Ytdyklly

I have a problem with installing the newest version of R, an error "fatal error: jni.h: No such file or directory" that I don't understand appeared.
Here is what I did before getting an error in the installation of R :

#download tar.gz file

https://cran.r-project.org/

#install because we need it for execution of "make"

sudo apt-get install libx11-dev

sudo apt-get install xorg-dev

sudo apt-get install libcurl4-openssl-dev

# decompile

# on terminal

./configure

make

What appeared to me at the end of the installation after installing libraries was this (can't paste everything because it is too long):

installing to /home/fafnyr/R/R-3.5.2/library/mgcv/libs

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

* DONE (mgcv)

make[2]: Leaving directory '/home/fafnyr/R/R-3.5.2/src/library/Recommended'

make[1]: Leaving directory '/home/fafnyr/R/R-3.5.2/src/library/Recommended'

make[1]: Entering directory '/home/fafnyr/R/R-3.5.2/src/library'

building/updating vignettes for package 'grid' ...

building/updating vignettes for package 'parallel' ...

building/updating vignettes for package 'utils' ...

make[1]: Leaving directory '/home/fafnyr/R/R-3.5.2/src/library'

make[1]: Entering directory '/home/fafnyr/R/R-3.5.2'

configuring Java ...

Java interpreter : /usr/bin/java

Java version     : 10.0.2

Java home path   : /usr/lib/jvm/java-11-openjdk-amd64

Java compiler    : not present

Java headers gen.: 

Java archive tool: 



trying to compile and link a JNI program 

detected JNI cpp flags    : 

detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm

make[2]: Entering directory '/tmp/Rjavareconf.VwU72a'

gcc -I"/home/fafnyr/R/R-3.5.2/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c conftest.c -o conftest.o

conftest.c:1:10: fatal error: jni.h: No such file or directory

 #include <jni.h>

          ^~~~~~~

compilation terminated.

/home/fafnyr/R/R-3.5.2/etc/Makeconf:162: recipe for target 'conftest.o' failed

make[2]: *** [conftest.o] Error 1

make[2]: Leaving directory '/tmp/Rjavareconf.VwU72a'

Unable to compile a JNI program





JAVA_HOME        : /usr/lib/jvm/java-11-openjdk-amd64

Java library path: 

JNI cpp flags    : 

JNI linker flags : 

Updating Java configuration in /home/fafnyr/R/R-3.5.2

Done.



make[1]: Leaving directory '/home/fafnyr/R/R-3.5.2'

For this problem, I found the solution:

sudo apt install default-jdk

For the makefile, I also had some problem so I installed this:

sudo apt-get install libx11-dev

sudo apt-get install xorg-dev

sudo apt-get install libcurl4-openssl-dev

Moreover for the installation of 3.5.2, I followed those instructions:

Install the packages necessary to add a new repository over HTTPS:

  sudo apt install apt-transport-https software-properties-common

Enable the CRAN repository and add the CRAN GPG key to your system using the following commands:

  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

  sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'

Now that the repository is added, update the packages list and install the R package by typing:

sudo apt update

sudo apt install r-base

To verify that the installation was successful run the following command which will print the R version:

  R --version

  # or #

  sudo -i R