[R-SIG-Mac] Problem with RJDBC in OS X 10.11
David Winsemius
dwinsemius at comcast.net
Sat Jun 18 17:04:23 CEST 2016
> On Jun 18, 2016, at 4:32 AM, Charles DiMaggio <charles.dimaggio at gmail.com> wrote:
>
> Recently came up against the same issue with package �RNetLogo�, so appears to not be an isolated issue. Solution for me was to
>
> (1) ensure latest version of java (type "java -version" without the quotes in your terminal), if less than 1.8, install Java SE Development Kit 8u91 (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html) and
>
> (2) run the program through JGR. I needed to tweak the settings a bit when running JGR:
>
> Sys.setenv(NOAWT=1)
> library(JGR)
> Sys.unsetenv("NOAWT")
> JGR()
>
> Wasn�t entirely happy about having to leave my preferred editor (Textmate), but it worked.
>
> Cheers
>
> Charles
> Charles DiMaggio, PhD, MPH
> Professor of Surgery and Population Health
>
I recently had failure on an El Capitan machine running R 3.3.0 RC to load pkg:XLConnect and got identical message attempting to load pkg:xlsx.
#------------
> library(XLConnect)
Loading required package: XLConnectJars
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so
Reason: image not found
Error: package ‘XLConnectJars’ could not be loaded
#------------
Searching StackOverflow I found an answer that reported success with this system level incantation:
david-winsemiuss-mac-pro:~ davidwinsemius$ sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
Password:
# I (think) this creates a link to the current libjvm in the "newly blessed" OSX library location under the tightened OSX rules of user engagement. Then success with both packages loading. Now get:
$ java -version
java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(™) 64-Bit Server VM (build 25.65-b01, mixed mode)
I didn't know if my R sessions would have the same result, since I had both a 1.6 which I thought was the designated Java version for R, and a 1.8 version of the Java RTE, but seems I'm now simply using 1.8.
> system("java -version")
java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(™) 64-Bit Server VM (build 25.65-b01, mixed mode)
>
> On Jun 18, 2016, at 3:43 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
>>>
>>>
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
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David Winsemius
Alameda, CA, USA
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