Hi Chris, > I think the problem may be options setting where R/rJava will look for Java so I tried: > > options(java.home="/usr/lib/jvm/java-8-openjdk-amd64/")
This should not be necessary. I would recommend to start a fresh R session in order to unset this. > As far as I can see Debian is happy with the setup of java and javac: > ... > And I have the full jdk not just the headless version I can see the header > files: > ... > But I can't reconfigure R for Java: > > root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf > *** JAVA_HOME is not a valid path, ignoring as above, I would not recommend setting JAVA_HOME manually. > Java interpreter : /usr/lib/jvm/default-java/jre/bin/java > /usr/lib/R/bin/javareconf: 1: /usr/lib/R/bin/javareconf: > /usr/lib/jvm/default-java/jre/bin/java: not found Obviously this file was not found. Again, apt-file can provide some help (but not when giving it the full path, because of the link maintained by update- alternatives: apt-file search jre/bin/java If you have openjdk-8-jre-headless installed, this file should be there on your system. Seems you don't have the jre installed? ... > Tangential question: surely I'm not rare in running R 3.5.2 on Stretch am I? I for sure am running it without issues on several computers. On my desktop, I am using openjdk-9 from stretch-backports, but on my laptop I just upgraded from R 3.4.x to R 3.5.2 using the stretch-cran35 packages on CRAN, and had no issues. I could install rJava from within R, and after that R CMD javareconf gives me: 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 : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/default-java/ include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -fdebug- prefix-map=/home/jranke/git/r-backports/stretch/r-base-3.4.3=. -fstack- protector-strong -Wformat -Werror=format-security -Wdate-time - D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/jre/lib/amd64/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm Updating Java configuration in /usr/lib/R Done. > Other tangential question: is there anything that can be done to fix the > r-api-3/r-api-3.5 issue. You can see I'm no programmer or sysadmin but if > there is anything I can do to help ...? Thanks for the offer. Personally, I am always glad to get some feedback from people using the Debian backports on CRAN, so thanks for that. On the other hand, I do not think that there is an error to be fixed. Of course it would be nice if we could provide more precompiled debs for these backports in order to avoid having to install them from sources. For me personally, this is not a priority, I am happy if I manage to get the base and recommended packages out on new releases. Johannes > > TIA all, > > Chris > > > > ----- Original Message ----- > > > From: "Dirk Eddelbuettel" <e...@debian.org> > > To: "Chris Evans" <chrish...@psyctc.org> > > Cc: "r-sig-debian" <r-sig-debian@r-project.org> > > Sent: Tuesday, 22 January, 2019 12:21:39 > > Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava > > > > On 22 January 2019 at 10:14, Chris Evans wrote: > >| root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install > >| openjdk-8-jdk-headless > >| Reading package lists... Done > >| Building dependency tree > >| Reading state information... Done > >| openjdk-8-jdk-headless is already the newest version > >| (8u181-b13-2~deb9u1). > >| openjdk-8-jdk-headless set to manually installed. > >| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > >| > >| Anyone else got any ideas? > > > > Install the full-blown jdk no just headless. > > > > In the sources for rJava I have as a build-depends > > > > openjdk-10-jdk > > > > which may of course be a virtual. At some point we had more than JDK > > implementation. See what you can find there. > > > > Dirk > > > > -- > > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org -- Johannes Ranke Wissenschaftlicher Berater https://jrwb.de/contact _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian