Simon, On 20 October 2017 at 10:14, Simon Urbanek wrote: | oh, no, rJava does not run javareconf - it only tells the user to do so if the configuration is broken. The R CMD javareconf occurrences in configure are always in the text section printed to the user. As you correctly said, it would be very bad if a package tried to change the system configuration. So please check who's calling what after the build - it's not rJava calling javareconf.
Fair enough and good to know. That said, we are still at an impasse. It fails to build, I have no idea why, don't know how to fix a (rather complicated) package so unless you can aid me here I fear the worst case of a "fails to build from source package" being auto-removed will kick in. (Partial) log is below. Dirk | | Thanks, | Simon | | | | | | > On Oct 19, 2017, at 9:34 PM, Dirk Eddelbuettel <e...@debian.org> wrote: | > | > | > Simon, | > | > On 19 October 2017 at 17:49, Simon Urbanek wrote: | > | Dirk, | > | | > | to clarify - this is about *R* configuration, not about rJava at all. rJava has nothing to do with those settings - it just uses what R was configured with. The only part rJava plays here is that it needs those R settings to be valid - just like other R packages that use Java. | > | | > | As you reported the R configuration is broken, because the JAVA entry points to a non-existent file. I don't know why or how that happens. At least that's what I saw in the log: | > | | > | checking Java support in R... present: | > | interpreter : '/usr/lib/jvm/default-java/jre/bin/java' | > | [...] | > | 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 | > | | > | I presume that setting should have been /usr/lib/jvm/default-java/bin/java -- or JRE is required and missing (again, I don't know what package is providing that /usr/lib/jvm/default-java/jre/bin/java file used in the configuration). | > | > I am confused. Once I added the call to 'R CMD javareconf' to be done | > before 'R CMD INSTALL ...your tarball...' happens, it _builds_ but then failed | > on a subsequent command that is not from me. I could patch that. | > | > Allow me to copy and paste again: | > | > ----------------------------------------------------------------------------- | > make[1]: Entering directory '/build/rjava-0.9-9' | > CDBS WARNING: simple-patchsys.mk is deprecated since 0.4.85 - please use source format 3.0 (quilt) instead | > set -e; mv ./jri/tools/config.guess ./jri/tools/config.guess.cdbs-orig; cp --remove-destination /usr/share/misc/config.guess ./jri/tools/config.guess; | > set -e; mv ./jri/tools/config.sub ./jri/tools/config.sub.cdbs-orig; cp --remove-destination /usr/share/misc/config.sub ./jri/tools/config.sub; | > make[1]: Leaving directory '/build/rjava-0.9-9' | > set -e; | > set -e; | > 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. | > | > debian/rules:9: recipe for target 'build/r-cran-rjava' failed | > make: *** [build/r-cran-rjava] Error 1 | > dpkg-buildpackage: error: debian/rules build gave error exit status 2 | > ----------------------------------------------------------------------------- | > | > So conftest.so is built. Can we skip the subsequent javareconf? If so, | > where? When I glance at your configure.ac I see several ... And the | > Makefile structure is not exactly trivial or standard either. | > | > Dirk | > | > | > | Cheers, | > | Simon | > | | > | | > | > On Oct 19, 2017, at 4:56 PM, Dirk Eddelbuettel <e...@debian.org> wrote: | > | > | > | > | > | > On 19 October 2017 at 16:31, Simon Urbanek wrote: | > | > | | > | > | > On Oct 19, 2017, at 4:12 PM, Dirk Eddelbuettel <e...@debian.org> wrote: | > | > | > | > | > | > | > | > | > 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. | > | > | > | > | > | | > | > | Right, you have to have write-access is /usr/lib/R/etc/ so it can update the configuration to record your Java settings. | > | > | > | > Well, in general we do _not_ have that and _cannot_ assume it, just like CRAN | > | > packages do _not_ get to write to $RHOME/bin. | > | > | > | > _For Debian systems_ I offer (us, mostly) /etc/R/ with softlinks. | > | > | > | > But if your package assumes /usr/lib for write only, we may be done here and | > | > it will get removed. | > | > | > | > | I was asking because the above it obviously non-portable - i.e. if I | > | > | install Oracle Java the path will be different and also it will be different | > | > | for Java 1.8 etc. Hence you'd need to re-run javareconf any time the Java | > | > | configuration changes (thanks to Sun/Oracle for that wonderful design) - | > | > | unless you have canonical place you can use. From your original settings it | > | > | looked like you have some default-java symlink which would help here - | > | > | > | > Not mine. That is the Debian Java folks. | > | > | > | > | except that it has the broken path to java which is where the trouble started in the first place. I suspect that fixing your default config to have a valid path to java should be enough as long as that default setting is maintained at the system level. | > | > | > | > No trouble _once I run R CMD javareconf_ earlier it built. But we died in in | > | > your post-processing, it seems. | > | > | > | > Dirk | > | > | > | > | Cheers, | > | > | Simon | > | > | | > | > | | > | > | | > | > | > 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 | > | > | > | > | > | | > | > | > | > -- | > | > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > | > | > | | > | > -- | > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > | -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
