R SIG Debian - Mar 2010 - rJava works on karmic for root but not for user sean

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

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
>
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