sudo R CMD javareconf and R CMD javareconf produce different output with Java 10

[luispuerto]

I just posted this in stackoverflow but I don't know if it's something to do with rJava. Perhaps, since it seems that with Java 10 rJava isn't building.

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I on macOS 10.13.3 and I just update to java 10 and when I've tried to update R to it I just realize that I get two different outputs if I run R CMD javareconf with or without sudo. If I run with sudo it sticks to Java 9, but if I run without sudo it configures java 10.

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 end result of this is: without sudo and in consequence with java 10, rJava doesn't build. With sudo and java 9, rJava build normally.

Does anyone know what is going on?

PS/ I have set $JAVA_HOME to JAVA_HOME="$(/usr/libexec/java_home)" in my zsh and bash profile.

PS2/ just for the sake of having all the info in one place... when building rJava with Java 10 I get the following error:

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.

[JackHo327]

Hi @luisspuerto , I also met the same problem here.
I also checked you thread here. Nice post!

---

Thanks @s-u , I tried that and it is working right now 👍

[s-u]

This has been worked around in latest rJava - please try rJava 0.9-10

[gsgxnet]

rJava 0.9-10 does not install with openjdk 10.0.1 on openSUSE Tumbleweed:

install.packages('rJava',,'http://www.rforge.net/')
Installing package into ‘/home/gsd/R/x86_64-suse-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
versuche URL 'http://www.rforge.net/src/contrib/rJava_0.9-10.tar.gz'
Content type 'application/x-gzip' length 654583 bytes (639 KB)
==================================================
downloaded 639 KB

* installing *source* package ‘rJava’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/lib64/jvm/java/bin/java'
archiver    : '/usr/lib64/jvm/java/bin/jar'
compiler    : '/usr/lib64/jvm/java/bin/javac'
header prep.: ''
cpp flags   : '-I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux'
java libs   : '-L/usr/lib64/jvm/java/lib/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes

...

checking for ANSI C header files... yes
checking Java version... 
checking whether  actually works... no
checking whether javah was replaced by javac -h... no
configure: error: one or more Java tools are missing.

...

it should detect that javah is replaced by javac -h

from /etc/os-release:

NAME="openSUSE Tumbleweed"
# VERSION="20180502"

/usr/lib64/jvm/java/bin/java -version

openjdk version "10.0.1" 2018-04-17
OpenJDK Runtime Environment (build 10.0.1+10-suse-1.2-x8664)
OpenJDK 64-Bit Server VM (build 10.0.1+10-suse-1.2-x8664, mixed mode)

[kapelner]

Ditto on Windows 10 with JDK 10 in RStudio running R 3.5.0.