[R-SIG-Mac] Problem with RJDBC in OS X 10.11

[Berend Hasselman]

> On 18 Jun 2016, at 00:28, MacQueen, Don <macqueen1 at llnl.gov> wrote:
> 
> I’m not sure the best place to ask about this, so I’ll start here, since the problem appears to be configuring Java on a Mac to support R packages. Unfortunately, my understanding of how to configure and manage Java is essentially non-existent, so any suggestions would be much appreciated. 
> 
> I have a script using RJDBC that is working on a Mac running OS X 10.10.5. The same script, with the same JDBC .jar files from Oracle, is not working on an OS X 10.11.4 machine, as shown below. Other packages that depend on Java, such as xlsx, are not working either.
> 
> I have run R CMD javareconf to no avail (output below).
> 
> The software management system used by our IT department claims that "Oracle Java 1.7 SDK and JRE" are installed.
> 

I had similar issues with rJava. See this thread: https://stat.ethz.ch/pipermail/r-sig-mac/2016-February/011836.html

I made a shell script for reinstalling rJava whenever the R version changes.
It runs in the folder where you have the rJava source tarball.

<script>
R -e 'Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")'
R CMD javareconf
R -e 'Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")'

RMAINLIB="$(R RHOME)/library"
# install rJava from source in to main library
R CMD INSTALL --library="$RMAINLIB" rJava_0.9-8.tar.gz > install.out
</script>

I've just tested this after removing the installed version of rJava.
I can load things like XLConnect etc. without problems.

Then you can use rJava etc. with R in Terminal. Using rJava doesn't work in/with R GUI.

Berend


> -Don
> 
> 
>> jdbm <- JDBC('oracle.jdbc.OracleDriver', '/opt/ora11g/instantclient_11_2/ojdbc6.jar', "`")
> JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
> JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
> JavaVM FATAL: Failed to load the jvm library.
> Error in .jinit(classPath) : JNI_GetCreatedJavaVMs returned -1
> 
>> sessionInfo()
> R version 3.3.0 (2016-05-03)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.11.4 (El Capitan)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RJDBC_0.2-5 rJava_0.9-8 DBI_0.4-1  
> 
> 
> 
> [macqueen1-ml:~]% sudo R CMD javareconf
> 
> Java interpreter : /usr/bin/java
> Java version     : 1.7.0_101
> Java home path   : /Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre
> Java compiler    : /usr/bin/javac
> Java headers gen.: /usr/bin/javah
> Java archive tool: /usr/bin/jar
> Non-system Java on OS X
> 
> trying to compile and link a JNI program 
> detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
> detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c conftest.c -o conftest.o
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> 
> 
> JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre
> Java library path: $(JAVA_HOME)/lib/server
> JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
> JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
> Updating Java configuration in /Library/Frameworks/R.framework/Resources
> Done.
> 
> 
> Also:
> [macqueen1-ml:~]% java -version
> java version "1.7.0_101"
> Java(TM) SE Runtime Environment (build 1.7.0_101-b14)
> Java HotSpot(TM) 64-Bit Server VM (build 24.101-b14, mixed mode)
> 
> 
> 
> Don MacQueen
> Lawrence Livermore National Laboratory
> macqueen1 at llnl.gov
> 925-423-1062
> 
> 
> 
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