstalled.

#15

Hi,

I had exactly the same problem here. In my case I found a solution to get R initialized which is reported below. (Unfortunately, I got stuck with a subsequent problem: http://tech.knime.org/forum/r-statistics-nodes-and-integration/r-interactive-error-in-identicalsimplify-false. Maybe you can help there?)

I'm running a Linux 64bit system, Knime 2.9.2, R 3.0.3, and followed the steps in the FAQ: http://tech.knime.org/faq#q25.

As mentioned in #8 above, my $R_HOME/library/rJava/jri/ only contains the two archives JRIEngine.jar and REngine.jar, but no *.so or *.jnilib and no x64 subfolder. Within the rJava folder, I only found one *.so file, which is rJava.so inside the $R_HOME/library/rJava/libs/ folder. However, pointing the knime.ini to this path doesn't make any difference. Whenever I tried to run (or configure) an R node, I got an error that R could not be initialized.

The important point was that I compiled R from the sources! When installing rJava within R, I found the following log messages:

checking whether JRI should be compiled (autodetect)... no
...
checking whether JRI is requested... no

So I tried to explicitly request JRI using the following command:

  > install.packages("rJava", configure.args=c("--enable-jri"))

which in turn required the R system to be build as a shared library:

  $ ./configure --enable-R-shlib  
  $ make

Finally, after re-building R with "enable-R-shlib" option and subsequently installing rJava (which than automatically enabled jri), I got a "libjri.so" in the folder $R_HOME/library/rJava/jri/ to which I pointed the knime.ini, and Knime is able to initialize R 3.0.3.

Best, Andreas

 

#16

Hello Andreas,

I followed what you did but at the end I still cannot initialize R in Knime...

I am curious to know which version of Java you are using?

Thanks

Nicolas

#17

Hi Nicolas,

in Knime the included JRE ( java version "1.7.0_07") is used. In R, our system default is used (java version "1.7.0_21").

Andreas

 

#18

I am seeing this problem as I attempt to move from Knime 2.9.4 to 2.10.0.

The R Snippet node in 2.9.4 was working fine, but when I attempt to configure the R Snippet node of 2.10.0 I get this in the R Snippet console:

  Error in unique.default(unlist(lapply(x, length))) :
    4 arguments passed to .Internal(unique) which requires 3
  Error in unique.default(unlist(lapply(x, length))) :
    4 arguments passed to .Internal(unique) which requires 3
  Error in unique.default(unlist(lapply(x, length))) :
    4 arguments passed to .Internal(unique) which requires 3

I found this thread and followed the instructions referred to above (http://tech.knime.org/faq#q25).  I added -Djava.library.path=/apps/source/R-3.0.2-mkl/lib64/R/library/rJava/jri to my knime.ini file.  Within that directory I see a libjri.so file.  When I attempted to remove org.knime.features.rengine.r2 feature.group it was already not present.  Among the features groups that are present is org.knime.features.r .

Thanks, Doug