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$(JAVA_HOME)/include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/local/Cellar/r/3.4.4/lib/R
Done.
The result of be pointed to Java 10 is rJava package not be able to build.
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
/usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah" (-1)
make[2]: *** [org_rosuda_JRI_Rengine.h] Error 2
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ?rJava?
* removing ?/Users/lpuerto/Library/R/3.x/library/rJava?
* restoring previous ?/Users/lpuerto/Library/R/3.x/library/rJava?
The downloaded source packages are in
?/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5h0000gn/T/RtmpT2kJMY/downloaded_packages?
Warning message:
In install.packages("rJava", repos = "cloud.r-project.org") :
installation of package ?rJava? had non-zero exit status
I've checked and there isn't a javah on /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah as in Java 9. Which make me think that either R CMD javareconf isn?t working properly with Java 10 or rJava is not yet compatible with Java 10.
Does anyone know what is going on?
Thanks!
PS/ I?ve opened an issue <https://github.com/s-u/rJava/issues/137> in rJava?s github and a question in stackoverflow <https://stackoverflow.com/questions/49519007/sudo-r-cmd-javareconf-and-r-cmd-javareconf-produce-different-output-with-java-10>.
Best Regards
Luis Puerto
http://luisspuerto.net
R and Java 10 ➜ rJava not able to build
5 messages · Luis Puerto, Jeff Newmiller, Brian Ripley +1 more
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 <luiss.puerto at gmail.com> 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$(JAVA_HOME)/include/darwin
>JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>Updating Java configuration in /usr/local/Cellar/r/3.4.4/lib/R
>Done.
>The result of be pointed to Java 10 is rJava package not be able to
>build.
>
>warning: [options] bootstrap class path not set in conjunction with
>-source 6
>warning: [options] source value 6 is obsolete and will be removed in a
>future release
>warning: [options] target value 1.6 is obsolete and will be removed in
>a future release
>warning: [options] To suppress warnings about obsolete options, use
>-Xlint:-options.
>Note: Some input files use or override a deprecated API.
>Note: Recompile with -Xlint:deprecation for details.
>Note: Some input files use unchecked or unsafe operations.
>Note: Recompile with -Xlint:unchecked for details.
>4 warnings
>/usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
>Unable to locate an executable at
>"/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah"
>(-1)
>make[2]: *** [org_rosuda_JRI_Rengine.h] Error 2
>make[1]: *** [src/JRI.jar] Error 2
>make: *** [jri] Error 2
>ERROR: compilation failed for package ?rJava?
>* removing ?/Users/lpuerto/Library/R/3.x/library/rJava?
>* restoring previous ?/Users/lpuerto/Library/R/3.x/library/rJava?
>
>The downloaded source packages are in
>?/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5h0000gn/T/RtmpT2kJMY/downloaded_packages?
>Warning message:
>In install.packages("rJava", repos = "cloud.r-project.org") :
> installation of package ?rJava? had non-zero exit status
>I've checked and there isn't a javah on
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah as
>in Java 9. Which make me think that either R CMD javareconf isn?t
>working properly with Java 10 or rJava is not yet compatible with Java
>10.
>
>Does anyone know what is going on?
>
>Thanks!
>
>PS/ I?ve opened an issue <https://github.com/s-u/rJava/issues/137> in
>rJava?s github and a question in stackoverflow
><https://stackoverflow.com/questions/49519007/sudo-r-cmd-javareconf-and-r-cmd-javareconf-produce-different-output-with-java-10>.
>
>
>
>Best Regards
>Luis Puerto
>http://luisspuerto.net
>
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
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, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford
On Tue, Mar 27, 2018 at 9:39 PM, Jeff Newmiller
<jdnewmil at dcn.davis.ca.us> wrote:
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.
I don't think this is reasonable advice, given that both R CMD javareconf and the rJava package makefile explicitly instruct you to run R CMD javareconf as root.
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.
I also disagree with this. You don't have to answer if you don't want to, but the question is about getting the rJava package to work with Java JDK 10, and I for one consider that to be on-topic here. Best, Ista
-- Sent from my phone. Please excuse my brevity. On March 27, 2018 12:25:33 PM PDT, Luis Puerto <luiss.puerto at gmail.com> 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$(JAVA_HOME)/include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/local/Cellar/r/3.4.4/lib/R
Done.
The result of be pointed to Java 10 is rJava package not be able to
build.
warning: [options] bootstrap class path not set in conjunction with
-source 6
warning: [options] source value 6 is obsolete and will be removed in a
future release
warning: [options] target value 1.6 is obsolete and will be removed in
a future release
warning: [options] To suppress warnings about obsolete options, use
-Xlint:-options.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
/usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
Unable to locate an executable at
"/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah"
(-1)
make[2]: *** [org_rosuda_JRI_Rengine.h] Error 2
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ?rJava?
* removing ?/Users/lpuerto/Library/R/3.x/library/rJava?
* restoring previous ?/Users/lpuerto/Library/R/3.x/library/rJava?
The downloaded source packages are in
?/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5h0000gn/T/RtmpT2kJMY/downloaded_packages?
Warning message:
In install.packages("rJava", repos = "cloud.r-project.org") :
installation of package ?rJava? had non-zero exit status
I've checked and there isn't a javah on
/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah as
in Java 9. Which make me think that either R CMD javareconf isn?t
working properly with Java 10 or rJava is not yet compatible with Java
10.
Does anyone know what is going on?
Thanks!
PS/ I?ve opened an issue <https://github.com/s-u/rJava/issues/137> in
rJava?s github and a question in stackoverflow
<https://stackoverflow.com/questions/49519007/sudo-r-cmd-javareconf-and-r-cmd-javareconf-produce-different-output-with-java-10>.
Best Regards
Luis Puerto
http://luisspuerto.net
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______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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 <ripley at stats.ox.ac.uk> 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, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford