javareconf issue

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

javareconf issue

rosseji
Hi,

Wasn't able to see a bug report on this issue yet... Hope I'm not doublng
up.

There seems to be little info around for what "R CMD javareconf" does but
it has some deprecation errors seemingly.

On running cmd in terminal:

Java interpreter : /usr/bin/java

Java version     : 9

Java home path   : /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home

Java compiler    : /usr/bin/javac

Java headers gen.: /usr/bin/javah

Java archive tool: /usr/bin/jar

System Java on macOS


*trying to compile and link a JNI program *

*detected JNI cpp flags    :
-I/System/Library/Frameworks/JavaVM.framework/Headers*

*detected JNI linker flags : -framework JavaVM*

*clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/System/Library/Frameworks/JavaVM.framework/Headers  -I/usr/local/include
  -fPIC  -Wall -g -O2  -c conftest.c -o conftest.o*

*conftest.c:4:5: warning: 'JNI_CreateJavaVM' is deprecated
[-Wdeprecated-declarations]*

*    JNI_CreateJavaVM(0, 0, 0);*

*    ^*

*/System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1936:39: note:
'JNI_CreateJavaVM' has*

*      been explicitly marked deprecated here*

*_JNI_IMPORT_OR_EXPORT_ __attribute__((deprecated)) jint JNICALL*

*                                      ^*

*1 warning generated.*

*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 -framework JavaVM
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation*



*JAVA_HOME        :
/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home*

*Java library path: *

*JNI cpp flags    : -I/System/Library/Frameworks/JavaVM.framework/Headers*

*JNI linker flags : -framework JavaVM*

*Updating Java configuration in /Library/Frameworks/R.framework/Resources*

*Done.*

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Reply | Threaded
Open this post in threaded view
|

Re: javareconf issue

Prof Brian Ripley
On 27/10/2017 04:13, rosseji wrote:

Using a real name and a signature are regarded as polite here.

> Hi,
>
> Wasn't able to see a bug report on this issue yet... Hope I'm not doublng
> up.

This is a problem on your system.  Also, macOS issues should be reported
to R-sig-mac ... and you should give the 'at a minimum' information
requested by the posting guide.

> There seems to be little info around for what "R CMD javareconf" does but
> it has some deprecation errors seemingly.

See R CMD javareconf --help , and the R-admin manual.

>
> On running cmd in terminal:
>
> Java interpreter : /usr/bin/java
>
> Java version     : 9
>
> Java home path   : /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home
>
> Java compiler    : /usr/bin/javac
>
> Java headers gen.: /usr/bin/javah
>
> Java archive tool: /usr/bin/jar
>
> System Java on macOS

Try updating your R (as suggested by the posting guide): javareconf did
not detect Java 9 on macOS until the it was released recently.  You are
trying to use an obsolete system installation of Java (not Oracle Java).

 From the NEWS for R 3.4.2.patched (and R-devel)

     • R CMD javareconf has been updated to recognize the use of a Java
       9 SDK on macOS.


>
>
> *trying to compile and link a JNI program *
>
> *detected JNI cpp flags    :
> -I/System/Library/Frameworks/JavaVM.framework/Headers*
>
> *detected JNI linker flags : -framework JavaVM*
>
> *clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/System/Library/Frameworks/JavaVM.framework/Headers  -I/usr/local/include
>    -fPIC  -Wall -g -O2  -c conftest.c -o conftest.o*
>
> *conftest.c:4:5: warning: 'JNI_CreateJavaVM' is deprecated
> [-Wdeprecated-declarations]*
>
> *    JNI_CreateJavaVM(0, 0, 0);*
>
> *    ^*
>
> */System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1936:39: note:
> 'JNI_CreateJavaVM' has*
>
> *      been explicitly marked deprecated here*
>
> *_JNI_IMPORT_OR_EXPORT_ __attribute__((deprecated)) jint JNICALL*
>
> *                                      ^*
>
> *1 warning generated.*
>
> *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 -framework JavaVM
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation*
>
>
>
> *JAVA_HOME        :
> /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home*
>
> *Java library path: *
>
> *JNI cpp flags    : -I/System/Library/Frameworks/JavaVM.framework/Headers*
>
> *JNI linker flags : -framework JavaVM*
>
> *Updating Java configuration in /Library/Frameworks/R.framework/Resources*
>
> *Done.*
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


--
Brian D. Ripley,                  [hidden email]
Emeritus Professor of Applied Statistics, University of Oxford

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel