В Ubuntu 18.04 я пытаюсь установить пакет rJava в R, но он не работает из-за отсутствия java:
> install.packages("rJava")
Installing package into ‘/home/t/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-12.tar.gz'
Content type 'application/x-gzip' length 1103629 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
* 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/lib/jvm/default-java/bin/java'
archiver : '/usr/lib/jvm/default-java/bin/jar'
compiler : '/usr/lib/jvm/default-java/bin/javac'
header prep.: ''
cpp flags : '-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux'
java libs : '-L/usr/lib/jvm/default-java/lib/server -ljvm'
checking whether Java run-time works... ./configure: line 3767: /usr/lib/jvm/default-java/bin/java: No such file or directory
no
configure: error: Java interpreter '/usr/lib/jvm/default-java/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/t/R/x86_64-pc-linux-gnu-library/3.6/rJava’
The downloaded source packages are in
‘/tmp/RtmpnCRl8C/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
, в частности:
configure: error: Java interpreter '/usr/lib/jvm/default-java/bin/java' does not work
В моем Ubuntu установлено java в /usr/lib/jvm/java-11-openjdk-amd64/bin/java:
$ which java
/usr/bin/java
$ ls -l /usr/bin/java
lrwxrwxrwx 1 root root 22 May 20 2018 /usr/bin/java -> /etc/alternatives/java
$ ls -l /etc/alternatives/java
lrwxrwxrwx 1 root root 43 Oct 4 2018 /etc/alternatives/java -> /usr/lib/jvm/java-11-openjdk-amd64/bin/java
$ ls -l /usr/lib/jvm/java-11-openjdk-amd64/bin/java
-rwxr-xr-x 1 root root 10304 Jan 15 10:14 /usr/lib/jvm/java-11-openjdk-amd64/bin/java
Мне было интересно, как решить проблему? Спасибо.
Первый подход: Я попробовал комментарий, но он не работает при установке, и что мне делать?
$ sudo apt install r-cran-rjava
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-rjava : Depends: r-api-3.4
E: Unable to correct problems, you have held broken packages.
Второй подход: вдохновлен { ссылка }, который изменяет JAVA_HOME в /usr/lib/R/etc/javaconf с
${JAVA_HOME=/usr/lib/jvm/default-java}
на
${JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64}
Перейдя по указанной выше ссылке, чтобы изменить /usr/lib/R/etc/javaconf, или создав ссылку из каталога по умолчанию на действительный каталог
ln -sr /usr/lib/jvm/java-11-openjdk-amd64/ /usr/lib/jvm/default-java/
Установка все равно не удалась
> install.packages("rJava")
Installing package into ‘/home/t/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-12.tar.gz'
Content type 'application/x-gzip' length 1103629 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
* 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/lib/jvm/default-java/bin/java'
archiver : '/usr/lib/jvm/default-java/bin/jar'
compiler : '/usr/lib/jvm/default-java/bin/javac'
header prep.: ''
cpp flags : '-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux'
java libs : '-L/usr/lib/jvm/default-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 JVM will be loaded dynamically... no
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/t/R/x86_64-pc-linux-gnu-library/3.6/rJava’
The downloaded source packages are in
‘/tmp/RtmpPUecfs/downloaded_packages’
Warning message:
In install.packages("rJava") :
Я обнаружил, что проблема является то, что я использую Java 11. Когда я переключаюсь на Java 8, второй подход работает. С какой Java версией может работать r Java?