On 19 October 2017 at 15:47, Simon Urbanek wrote: | R CMD javareconf is always needed to register Java support with R (on all unix platforms).
s/always/sometimes/ The values get encoded when I build R binaries. For many years now, that was good enough. | Like I said, I don't know what deb packages do here - 'R CMD INSTALL sourceTarball_1.2-3.tar.gz -- what else do you think I do? | I presume you must do something in your R binary and all I can presume is that whatever the setup is then doesn't match what's there now. 500+ CRAN packages packaged _exactly_ this. rJava is a little different (for an understandable reason; RInside is different too). So ... tried that, still no luck: --- [...] R CMD javareconf *** JAVA_HOME is not a valid path, ignoring Java interpreter : /usr/bin/java Java version : 9-Debian Java home path : /usr/lib/jvm/java-9-openjdk-amd64 Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/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)/lib/server -ljvm make[1]: Entering directory '/tmp/Rjavareconf.e0Jzrq' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-9-openjdk-amd64/include -I/usr/lib/jvm/java-9-openjdk-amd64/include/linux -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.2=. -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/java-9-openjdk-amd64/lib/server -ljvm -L/usr/lib/R/lib -lR make[1]: Leaving directory '/tmp/Rjavareconf.e0Jzrq' JAVA_HOME : /usr/lib/jvm/java-9-openjdk-amd64 Java library path: $(JAVA_HOME)/lib/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm Updating Java configuration in /usr/lib/R /usr/lib/R/bin/javareconf: 406: /usr/lib/R/bin/javareconf: cannot create /usr/lib/R/etc/Makeconf.new: Permission denied *** cannot create /usr/lib/R/etc/Makeconf.new *** Please run as root if required. [...] --- All this is running as root. But /usr may be mounted read-only. Dirk | | Cheers, | Simon | | | > On Oct 18, 2017, at 9:50 PM, Dirk Eddelbuettel <e...@debian.org> wrote: | > | > | > Simon, | > | > On 18 October 2017 at 21:34, Simon Urbanek wrote: | > | Dirk, | > | | > | I don't have the details but this looks like as incorrect Java configuration in R - the Java home is obviously incomplete as it's missing bin/java and/or that path is wrong. Also I'm surprised to the the odd paths "/usr/lib/jvm/default-java/" since at least in my installations I see the actual JVM being used - but then I don't know how your package (or Debian?) abstracts the Java version mess. | > | > This was vanilla 'openjdk-9-jdk' and nothing else. | > | > Could I / should invoke 'R CMD javareconf' ? | > | > Dirk | > | > | Cheers, | > | Simon | > | | > | | > | > On Oct 17, 2017, at 10:24 PM, Dirk Eddelbuettel <e...@debian.org> wrote: | > | > | > | > | > | > Simon, | > | > | > | > With your new rJava_0.9-9 I tried this against Debian's openjdk-9-jdk -- but | > | > with R 3.4.2 as built against openjdk-7 -- and it still fails: | > | > | > | > 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/jre/bin/java' | > | > archiver : '/usr/lib/jvm/default-java/bin/jar' | > | > compiler : '/usr/lib/jvm/default-java/bin/javac' | > | > header prep.: '/usr/lib/jvm/default-java/bin/javah' | > | > cpp flags : '-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux' | > | > java libs : '-L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm' | > | > checking whether Java run-time works... ./configure: line 3736: /usr/lib/jvm/default-java/jre/bin/java: No such file or directory | > | > no | > | > configure: error: Java interpreter '/usr/lib/jvm/default-java/jre/bin/java' does not work | > | > ERROR: configuration failed for package 'rJava' | > | > * removing '/build/rjava-0.9-9/debian/r-cran-rjava/usr/lib/R/site-library/rJava' | > | > /usr/share/R/debian/r-cran.mk:101: recipe for target 'R_any_arch' failed | > | > make: *** [R_any_arch] Error 1 | > | > dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2 | > | > | > | > | > | > Any ideas? I saw that r-devel got some changes related to javareconf. Do we | > | > need to port that to r-patched? Can you advise? | > | > | > | > Many thanks, Dirk | > | > | > | > -- | > | > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > | > | > | | > | > -- | > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > | -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
