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

[MacQueen, Don]

Berend,

I now have  working packages, thanks!

The key was installing rJava from source rather than binary (binary being the default when using install.packages(); I had already run javareconf so there was no change there).

And apologies to everyone for failing to search hard enough to find the solution that was already available on R-sig-mac. As an aside, yes, my Java is indeed old, but my institution, for whatever reason, is not offering a more recent version in its software deployment system.

-Don

Don MacQueen
Lawrence Livermore National Laboratory
macqueen1 at llnl.gov
925-423-1062



> On Jun 18, 2016, at 12:43 AM, Berend Hasselman <bhh at xs4all.nl> wrote:
> 
> 
>> 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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