Issues with rJava on OS X El Capitan

On 14 Feb 2016, at 23:13, Simon Urbanek <simon.urbanek at r-project.org>

wrote:

Check DYLD_FALLBACK_LIBRARY_PATH - it must include your Java:

Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")

[1]

"/Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/server"

if it doesn't, your R is not correctly configured. Oracle's Java

requires the above setting, it doesn't work without it (unlike the system
Java). The above is set by the R script based on etc/ldpaths - so make sure
that one is correct (it should be by javareconf if your system is setup
correctly).

Thanks; this lead to resolving the problem.
I should have mentioned I was using library(rJava) and the others in the
GUI R.app.

In Terminal R shows

Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")

[1]
"/Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_74.jdk/Contents/Home/jre/lib/server"

as required.


I've had to compile rJava from source as suggested by Brian Ripley (if I
use the binary on CRAN I get  errors)(on OS X 10.11.3).
I've installed the binaries of XLConnect, etc.

I can now run things like XLConnect from R in the Terminal and from bash
scripts.
I can't run anything using rJava in the GUI R.app or in Rstudio.


BTW. R.app ([R.app GUI 1.67 (7129) x86_64-apple-darwin13.4.0]) shows

Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")

[1] ""

and Rstudio (Version 0.99.878) shows this

Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")

[1]
"/Library/Frameworks/R.framework/Resources/lib:/Users/berendhasselman/lib:/usr/local/lib:/usr/lib::"

Where it got "/Users/berendhasselman/lib" from I wouldn't know; the folder
does not exist.

thanks a lot

Berend

Cheers,
Simon


On Feb 14, 2016, at 6:47 AM, Berend Hasselman <bhh at xs4all.nl> wrote:

On 14 Feb 2016, at 12:31, Prof Brian Ripley <ripley at stats.ox.ac.uk>

wrote:

On 14/02/2016 11:24, Berend Hasselman wrote:

On 14 Feb 2016, at 11:48, Prof Brian Ripley <ripley at stats.ox.ac.uk>

wrote:

Your Java is seriously old.  Start by updating it (1.8.0_74 is

current, AFAIK).

I can reproduce this with the CRAN binary packages, but installing

the packages from source works for me on El Capitan (using the CRAN binary
R).  So I suspect a problem with the CRAN binary package of rJava, which
seems to be hard-coded to use /System/Library/Frameworks/JavaVM.framework
and not Oracle Java.

I've just updated to Java 1.8.0_74.
I get the same issues.


And I have now also installed rJava, XLConnect end XLConnectJars from

source.

library(XLConnect) gives this error

<message>
Loading required package: XLConnectJars
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object

'/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so':

dlopen(/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so,
6): Library not loaded: @rpath/libjvm.dylib

Referenced from:

/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so

Reason: image not found
Error: package 'XLConnectJars' could not be loaded
</message>

Apparently rJava.so can't be found. But I had already installed it

from source.

That is not what the message says ... it is libjvm which is not being

found.

Correct. Sorry about that.

Did you re-run R CMD javareconf?  (You might need to reinstall rJava

from source once you do.)

Yes I did and have done so again. I've reinstalled rJava from source

and get the same error and the same output of running otool -L  on rJava.so.

Berend

Output of R CMD javareconf:

Java interpreter : /usr/bin/java
Java version     : 1.8.0_74
Java home path   :

/Library/Java/JavaVirtualMachines/jdk1.8.0_74.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/jdk1.8.0_74.jdk/Contents/Home/jre/../include
-I/Library/Java/JavaVirtualMachines/jdk1.8.0_74.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/jdk1.8.0_74.jdk/Contents/Home/jre/lib/server
-ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation

JAVA_HOME        :

/Library/Java/JavaVirtualMachines/jdk1.8.0_74.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.

I have run otool on the installed rJava.so

otool -L rJava.so
rJava.so:
   rJava.so (compatibility version 0.0.0, current version 0.0.0)
   @rpath/libjvm.dylib (compatibility version 1.0.0, current version

1.0.0)

/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libR.dylib
(compatibility version 3.2.0, current version 3.2.3)

/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 1256.14.0)

   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current

version 1226.10.1)

Berend

On 14/02/2016 09:22, Berend Hasselman wrote:

I have installed rJava, xlsx, xlsxjars, XLConnect and XLConnectJars.

Executing library(xlsx) gives this output

Loading required package: rJava
Loading required package: xlsxjars
Error : .onLoad failed in loadNamespace() for 'xlsx', details:
call: .jinit()
error: JNI_GetCreatedJavaVMs returned -1

Error: package or namespace load failed for 'xlsx'
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.


Executing library(XLConnect) gives this output

Loading required package: XLConnectJars
Error : .onLoad failed in loadNamespace() for 'XLConnectJars',

details:

call: .jinit()
error: JNI_GetCreatedJavaVMs returned -1

Error: package 'XLConnectJars' could not be loaded
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.


sessionInfo (after library(xlsx) and library(XLConnect)) and

javareconf output below.

What is going on?
What is the solution for this problem?

Berend Hasselman


SessionInfo:

R version 3.2.3 Patched (2016-02-13 r70160)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] xlsxjars_0.6.1 rJava_0.9-8

loaded via a namespace (and not attached):
[1] tools_3.2.3


Output of R CMD javareconf

[.../~]: R CMD javareconf -n
Java interpreter : /usr/bin/java
Java version     : 1.8.0_25
Java home path   :

/Library/Java/JavaVirtualMachines/jdk1.8.0_25.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/jdk1.8.0_25.jdk/Contents/Home/jre/../include
-I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.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/jdk1.8.0_25.jdk/Contents/Home/jre/lib/server
-ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation

JAVA_HOME        :

/Library/Java/JavaVirtualMachines/jdk1.8.0_25.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

--
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

--
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford