[R-sig-Debian] So nearly there, but can't install rJava

[Chris Evans]

Wow, this has amplified my respect and gratitude for the R Debian repositories. Doing all the install.packages() and following the clues about missing dependencies has taken hours! However, I have almost all the packages I want installed on this machine and Rstudio and the shiny server are installed and running fine. Bizarrely, to my mind, I am totally failing on rJava and hence a number of packages that depend on it. In R I get: 

checking Java support in R... present: 
interpreter : '/usr/lib/jvm/default-java/jre/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. 


When I do R CMD javareconf I get this: 

root using DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf 
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java 
Java version : 1.8.0_181 
Java home path : /usr/lib/jvm/default-java 
Java compiler : /usr/lib/jvm/default-java/bin/javac 
Java headers gen.: /usr/lib/jvm/default-java/bin/javah 
Java archive tool: /usr/lib/jvm/default-java/bin/jar 

trying to compile and link a JNI program 
detected JNI cpp flags : 
detected JNI linker flags : 
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o 
conftest.c:1:17: fatal error: jni.h: No such file or directory 
#include <jni.h> 
^ 
compilation terminated. 
/usr/lib/R/etc/Makeconf:162: recipe for target 'conftest.o' failed 
make: *** [conftest.o] Error 1 
Unable to compile a JNI program 


JAVA_HOME : /usr/lib/jvm/default-java 
Java library path: 
JNI cpp flags : 
JNI linker flags : 
Updating Java configuration in /usr/lib/R 
Done. 

I'm pretty sure that the problem is with some missing path but I also know I'm out of my depth (again). I'm a bit puzzled because I have only installed default Debian things. Do I need particular non-default Java or Java related components? 

TIA (again!), 

Chris 

-- 
Chris Evans <chris using psyctc.org> Skype: chris-psyctc 
Visiting Professor, University of Sheffield <chris.evans using sheffield.ac.uk> 
I do some consultation work for the University of Roehampton <chris.evans using roehampton.ac.uk> and other places but this <chris using psyctc.org> remains my main Email address. 
I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book to talk, I am trying to keep that to Thursdays and my diary is now available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/ 
Beware: French time, generally an hour ahead of UK. That page will also take you to my blog which started with earlier joys in France and Spain! 


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