Non-Zero Exist Status Installing openNLP - r

Question

I am attempting to learn how to find co-occurrences in R using the openNLP package. However, when I run > install.packages(openNLP) I get the following output:
Installing package into ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openNLPdata’, ‘rJava’
trying URL 'https://cloud.r-project.org/src/contrib/openNLPdata_1.5.3-4.tar.gz'
Content type 'application/x-gzip' length 7318770 bytes (7.0 MB)
==================================================
downloaded 7.0 MB
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
trying URL 'https://cloud.r-project.org/src/contrib/openNLP_0.2-6.tar.gz'
Content type 'application/x-gzip' length 6656 bytes
==================================================
downloaded 6656 bytes
* 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/default-java/bin/java'
archiver : ''
compiler : ''
header prep.: ''
cpp flags : ''
java libs : ''
configure: error: Java Development Kit (JDK) is missing or not registered in R
Make sure R is configuInstalling package into ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openNLPdata’, ‘rJava’
trying URL 'https://cloud.r-project.org/src/contrib/openNLPdata_1.5.3-4.tar.gz'
Content type 'application/x-gzip' length 7318770 bytes (7.0 MB)
==================================================
downloaded 7.0 MB
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
trying URL 'https://cloud.r-project.org/src/contrib/openNLP_0.2-6.tar.gz'
Content type 'application/x-gzip' length 6656 bytes
==================================================
downloaded 6656 bytes
* 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/default-java/bin/java'
archiver : ''
compiler : ''
header prep.: ''
cpp flags : ''
java libs : ''
configure: error: Java Development Kit (JDK) is missing or not registered in R
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘openNLPdata’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLPdata’
Warning in install.packages :
installation of package ‘openNLPdata’ had non-zero exit status
ERROR: dependencies ‘openNLPdata’, ‘rJava’ are not available for package ‘openNLP’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLP’
Warning in install.packages :
installation of package ‘openNLP’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpyeXutE/downloaded_packages’red with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘openNLPdata’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLPdata’
Warning in install.packages :
installation of package ‘openNLPdata’ had non-zero exit status
ERROR: dependencies ‘openNLPdata’, ‘rJava’ are not available for package ‘openNLP’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLP’
Warning in install.packages :
installation of package ‘openNLP’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpyeXutE/downloaded_packages’
If it's possible to get openNLP running, how do I do so? If not, are there other packages which can do co-occurrences in text strings?
If it helps any, I'm running this from Ubuntu 18.+ and R 3.5.3.

Answer 1

Okay, so, I figured this out myself but I thought it might help someone else. Long story short, read the output carefully. Output says:
configure: error: Java Development Kit (JDK) is missing or not registered in R
Make sure R is configuInstalling package into ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openNLPdata’, ‘rJava’
To solve my dependency problems, I opened terminal and ran the following lines:
1. $ sudo apt-get install -y default-jre to install Java Runtime Environment
2. $ sudo apt-get install -y default-jdk to install Java Development Kit
3. $ sudo R CMD javareconf to tell R where to find things
4. Then in R, > install.packages("rJava")
5. > install.packages("openNLP")
That should work.