R help - Aug 2012 - littler and rJava

Hello list,

I'm having some difficulty getting rJava to load in littler. Even
after a R CMD javareconf and a reinstall of littler, I get this:
jlaing at xenon:~$ r -e "require(rJava)"
Loading required package: rJava
Loading required package: methods
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object
'/usr/local/lib/R/site-library/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory

It works fine with Rscript:
jlaing at xenon:~$ Rscript -e "require(rJava)"
Loading required package: rJava
Loading required package: methods

Presumably my load paths are misconfigured, but I can't figure out where:
jlaing at xenon:~$ R CMD javareconf
Java interpreter : /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java
Java version     : 1.6.0_24
Java home path   : /usr/lib/jvm/java-6-openjdk-amd64/jre
Java compiler    : /usr/lib/jvm/java-6-openjdk-amd64/jre/../bin/javac
Java headers gen.: /usr/lib/jvm/java-6-openjdk-amd64/jre/../bin/javah
Java archive tool: /usr/lib/jvm/java-6-openjdk-amd64/jre/../bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64
-L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni
-L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni
-L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I$(JAVA_HOME)/../include

System info:
jlaing at xenon:~$ R --version
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

jlaing at xenon:~$ r --version
r ('littler') version 0.1.5
        svn revision 185 as of 2011-09-17 09:35:56
        built at 15:30:55 on Sep 17 2011
        using GNU R Version 2.13.1 (2011-07-08)

Copyright (C) 2006 - 2011 Jeffrey Horner and Dirk Eddelbuettel


Thanks,
John

John,

I see this:

edd at max:~$ r -e'require(rJava)'
Loading required package: rJava
Loading required package: methods
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object
'/usr/lib/R/site-library/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory

but also

edd at max:~$ locate libjvm.so
/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/cacao/libjvm.so
/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server/libjvm.so
edd at max:~$
LD_LIBRARY_PATH="/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server"
r -e'require(rJava)'
Loading required package: rJava
Loading required package: methods
edd at max:~$ 

Java is a bit of a moving target. We did add 

edd at max:~/svn/littler$ ./configure --help|grep java
  --with-java-libs        Link littler to R's java libraries
edd at max:~/svn/littler$ 

a while back but that may not be sufficient.  Would you have time to poke
around at your end how we could make this better (presuming that you want
something more solid than the LD_LIBRARY_PATH adjustment you could also do on
your system-side).

Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

Hi:

I am trying to understand the link between ".csv" and 
".rda" files.
Is there any easy to follow tutorial on this?

(I could do some of the operations below, but I got lost in the details.)

1.  Reading .rda file ?

data <- load("profit.rda")         # supposed to have four variable
--y
x1 x2 state_name

--how do I find out about the variable names,
--take the log of y and x1
--extract y and calculate mean etc..

(I want to use it in lm regression lny = f(lnx1,x2))

****************

2. How could I save this profit.rda file as a csv file  with the 
variable names attached?
I tried doing this:

profit_data <- load("profit.rda")

#Could I do this?
write.csv(profit_data, file="profit.csv", col.names=TRUE)
data2 <- read.csv("profit.csv", head = TRUE)

# saving .rda file without the header?
write.csv(profit_data, file="profit2.csv", col.names=FALSE)

***********

3. Creating a .rda file  from a csv file  using the save command

data2 <- read.csv("poverty.csv", head = T, sep = ",")   #
poverty.csv
file has 4 variables -- Q L K  country_name
save(data2, file="poverty.rda")

--How do I  attach names from the csv file to this .rda file?



Best,
Alok Bohara
UNM