[BioC] Failed installing SJava on MacOS

[Seth Falcon]

On 1/19/10 8:58 AM, Martin Morgan wrote:
> Michael Dondrup wrote:
>> Am Jan 19, 2010 um 3:39 PM schrieb Martin Morgan:
>>
>>> Michael Dondrup wrote:
>>>> Hi,
>>>> I would like to use RWebServices and therefore SJava on Mac OS snow leopard. The documentation does not explicitly mention Mac os, so it's
>>>> maybe not supported, but i hope it can be made working anyway.
>>>> Maybe somebody out there got this configuration running and could help? I am trying to install SJava 0.72. I try the following:
>>>>
>>>>> library(SJava)
>>>> Load the Java VM with .JavaInit()
>>>>> .JavaInit()
>>>>> example(.Java)
>>>> .Java>    v<- .JavaConstructor("java.util.Vector", as.integer(10))
>>>>
>>>> .Java>   .Java(v, "add", "A string element")
>>>> Error in .Java(v, "add", "A string element") :
>>>>   Can't find org.omegahat.R.Java.RForeignReference
>
> this is in org.omegahat/Jars/RJava.jar, e.g.,
>
>    jar tf org.omegahat/Jars/RJava.jar
>

Curious, as this jar did not appear on your classpath in your previous mail.

I'm able to reproduce the error on my Snow Leopard laptop.  I also 
notice that I don't have this jar.  There are .class files under the 
package structure in org/omegahat/R/Java/*.class. 
RForeignReference.class is among them and this would seem to be the 
purpose of the "<...>/SJava/org/.." entry in class path.

> more below...
>> Here is the output of javaConfig().
>>
>>> javaConfig()
>> An object of class "JavaConfiguration"
>> Slot "classPath":
>> [1] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/Environment.jar"
>> [2] "/Library/Frameworks/R.framework/Resources/library/SJava/org/.."
>> [3] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/antlr.jar"
>> [4] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/jas.jar"
>> [5] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/jhall.jar"
>>
>> Slot "libraryPath":
>> [1] "/Library/Frameworks/R.framework/Resources/library/SJava/libs"
>>
>> Slot "properties":
>>                                                                   EmbeddedInR
>>                                                                        "true"
>>                                                         InterfaceManagerClass
>>               "org/omegahat/Interfaces/NativeInterface/OmegaInterfaceManager"
>>                                                     ForeignReferenceBaseClass
>>                                           "org/omegahat/R/Java/RJavaInstance"
>>                                                                 java.compiler
>>                                                                        "NONE"
>>                                                                    OMEGA_HOME
>>        "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat"
>>                                                            OmegahatSearchPath
>> ".,${OMEGA_HOME}/Environment/Scripts/Run,${OMEGA_HOME}/Jars/Environment.jar"
>
> My javaConfig() (not on Mac) has ${OMEGA_HOME} expanded

Mine is not expanded.  I tried expanding it, but that didn't seem to 
make a difference either. :-(


-- 
Seth Falcon
Bioconductor Core Team | FHCRC