rJava works on karmic for root but not for user sean
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, Se?n
_______________________________________________ R-SIG-Debian mailing list R-SIG-Debian at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian