Re: [R-SIG-Mac] R and Java 10 ➜ rJava not able to build

2018-03-28 Thread Luis Puerto 
Hi Jeff, 

Sorry if I’ve done something wrong posting to more that one list. Perhaps I 
should have written just different emails for each list so people from one list 
don’t reply to the other lists. Apologies for that. 

On another note, thanks for your reply. Let’s hope that we soon can have only 
one version of Java. 


Best Regards
Luis Puerto
http://luisspuerto.net

> On 28 Mar 2018, at 14:10, Prof Brian Ripley  wrote:
> 
> On 27/03/2018 20:25, Luis Puerto wrote:
> ...
>> rJava is not yet compatible with Java 10
> 
> Is the correct answer.  How to work around this is in the current manual, 
> specifically R-admin for R 3.5.0 alpha or R-devel.
> 
> Java 10 has been out for 8 days, and the rJava maintainer was made aware of 
> the issues early this month, several other package maintainers only today.  
> The advice is to stick to an LTS release of Java (currently 8) unless you 
> know what you are doing.
> 
> And don't post to multiple lists!
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford


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Re: [R-SIG-Mac] R and Java 10 ➜ rJava not able to build

2018-03-28 Thread Prof Brian Ripley 

On 27/03/2018 20:25, Luis Puerto wrote:
...

rJava is not yet compatible with Java 10


Is the correct answer.  How to work around this is in the current 
manual, specifically R-admin for R 3.5.0 alpha or R-devel.


Java 10 has been out for 8 days, and the rJava maintainer was made aware 
of the issues early this month, several other package maintainers only 
today.  The advice is to stick to an LTS release of Java (currently 8) 
unless you know what you are doing.


And don't post to multiple lists!

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

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Re: [R-SIG-Mac] [R] R and Java 10 ➜ rJava not able to build

2018-03-28 Thread Jeff Newmiller 
I am not a Mac user, but I do use Linux and I would recommend not running R 
with sudo unless you are an admin ninja. That defensive practice would render 
the answer to your question moot.

It is possible that your problem may have started with inappropriate use of 
sudo in configuring java, but configuring Java is not on-topic here.
-- 
Sent from my phone. Please excuse my brevity.

On March 27, 2018 12:25:33 PM PDT, Luis Puerto  wrote:
>Hi! 
>
>I’m on macOS 10.13.3 and just installed the new Java 10 using Homebrew
>Cask. I also have installed R with Homebrew. Everything seems to work
>fine, however I just get different outputs if I run sudo R CMD
>javareconf or R CMD javareconf. With sudo I get pointed to Java 9 and
>without sudo I get pointed to Java 10. I really don’t know why. 
>
>Without sudo:
>
>$ R CMD javareconf 
>  
>Java interpreter :
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/java
>Java version : 10
>Java home path   :
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home
>Java compiler:
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javac
>Java headers gen.: /usr/bin/javah
>Java archive tool:
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/jar
>Non-system Java on macOS
>
>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
>/usr/local/opt/llvm/bin/clang 
>-I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG
>-I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include
>-I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin
>-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC 
>-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o
>conftest.o
>/usr/local/opt/llvm/bin/clang++ -dynamiclib
>-Wl,-headerpad_max_install_names -undefined dynamic_lookup
>-single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
>-L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o
>conftest.so conftest.o
>-L/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/lib/server
>-ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework
>-Wl,CoreFoundation
>
>
>JAVA_HOME:
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home
>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 /usr/local/Cellar/r/3.4.4/lib/R
>override rw-r--r--  root/admin for
>/usr/local/Cellar/r/3.4.4/lib/R/etc/Makeconf? (y/n [n]) y
>override rw-r--r--  root/admin for
>/usr/local/Cellar/r/3.4.4/lib/R/etc/ldpaths? (y/n [n]) y
>Done.
>With sudo:
>
>$ sudo R CMD javareconf
>  
>Java interpreter :
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/java
>Java version : 9.0.4
>Java home path   :
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home
>Java compiler:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/javac
>Java headers gen.:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/javah
>Java archive tool:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/jar
>Non-system Java on macOS
>
>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
>/usr/local/opt/llvm/bin/clang 
>-I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG
>-I/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include
>-I/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include/darwin
>-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC 
>-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o
>conftest.o
>/usr/local/opt/llvm/bin/clang++ -dynamiclib
>-Wl,-headerpad_max_install_names -undefined dynamic_lookup
>-single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
>-L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o
>conftest.so conftest.o
>-L/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/lib/server
>-ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework
>-Wl,CoreFoundation
>
>
>JAVA_HOME:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home
>Java library path: $(JAVA_HOME)/lib/server
>JNI cpp flags: -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
>JNI linker flags :