[BioC] Failed installing SJava on MacOS
Michael Dondrup
Michael.Dondrup at uni.no
Tue Jan 19 18:35:28 CET 2010
Am Jan 19, 2010 um 5:58 PM schrieb Martin Morgan:
> 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
>
> more below...
Thank you for this information, this seems to be the crucial point, because my install is lacking this file!
I have only these:
Seneca:SJava mdondrup$ find . -name "*.jar"
./org/omegahat/Jars/antlr.jar
./org/omegahat/Jars/Environment.jar
./org/omegahat/Jars/jas.jar
./org/omegahat/Jars/jhall.jar
./org/omegahat/Jars/ROmegahatExamples.jar
I wonder what went wrong, as there was no error message during build. I have to further investigate the sources I think.
Do you know at which point during install the jar's are being built? While the other jar's are already contained in the package,
RJava.jar could be built from the files in inst/org/omegahat/R/Java ,correct?
Thanks again
>
>>> Hi Michael --
>>>
>>> .JavaInit has an argument default=javaConfig() which sets the class path
>>> and other variables. My guess is that javaConfig() needs to be augmented
>>> to return the correct class path. On my system it is
>>>
>>>> javaConfig()@classPath
>>> [1] "<...>/library/SJava/org/omegahat/Jars/Environment.jar"
>>> [2] "<...>/library/SJava/org/.."
>>> [3] "<...>/library/SJava/org/omegahat/Jars/antlr.jar"
>>> [4] "<...>/library/SJava/org/omegahat/Jars/jas.jar"
>>> [5] "<...>/library/SJava/org/omegahat/Jars/jhall.jar"
>>>
>>> where <...> is the path to my R installation.
>>>
>>> Martin
>>
>> Hi Martin,
>> thank you very much for your reply. My configuration looks pretty much like yours. All jars exist and readable.
>> I tried messing around
>> with the paths in addition, adding "/Library/Frameworks/R.framework/Resources/library/SJava/org/" (without the ..), to no avail.
>> Are you using a Mac? It would be good to compare the full output of javaConfig() for a functioning version,
>> maybe you could send that to me?
>> And might be good to know in which jar the class org.omegahat.R.Java.RForeignReference is contained.
>>
>>
>> If that is relevant:
>>
>> java version "1.6.0_17"
>> Java(TM) SE Runtime Environment (build 1.6.0_17-b04-248-10M3025)
>> Java HotSpot(TM) 64-Bit Server VM (build 14.3-b01-101, mixed mode)
>>
>>
>> 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
>
> Slot "properties":
>
>
> EmbeddedInR
>
>
> "true"
>
>
> InterfaceManagerClass
>
>
> "org/omegahat/Interfaces/NativeInterface/OmegaInterfaceManager"
>
>
> ForeignReferenceBaseClass
>
>
> "org/omegahat/R/Java/RJavaInstance"
>
>
> java.compiler
>
>
> "NONE"
>
>
> OMEGA_HOME
>
>
> "/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat"
>
>
> OmegahatSearchPath
> ".,/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat/Environment/Scripts/Run,/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat/Jars/Environment.jar"
>
>
> java.library.path
>
>
> "/home/mtmorgan/arch/x86_64/R-devel/library/SJava/libs"
>
>
>> java.library.path
>> "/Library/Frameworks/R.framework/Resources/library/SJava/libs"
>>
>> Slot "options":
>> character(0)
>>
>> Slot "args":
>> character(0)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>>> During installation I got the following error message, which I suspect to be relevant:
>>>>
>>>> ...
>>>> ** R
>>>> ** inst
>>>> cp: cannot overwrite directory /Library/Frameworks/R.framework/Resources/library/SJava/libs with non-directory inst/libs
>>>> sh: /usr/bin/tarxf: No such file or directory
>>>> ....
>>>>
>>>> I also manually copied src/SJava.so to /Library/Frameworks/R.framework/Resources/library/SJava/libs but that didn't change anything.
>>>> I put the full output of javareconf, R CMD INSTALL, and sessionInfo() here. Any help would be appreciated.
>>>>
>>>> Michael
>>>>
>>>> [snip]
>>>>
>>>>
>>>>
>>>>> sessionInfo()
>>>> R version 2.10.1 (2009-12-14)
>>>> x86_64-apple-darwin9.8.0
>>>>
>>>> locale:
>>>> [1] C
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] SJava_0.72.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.10.1
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>> --
>>> Martin Morgan
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
More information about the Bioconductor
mailing list