* Using: sun-jdk-1.6 >>> Unpacking source... >>> Unpacking hdf-java-2.5-src.tar to /var/tmp/portage/dev-java/hdf-java-2.5/work >>> Source unpacked in /var/tmp/portage/dev-java/hdf-java-2.5/work >>> Preparing source in /var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java ... * econf: updating hdf-java/Config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating hdf-java/Config/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --with-libz=/usr/include,/usr/lib64 --with-libjpeg=/usr/include,/usr/lib64 --with-hdf5=/usr/include,/usr/lib64 --with-jdk=/opt/sun-jdk-1.6.0.17/include,/opt/sun-jdk-1.6.0.17/jre/lib checking if tr works... yes checking for gawk... gawk checking if expr works... yes checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc 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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ANSI C... none needed checking whether make sets $(MAKE)... yes checking for a BSD-compatible install... /usr/bin/install -c checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for ceil in -lm... yes checking for rm... /bin/rm checking for find... /usr/bin/find checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu FYI the target here is: x86_64-pc-linux-gnu checking gzip compression... yes zlib found: /usr/lib64/libz.a checking jpeg compression... yes jpeg found: /usr/lib64/libjpeg.a checking szip compression... no checking HDF4 library... no checking HDF5 library... yes HDF5 found: /usr/lib64 checking dependencies for HDF5 library... OK checking HDF4to5 library... no checking jni.h usability... yes checking jni.h presence... yes checking for jni.h... yes checking for java... /opt/sun-jdk-1.6.0.17/bin/java checking for javac... /opt/sun-jdk-1.6.0.17/bin/javac checking for javadoc... /opt/sun-jdk-1.6.0.17/bin/javadoc checking for jar... /opt/sun-jdk-1.6.0.17/bin/jar configure: creating ./config.status config.status: creating Makefile config.status: creating native/Makefile config.status: creating native/hdflib/Makefile config.status: creating native/hdf5lib/Makefile config.status: creating bin/hdfview.sh config.status: creating test/linktest/Makefile config.status: creating test/linktest/testlink config.status: creating test/linktest/testh4link config.status: creating test/Makefile config.status: creating test/object/Makefile config.status: creating test/object/testh4file.sh config.status: creating test/object/testh5file.sh config.status: creating test/object/runtests.sh config.status: creating test/h5/TestHDF5.sh config.status: creating test/object/TestH5Object.sh config.status: creating test/object/TestH5Table.sh config.status: creating test/object/TestH5MemoryLeak.sh config.status: creating test/unittests/Makefile config.status: creating test/unittests/unittests.sh config.status: creating examples/Makefile config.status: creating examples/intro/Makefile config.status: creating examples/datasets/Makefile config.status: creating examples/datatypes/Makefile config.status: creating examples/groups/Makefile config.status: creating examples/runExample.sh >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java ... make -j4 cd native; \ make /opt/sun-jdk-1.6.0.17/bin/javac -classpath /opt/sun-jdk-1.6.0.17/jre/lib/rt.jar:/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java:lib/fits.jar:lib/netcdf.jar ncsa/hdf/hdf5lib/exceptions/HDF5AtomException.java /opt/sun-jdk-1.6.0.17/bin/javac -classpath /opt/sun-jdk-1.6.0.17/jre/lib/rt.jar:/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java:lib/fits.jar:lib/netcdf.jar ncsa/hdf/hdf5lib/exceptions/HDF5AttributeException.java /opt/sun-jdk-1.6.0.17/bin/javac -classpath /opt/sun-jdk-1.6.0.17/jre/lib/rt.jar:/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java:lib/fits.jar:lib/netcdf.jar ncsa/hdf/hdf5lib/exceptions/HDF5BtreeException.java make[1]: Entering directory `/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java/native' make[2]: Entering directory `/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java/native' cd hdf5lib; \ make ; make[3]: Entering directory `/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java/native/hdf5lib' x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o exceptionImp.o exceptionImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5Constants.o h5Constants.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5Imp.o h5Imp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5aImp.o h5aImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5dImp.o h5dImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5fImp.o h5fImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5gImp.o h5gImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5iImp.o h5iImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5pImp.o h5pImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5rImp.o h5rImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5sImp.o h5sImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5tImp.o h5tImp.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o nativeData.o nativeData.c x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5util.o h5util.c h5util.c: In function 'h5str_sprintf': h5util.c:171: warning: format '%d' expects type 'int', but argument 3 has type 'long int' h5util.c:176: warning: format '%u' expects type 'unsigned int', but argument 3 has type 'long unsigned int' h5util.c:181: warning: format '%u' expects type 'unsigned int', but argument 3 has type 'long unsigned int' x86_64-pc-linux-gnu-gcc -shared -Dx86_64 -fPIC -DH5_USE_16_API -D_FILE_OFFSET_BITS=64 -I. -I/usr/include -I/opt/sun-jdk-1.6.0.17/include -I/opt/sun-jdk-1.6.0.17/include/linux -c -o h5zImp.o h5zImp.c mkdir -p ../../lib/linux; x86_64-pc-linux-gnu-gcc -shared -o ../../lib/linux/libjhdf5.so exceptionImp.o h5Constants.o h5Imp.o h5aImp.o h5dImp.o h5fImp.o h5gImp.o h5iImp.o h5pImp.o h5rImp.o h5sImp.o h5tImp.o nativeData.o h5util.o h5zImp.o /usr/lib64/libhdf5.a /usr/lib64/libz.a -lm /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libhdf5.a(H5.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/libhdf5.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libjhdf5] Error 1 make[3]: Leaving directory `/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java/native/hdf5lib' make[2]: *** [do-hdf5lib] Error 2 make[2]: Leaving directory `/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java/native' make[1]: *** [hdf5lib] Error 2 make[1]: Leaving directory `/var/tmp/portage/dev-java/hdf-java-2.5/work/hdf-java/native' make: *** [natives] Error 2 make: *** Waiting for unfinished jobs.... * * ERROR: dev-java/hdf-java-2.5 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 4108: Called die * The specific snippet of code: * emake || die * The die message: * (no error message) * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/dev-java/hdf-java-2.5/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-java/hdf-java-2.5/temp/environment'. * This ebuild is from an overlay: '/usr/local/portage/' * !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.17" JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="" and of course, the output of emerge --info