here is the error of compilation 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.... Reproducible: Always Steps to Reproduce: emerge hdf-java GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.17" JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="" emerge --info Portage 2.1.6.13 (default/linux/amd64/10.0/desktop, gcc-4.3.4, glibc-2.10.1-r1, 2.6.32-tuxonice x86_64) ================================================================= System uname: Linux-2.6.32-tuxonice-x86_64-AMD_Turion-tm-_64_X2_Mobile_Technology_TL-56-with-gentoo-1.12.13 Timestamp of tree: Wed, 13 Jan 2010 23:30:01 +0000 app-shells/bash: 4.0_p35 dev-java/java-config: 2.1.9-r2 dev-lang/python: 2.6.4 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -msse3 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-march=k8 -msse3 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="en_US fr it ru" MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage /usr/local/layman/kde-testing /usr/local/layman/science /usr/local/layman/java-overlay" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow X a52 aac acl acpi alsa amd64 bash-completion berkdb branding bzip2 cairo cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr dvdread emboss encode fam ffmpeg firefox fortran ftp gdbm gif gimp gnuplot hal hddtemp iconv icq ipod ipv6 jabber jpeg kde lame laptop ldap libnotify mad matroska mikmod mmx mng modules mozilla mp3 mp4 mpeg mudflap multilib ncurses networkmanager nls nptl nptlonly nsplugin ogg opengl openmp pam pcre pdf perl plasma plotutils png posix ppds pppd python qt3support qt4 quicktime raw readline reflection sdl session spell spl sse sse2 ssl startup-notification svg sysfs tcpd theora thunar tiff truetype unicode usb vorbis wifi x264 xcb xcomposite xml xorg xprint xscreensaver xulrunner xv xvid zlib" ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en_US fr it ru" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa radeon" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 216630 [details] build.log
I don't see such a package in main tree or our overlays: betelgeuse@pena /mnt/checkouts/java $ echo */dev-java/hdf5* */dev-java/hdf5* betelgeuse@pena /usr/portage/dev-java $ ls -l hdf* ls: cannot access hdf*: No such file or directory Reopen when you can figure out where you got the ebuild from.
you can find it here: http://bugs.gentoo.org/show_bug.cgi?id=301049
(In reply to comment #3) > you can find it here: > http://bugs.gentoo.org/show_bug.cgi?id=301049 > You aren't supposed to open new bugs about ebuilds you find in bugzilla failing. Just comment on the existing bug in the future.
Could you try with the ebuild from the science-overlay? This is for hdf-java-2.6, but there is a patch in it which could help.
