Your message dated Tue, 21 Nov 2017 06:52:58 -0600 with message-id <23060.8618.726099.41...@bud.eddelbuettel.com> has caused the report #882321, regarding rjava fails to build to be marked as having been forwarded to the upstream software author(s) simon.urba...@r-project.org
(NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 882321: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=882321 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---On 21 November 2017 at 13:41, Matthias Klose wrote: | Package: src:rjava | Version: 0.9-9-1 | Severity: serious | Tags: sid buster | | the package fails to build: | | checking for sys/time.h... yes | checking for unistd.h... (cached) yes | checking for an ANSI C-conforming const... yes | checking whether time.h and sys/time.h may both be included... yes | configure: checking whether gcc -std=gnu99 supports static inline... | yes | 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 ‘/<<PKGBUILDDIR>>/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 subprocess returned exit | status 2 | -------------------------------------------------------------------------------- | Build finished at 20171112-0120 Crap. We just fixed this by making sure jdk-9 is used. And the (new, first beta build of R 3.4.3) r-base I created yesterday had this in its log which looks good: *** JAVA_HOME is not a valid path, ignoring Java interpreter : /usr/bin/java Java version : 9.0.1 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[3]: Entering directory '/tmp/Rjavareconf.MCDKwf' gcc -std=gnu99 -I/build/r-base-3.4.2.20171120/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- 3.4.2.20171120=. -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/build/r-base-3.4.2.20171120/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-9-openjdk-amd64/lib/server -ljvm -L/build/r-base-3.4.2.20171120/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.MCDKwf' 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 /build/r-base-3.4.2.20171120 Done. What version of r-base core was used here, and what arch was this? Dirk | Finished -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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