[R-sig-Debian] rJava works on karmic for root but not for user sean
Sean O'Riordain
seanpor at acm.org
Wed Mar 10 06:38:01 CET 2010
Thanks Whit! That did the trick!!!
cheers,
Seán
On Tue, Mar 9, 2010 at 9:32 PM, Whit Armstrong <armstrong.whit at gmail.com> wrote:
> make sure you don't have JAVA_HOME set in your environment for user sean.
>
> just a guess, but have been stung by that one before.
>
> -Whit
>
>
> On Tue, Mar 9, 2010 at 1:32 PM, Sean O'Riordain <seanpor at acm.org> wrote:
>> Good afternoon,
>> A strange one - library(rJava) works for root but not for user sean
>>
>> On 64-bit Ubuntu 9.10, using R as root (sudo -i), I can say
>> library(rJava)
>> and it works fine with no error message of any kind. But logged in as
>> myself user "sean", it can't start...
>>
>> sean at SeansPC:~$ R --no-save --vanilla
>>
>> R version 2.10.1 (2009-12-14)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> library(rJava)
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared library
>> '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
>> libjvm.so: cannot open shared object file: No such file or directory
>> Error : .onLoad failed in 'loadNamespace' for 'rJava'
>> Error: package/namespace load failed for 'rJava'
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-pc-linux-gnu
>>
>> locale:
>> [1] LC_CTYPE=en_IE.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_IE.UTF-8 LC_COLLATE=en_IE.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_IE.UTF-8
>> [7] LC_PAPER=en_IE.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>>
>>
>> root at SeansPC:~# R CMD javareconf
>> Java interpreter : /usr/bin/java
>> Java version : 1.6.0_15
>> Java home path : /usr/lib/jvm/java-6-sun-1.6.0.15/jre
>> Java compiler : /usr/bin/javac
>> Java headers gen.: /usr/bin/javah
>> Java archive tool: /usr/bin/jar
>> Java library path:
>> $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
>> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
>> -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
>> -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
>> JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
>>
>> Updating Java configuration in /etc/R
>> Done.
>>
>>
>>
>> The sessionInfo is identical for root
>>
>> I've un-installed and re-installed r-base and r-cran-*
>>
>> I've done a reboot; I've done 'R CMD javareconf'
>>
>> The file /usr/local/lib/R/site-library/rJava/libs/rJava.so and any
>> nearby files and paths are readable by user sean...
>>
>> I've searched the archives, I've googled... (possibly missing some
>> vital clue of course!)
>>
>> I've removed the personal R library completely - I've checked libPath()
>>
>> java is available at the commandline both as root and as sean
>>
>> I've tried adding files to a new file in /etc/ld.so.conf.d and doing
>> an ldconfig ... but I can't see how this would be different for root
>> and sean.
>>
>> The only thing that I think changed was there was various ubuntu
>> updates this morning which asked for a reboot - so I did... and was
>> unable to go with the latest kernel so I'm with a previous version -
>> I'm not sure it is the same as before.
>>
>> If I say do a R CMD javareconf I get different results which may be a
>> clue... but it does appear to point to the same place in the end...
>>
>> sean at SeansPC:~$ R CMD javareconf
>> Java interpreter : /usr/lib/jvm/java-6-sun-1.6.0.15/jre/bin/java
>> Java version : 1.6.0_15
>> Java home path : /usr/lib/jvm/java-6-sun-1.6.0.15
>> Java compiler : /usr/lib/jvm/java-6-sun-1.6.0.15/bin/javac
>> Java headers gen.: /usr/lib/jvm/java-6-sun-1.6.0.15/bin/javah
>> Java archive tool: /usr/lib/jvm/java-6-sun-1.6.0.15/bin/jar
>> Java library path:
>> $(JAVA_HOME)/jre/lib/amd64/server:$(JAVA_HOME)/jre/lib/amd64:$(JAVA_HOME)/jre/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
>> JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server
>> -L$(JAVA_HOME)/jre/lib/amd64 -L$(JAVA_HOME)/jre/../lib/amd64 -L
>> -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
>> JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
>>
>> Updating Java configuration in /etc/R
>> /usr/lib64/R/bin/javareconf: line 323: /etc/R/Makeconf.new: Permission denied
>> *** cannot create /etc/R/Makeconf.new
>> *** Please run as root if required.
>> sean at SeansPC:~$ sudo -i
>> [sudo] password for sean:
>> root at SeansPC:~# R CMD javareconf
>> Java interpreter : /usr/bin/java
>> Java version : 1.6.0_15
>> Java home path : /usr/lib/jvm/java-6-sun-1.6.0.15/jre
>> Java compiler : /usr/bin/javac
>> Java headers gen.: /usr/bin/javah
>> Java archive tool: /usr/bin/jar
>> Java library path:
>> $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
>> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
>> -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
>> -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
>> JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
>>
>> Updating Java configuration in /etc/R
>> Done.
>>
>> Any help would be appreciated.
>>
>> Thanks in advance,
>> Seán
>>
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