Estou tentando instalar o rJava no R 3.6.1 no Ubuntu 18.04. Procurei perguntas semelhantes, mas as respostas fornecidas não parecem ter funcionado para mim.
Eu tentei inicialmente sudo apt install r-cran-rjavaseguido porinstall.packages("rJava")
sudo apt install r-cran-rjavaretornou um problema de dependência que parecia ter sido resolvido adicionando o repositório Debian Buster ao etc/apt/sources.listqual fiz seguindo as instruções fornecidas em:https://cran.r-project.org/bin/linux/debian/. r-cran-rjava agora parece estar instalado corretamente:
$ 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.
Porém, quando executei install.packages("rJava")do R ele retornou a seguinte mensagem de erro:
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
As instruções postadas aquihttps://thishosting.rocks/install-java-ubuntu/leve-me a instalar várias versões de java, incluindo java-11-oracle. Defino java-11-oracle como padrão usando sudo update-alternatives --config javaantes de atualizar JAVA_HOME usando sudo nano /etc/environmente echo $JAVA_HOMEfornece:
$ echo $JAVA_HOME
/usr/lib/jvm/java-11-oracle/bin/java
Mas quando eu corri sudo R CMD javareconfele retornou:
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 11.0.4
Java home path : /usr/lib/jvm/java-11-oracle
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(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.
e install.packages("rJava")retorna a mesma mensagem de erro de antes. Tentei definir java-11-openjdk e java-8-openjdk como padrão usando o mesmo método e tentei usar diversas variações do caminho JAVA_HOME conforme sugerido por alguns posts mais antigos sobre o tópico (https://stackoverflow.com/questions/3311940/r-rjava-package-install-failing& https://stackoverflow.com/questions/31684236/java-home-not-working-in-ubuntu), mas até agora R CMD javareconfe install.packages("rjava")estão retornando resultados semelhantes.
Sou bastante novo no R e no Ubuntu e sinto que cheguei a um beco sem saída. Alguém pode ver o que estou perdendo? Devo reverter para uma versão mais antiga do R? Qualquer ajuda seria muito apreciada.