On 16 February 2016 at 07:40, Dirk Eddelbuettel wrote: | | On 15 February 2016 at 13:20, Chris Lamb wrote: | | Source: rjava | | Version: 0.9-8-1 | | Severity: serious | | Justification: fails to build from source | | User: reproducible-bui...@lists.alioth.debian.org | | Usertags: ftbfs | | X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org | | | | Dear Maintainer, | | | | rjava fails to build from source in unstable/amd64: | | | | [..] | | | | 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' | | java libs : '-L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm' | | checking whether Java run-time works... yes | | checking whether -Xrs is supported... yes | | checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. | | | | Make sure you have Java Development Kit installed and correctly registered in R. | | If in doubt, re-run "R CMD javareconf" as root. | | | | ERROR: configuration failed for package 'rJava' | | * removing '/home/lamby/temp/cdt.20160215130417.8nrJupJ3Ai/rjava-0.9-8/debian/r-cran-rjava/usr/lib/R/site-library/rJava' | | /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed | | make: *** [R_any_arch] Error 1 | | | | [..] | | | | The full build log is attached. | | Could be a change in default-java. Here is me trying to install a given | Java-using package from CRAN once r-cran-rjava has been loaded in a 'Debian | unstable' container | | 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' | 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 '/usr/local/lib/R/site-library/rJava' | | The downloaded source packages are in | '/tmp/Rtmp8m9GKv/downloaded_packages' | Warning message: | In install.packages("rJava", repos = "http://cloud.r-project.org") : | installation of package 'rJava' had non-zero exit status | > | | I'll take another look later.
Could it be a recent change of default-jdk (which R itself build-depends upon, as does the r-cran-rjava package breaking) from java7 to java8? All this used to work, but as you notice, had a sudden breakage. Everything still works if we install 'openjdk-7-jdk' -- but that should not be necessary. Shall I just add a Build-Depends: on 'openjdk-7-jdk | openjdk-8-jdk' ? Seems like a kludge. Better ideas? Dirk | | Dirk | | | | | | Regards, | | | | -- | | ,''`. | | : :' : Chris Lamb | | `. `'` la...@debian.org / chris-lamb.co.uk | | `- | | x[DELETED ATTACHMENT rjava.0.9-8-1.unstable.amd64.log.txt.gz, Untyped binary data] | | -- | http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org