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

[Dirk Eddelbuettel]

On 18 April 2019 at 15:51, Christofer Bogaso wrote:
| Hi,
| 
| I was trying install rJava package but failed to install with below error:

You misspelled

   sudo apt-get install r-cran-rjava

Dirk

| 
| *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.
| 
| 	[[alternative HTML version deleted]]
| 
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