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@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 <ch...@psyctc.org> Skype: chris-psyctc Visiting Professor, University of Sheffield <chris.ev...@sheffield.ac.uk> I do some consultation work for the University of Roehampton <chris.ev...@roehampton.ac.uk> and other places but this <ch...@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! [[alternative HTML version deleted]] _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
