[R-sig-Debian] rJava failed to install in Ubuntu

[Christofer Bogaso]

Hi,

I was trying install rJava package but failed to install with below error:

*trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz
<https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz>'*
*Content type 'application/x-gzip' length 675188 bytes (659 KB)*
*==================================================*
*downloaded 659 KB*

** installing *source* package ‘rJava’ ...*
*** package ‘rJava’ successfully unpacked and MD5 sums checked*
*checking for gcc... gcc -std=gnu99*
*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 -std=gnu99 accepts -g... yes*
*checking for gcc -std=gnu99 option to accept ISO C89... none needed*
*checking how to run the C preprocessor... gcc -std=gnu99 -E*
*checking for grep that handles long lines and -e... /bin/grep*
*checking for egrep... /bin/grep -E*
*checking for ANSI C header files... yes*
*checking for sys/wait.h that is POSIX.1 compatible... yes*
*checking for sys/types.h... yes*
*checking for sys/stat.h... yes*
*checking for stdlib.h... yes*
*checking for string.h... yes*
*checking for memory.h... yes*
*checking for strings.h... yes*
*checking for inttypes.h... yes*
*checking for stdint.h... yes*
*checking for unistd.h... yes*
*checking for string.h... (cached) yes*
*checking sys/time.h usability... yes*
*checking sys/time.h presence... yes*
*checking for sys/time.h... yes*
*checking for unistd.h... (cached) yes*
*checking for an ANSI C-conforming const... yes*
*checking whether time.h and sys/time.h may both be included... yes*
*configure: checking whether gcc -std=gnu99 supports static inline...*
*yes*
*checking whether setjmp.h 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/lib/jvm/java-12-oracle/bin/java'*
*archiver    : '/usr/lib/jvm/java-12-oracle/bin/jar'*
*compiler    : '/usr/lib/jvm/java-12-oracle/bin/javac'*
*header prep.: '/usr/bin/javah'*
*cpp flags   : '-I/usr/lib/jvm/java-12-oracle/include
-I/usr/lib/jvm/java-12-oracle/include/linux'*
*java libs   : '-L/usr/lib/jvm/java-12-oracle/lib/server -ljvm -ldl'*
*checking whether Java run-time works... ./configure: line 3766:
/usr/lib/jvm/java-12-oracle/bin/java: No such file or directory*
*no*
*configure: error: Java interpreter '/usr/lib/jvm/java-12-oracle/bin/java'
does not work*
*ERROR: configuration failed for package ‘rJava’*
** removing ‘/home/asaha/R/x86_64-pc-linux-gnu-library/3.4/rJava’*

*The downloaded source packages are in*
*        ‘/tmp/RtmpAHaE0V/downloaded_packages’*
*Warning message:*
*In install.packages("rJava") :*
*  installation of package ‘rJava’ had non-zero exit status*

below is my *javareconf*

*sudo R CMD javareconf*
*Java interpreter : /usr/lib/jvm/java-11-oracle/bin/java*
*Java version     : 11.0.2*
*Java home path   : /usr/lib/jvm/java-11-oracle*
*Java compiler    : /usr/lib/jvm/java-11-oracle/bin/javac*
*Java headers gen.: /usr/bin/javah*
*Java archive tool: /usr/lib/jvm/java-11-oracle/bin/jar*

*trying to compile and link a JNI program*
*detected JNI cpp flags    : -I$(JAVA_HOME)/include
-I$(JAVA_HOME)/include/linux*
*detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm*
*gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I/usr/lib/jvm/java-11-oracle/include
-I/usr/lib/jvm/java-11-oracle/include/linux     -fpic  -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o*
*g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o
conftest.so conftest.o -L/usr/lib/jvm/java-11-oracle/lib/server -ljvm
-L/usr/lib/R/lib -lR*


*JAVA_HOME        : /usr/lib/jvm/java-11-oracle*
*Java library path: $(JAVA_HOME)/lib/server*
*JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux*
*JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm*
*Updating Java configuration in /usr/lib/R*
*Done.*

*I dont understand despite having version Java-11, at the time of
installation R is showing interpreter as 12.*

Any idea to resolve this issue will be highly helpful.

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