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.
Given that my chroot works, I can't think of a missing depends.
One more thing to try would be to wait a day for the most recent r-base-core
upload, but then nothing changed there either.
Dirk
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