Estoy intentando instalar rJava en R 3.6.1 en Ubuntu 18.04. He buscado preguntas similares pero las respuestas proporcionadas no parecen haber funcionado para mí.
Inicialmente lo intenté sudo apt install r-cran-rjavaseguido deinstall.packages("rJava")
sudo apt install r-cran-rjavadevolvió un problema de dependencia que pareció resolverse agregando el repositorio de Debian Buster, lo etc/apt/sources.listcual hice siguiendo las instrucciones proporcionadas en:https://cran.r-project.org/bin/linux/debian/. r-cran-rjava ahora parece estar instalado correctamente:
$ sudo apt install r-cran-rjava
[sudo] password for tj:
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-cran-rjava is already the newest version (0.9-11-1cran1ppabionic0).
0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade.
Sin embargo, cuando ejecuté install.packages("rJava")desde R me devolvió el siguiente mensaje de error:
install.packages("rJava")
Installing package into ‘/home/tj/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL '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
** using staged installation
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/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-11-oracle/include -I/usr/lib/jvm/java-11-oracle/include/linux'
java libs : '-L/usr/lib/jvm/java-11-oracle/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 whether JNI programs run... configure: error: Unable to run a simple JNI program. Make sure you have configured R with Java support (see R documentation) and check config.log for failure reason.
Warning in system(cmd) : error in running command
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/tj/R/x86_64-pc-linux-gnu-library/3.6/rJava’
The downloaded source packages are in
‘/tmp/Rtmp9GstQE/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
Las instrucciones publicadas aquí.https://thishosting.rocks/install-java-ubuntu/Llévame a instalar varias versiones de Java, incluida Java-11-Oracle. Configuré java-11-oracle en el uso predeterminado sudo update-alternatives --config javaantes de actualizar JAVA_HOME sudo nano /etc/environmenty echo $JAVA_HOMEobtengo:
$ echo $JAVA_HOME
/usr/lib/jvm/java-11-oracle/bin/java
Pero cuando lo ejecuté sudo R CMD javareconfme devolvió:
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 11.0.4
Java home path : /usr/lib/jvm/java-11-oracle
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(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 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
gcc -std=gnu99 -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.
y install.packages("rJava")devuelve el mismo mensaje de error que antes. Intenté configurar java-11-openjdk y java-8-openjdk como predeterminados usando el mismo método e intenté usar varias variaciones de la ruta JAVA_HOME como lo sugieren algunas publicaciones anteriores sobre el tema (https://stackoverflow.com/questions/3311940/r-rjava-package-install-failing& https://stackoverflow.com/questions/31684236/java-home-not-working-in-ubuntu) pero hasta ahora R CMD javareconfestán install.packages("rjava")arrojando resultados similares.
Soy bastante nuevo en R y Ubuntu y siento que he llegado a un callejón sin salida en este caso, ¿alguien puede ver lo que me estoy perdiendo? ¿Debo volver a una versión anterior de R? Cualquier ayuda sería muy apreciada.