On 22/06/09 at 08:04 -0500, Dirk Eddelbuettel wrote: > > On 22 June 2009 at 13:40, Lucas Nussbaum wrote: > | On 22/06/09 at 05:56 -0500, Dirk Eddelbuettel wrote: > | > > | > On 22 June 2009 at 11:02, Lucas Nussbaum wrote: > | > | On 21/06/09 at 21:12 -0500, Dirk Eddelbuettel wrote: > | > | > > | > | > On 21 June 2009 at 16:55, Lucas Nussbaum wrote: > | > | > | Hi, > | > | > | > | > | > | During a rebuild of all packages in sid, your package failed to > build on > | > | > | amd64. > | > | > | > | > | > | Relevant part: > | > | > | > /usr/bin/fakeroot debian/rules binary > | > | > | > test -x debian/rules > | > | > | > dh_clean -k > | > | > | > dh_installdirs -A > | > | > | > mkdir -p "." > | > | > | > if test -e /usr/share/misc/config.guess ; then \ > | > | > | > for i in ./jri/tools/config.guess ; do \ > | > | > | > if ! test -e $i.cdbs-orig ; then \ > | > | > | > mv $i $i.cdbs-orig ; \ > | > | > | > cp --remove-destination > /usr/share/misc/config.guess $i ; \ > | > | > | > fi ; \ > | > | > | > done ; \ > | > | > | > fi > | > | > | > if test -e /usr/share/misc/config.sub ; then \ > | > | > | > for i in ./jri/tools/config.sub ; do \ > | > | > | > if ! test -e $i.cdbs-orig ; then \ > | > | > | > mv $i $i.cdbs-orig ; \ > | > | > | > cp --remove-destination > /usr/share/misc/config.sub $i ; \ > | > | > | > fi ; \ > | > | > | > done ; \ > | > | > | > fi > | > | > | > dh_installdirs usr/lib/R/site-library > | > | > | > if test -f /usr/bin/xvfb-run; then \ > | > | > | > xvfb-run \ > | > | > | > R CMD INSTALL -l > /build/user-rjava_0.6-3-1-amd64-l63FQQ/rjava-0.6-3/debian/r-cran-rjava/usr/lib/R/site-library > --clean \ > | > | > | > . ; \ > | > | > | > else > \ > | > | > | > R CMD INSTALL -l > /build/user-rjava_0.6-3-1-amd64-l63FQQ/rjava-0.6-3/debian/r-cran-rjava/usr/lib/R/site-library > \ > | > | > | > --clean . ;\ > | > | > | > fi > | > | > | > * Installing *source* package 'rJava' ... > | > | > | > checking for gcc... gcc -std=gnu99 > | > | > | > checking for C compiler default output file name... a.out > | > | > | > checking whether the C compiler works... yes > | > | > | > checking whether we are cross compiling... no > | > | > | > checking for suffix of executables... > | > | > | > checking for suffix of object files... o > | > | > | > checking whether we are using the GNU C compiler... yes > | > | > | > checking whether gcc -std=gnu99 accepts -g... yes > | > | > | > checking for gcc -std=gnu99 option to accept ISO C89... none > needed > | > | > | > checking how to run the C preprocessor... gcc -std=gnu99 -E > | > | > | > checking for grep that handles long lines and -e... /bin/grep > | > | > | > checking for egrep... /bin/grep -E > | > | > | > checking for ANSI C header files... yes > | > | > | > checking for sys/wait.h that is POSIX.1 compatible... yes > | > | > | > checking for sys/types.h... yes > | > | > | > checking for sys/stat.h... yes > | > | > | > checking for stdlib.h... yes > | > | > | > checking for string.h... yes > | > | > | > checking for memory.h... yes > | > | > | > checking for strings.h... yes > | > | > | > checking for inttypes.h... yes > | > | > | > checking for stdint.h... yes > | > | > | > checking for unistd.h... yes > | > | > | > checking for string.h... (cached) yes > | > | > | > checking sys/time.h usability... yes > | > | > | > checking sys/time.h presence... yes > | > | > | > 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 > | > | > | > configure: error: One or more Java configuration variables are > not set. > | > | > | > Make sure R is configured with full Java support (including JDK). > Run > | > | > | > R CMD javareconf > | > | > | > as root to add Java support to R. > | > | > | > > | > | > | > If you don't have root privileges, run > | > | > | > R CMD javareconf -e > | > | > | > to set all Java-related variables and then install rJava. > | > | > | > > | > | > | > checking Java support in R... present: > | > | > | > interpreter : '/usr/bin/java' > | > | > | > archiver : '/usr/bin/jar' > | > | > | > compiler : '/usr/bin/javac' > | > | > | > header prep.: '' > | > | > > | > | > That variable is set on my system and ... > | > | > > | > | > | > cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' > | > | > | > java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server > -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 > -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L > -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' > | > | > | > ERROR: configuration failed for package 'rJava' > | > | > | > * Removing > '/build/user-rjava_0.6-3-1-amd64-l63FQQ/rjava-0.6-3/debian/r-cran-rjava/usr/lib/R/site-library/rJava' > | > | > | > make: *** [R_any_arch] Error 1 > | > | > > | > | > ... the build proceeds fine here. > | > | > > | > | > So I cannot reproduce this. > | > | > | > | Hi Dirk, > | > | > | > | I just tried, and I could reproduce the failure in a clean chroot. > | > | beaujolais:/tmp/rjava-0.6-3# R CMD config JAVAH > | > | > | > | Couldn't that be caused by a missing dependancy? > | > > | > Is your system amd64 ? My i386 handles building rJava (aka r-cran-rjava) > | > just fine. > | > | Yes > > Ok, so want can we do to tie this down?
I confirm that it builds fine on i386. i386: # R CMD config JAVAH /usr/bin/javah # ls -l /usr/bin/javah lrwxrwxrwx 1 root root 23 Jun 22 15:56 /usr/bin/javah -> /etc/alternatives/javah # ls -l /etc/alternatives/javah lrwxrwxrwx 1 root root 37 Jun 22 15:56 /etc/alternatives/javah -> /usr/lib/jvm/java-6-openjdk/bin/javah amd64: # R CMD config JAVAH # ls -l /usr/bin/javah lrwxrwxrwx 1 root root 23 Jun 22 15:59 /usr/bin/javah -> /etc/alternatives/javah # ls -l /etc/alternatives/javah lrwxrwxrwx 1 root root 37 Jun 22 15:59 /etc/alternatives/javah -> /usr/lib/jvm/java-6-openjdk/bin/javah So, there's really no reason why R couldn't find javah on amd64 as well. Looks like a problem in R. -- | Lucas Nussbaum | lu...@lucas-nussbaum.net http://www.lucas-nussbaum.net/ | | jabber: lu...@nussbaum.fr GPG: 1024D/023B3F4F | -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
