Created attachment 314247 [details] build log gentoo $ for l in usr/lib/libhdf5*.so ; do echo "${l}" ; ldd "${l}" | grep ' /usr' ; done usr/lib/libhdf5.so libz.so.1 => /usr/lib64/libz.so.1 (0x00002b3a59122000) usr/lib/libhdf5_cpp.so libz.so.1 => /usr/lib64/libz.so.1 (0x00002b4ac6f8c000) usr/lib/libhdf5_fortran.so libz.so.1 => /usr/lib64/libz.so.1 (0x00002b28417c0000) usr/lib/libhdf5_hl.so libhdf5.so.7 => /usr/lib64/libhdf5.so.7 (0x00002b71328c4000) libz.so.1 => /usr/lib64/libz.so.1 (0x00002b7132d63000) usr/lib/libhdf5_hl_cpp.so libz.so.1 => /usr/lib64/libz.so.1 (0x00002adec9f68000) usr/lib/libhdf5hl_fortran.so libz.so.1 => /usr/lib64/libz.so.1 (0x00002ac7fc2d9000) Additionally, none of the h5* executables link against prefix libraries. The libraries other than libhdf5_hl.so correctly link against the prefix libhdf5.so . $ emerge --info hdf5 Portage 2.2.01.20430-prefix (prefix/linux/amd64, gcc-4.6.3, unavailable, 2.6.18-238.12.1.el5 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.18-238.12.1.el5-x86_64-Intel-R-_Core-TM-2_CPU_6700_@_2.66GHz-with-redhat-5.5-Boron Timestamp of tree: Mon, 04 Jun 2012 01:54:04 +0000 app-shells/bash: 4.2_p29::gentoo_prefix dev-lang/python: 2.7.3-r2::gentoo_prefix dev-util/pkgconfig: 0.26::gentoo_prefix sys-devel/autoconf: 2.69::gentoo_prefix sys-devel/automake: 1.11.5::gentoo_prefix sys-devel/binutils: 2.22-r1::gentoo_prefix sys-devel/gcc: 4.6.3::gentoo_prefix sys-devel/gcc-config: 1.5-r2::gentoo_prefix sys-devel/libtool: 2.4.2::gentoo_prefix sys-devel/make: 3.82::gentoo_prefix sys-kernel/linux-headers: 3.4::gentoo_prefix (virtual/os-headers) Repositories: gentoo_prefix Installed sets: ACCEPT_KEYWORDS="~amd64-linux" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/portage /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/home/astrosun/wthrowe/tmp/distfiles" EMERGE_DEFAULT_OPTS="--ask" FEATURES="assume-digests binpkg-logs clean-logs collision-protect compress-build-logs distlocks ebuild-locks fixlafiles force-prefix news parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="POSIX" LDFLAGS="-Wl,-O1 -Wl,--hash-style=gnu" MAKEOPTS="-j3" PKGDIR="/home/supernova/wthrowe/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/home/supernova/wthrowe/gentoo/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/home/supernova/wthrowe/gentoo/var/tmp" PORTDIR="/home/supernova/wthrowe/gentoo/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix" USE="amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules mudflap ncurses nls nptl openmp pcre pppd prefix readline session sse sse2 ssl tcpd unicode xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-libs/hdf5-1.8.9 was built with the following: USE="cxx fortran (prefix) zlib -debug -examples -fortran2003 -mpi -static-libs -szip -threads"
Are you in prefix environment? ldd will show you different things wrt to your LD_LIBRARY_PATH settings. Try e.g. LD_LIBRARY_PATH="${EPREFIX}/usr/lib" ldd ${EPREFIX}/usr/lib/libhdf5.so
(In reply to comment #1) > Are you in prefix environment? ldd will show you different things wrt to > your LD_LIBRARY_PATH settings. > Try e.g. LD_LIBRARY_PATH="${EPREFIX}/usr/lib" ldd > ${EPREFIX}/usr/lib/libhdf5.so This was all done in the prefix environment, but the prefix environmnet doesn't set LD_LIBRARY_PATH. Explicitly specifying LD_LIBRARY_PATH="${EPREFIX}/usr/lib:${EPREFIX}/lib" gets ldd to show the correct libraries, but everything in the prefix except hdf5 works without LD_LIBRARY_PATH. It looks like all the hdf5 executables and libraries are missing ${EPREFIX}{,/usr}/lib from their RPATH/RUNPATH headers.
+*hdf5-1.8.9-r1 (06 Jun 2012) + + 06 Jun 2012; Kacper Kowalik <xarthisius@gentoo.org> +hdf5-1.8.9-r1.ebuild, + -hdf5-1.8.9.ebuild: + Don't disable rpath for shared libraries wrt #419677 by William Throwe + <wtt6@cornell.edu> +
Unfortunately, not fixed. It no longer tries to use the host libhdf5, but still uses the host libz. (I don't seem to be able to reopen the bug.) Some of the RPATHs now have ${EPREFIX}/usr/lib, but still not ${EPREFIX}/lib, which is where libz is. (libhdf5.so itself still has neither.)
I was about to open another bug for this, but on inspection I think it is the same issue we're seeing here. The package no longer builds with USE=fortran because it tries to use the host libgcc_s.so to run H5test_kind after (apparently) originally linking it against the prefix version. (Related to bug 419895 somehow?) make[2]: Entering directory `/home/supernova/wthrowe/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.9-r1/work/hdf5-1.8.9/fortran/src' x86_64-pc-linux-gnu-gfortran -I../../src -I../../fortran/src -c -o H5test_kind_SIZEOF.o `test -f './H5test_kind_SIZEOF.f90' || echo './'`./H5test_kind_SIZEOF.f90 /home/supernova/wthrowe/gentoo/bin/bash ../../libtool --tag=FC --mode=link x86_64-pc-linux-gnu-gfortran -I../../src -I../../fortran/src -static-libgfortran -Wl,-O1 -Wl,--hash-style=gnu -o H5test_kind H5test_kind_SIZEOF.o -lz -lrt -lm libtool: link: x86_64-pc-linux-gnu-gfortran -I../../src -I../../fortran/src -static-libgfortran -Wl,-O1 -Wl,--hash-style=gnu -o H5test_kind H5test_kind_SIZEOF.o -lz -lrt -lm ./H5test_kind > H5fortran_detect.f90 ./H5test_kind: /lib64/libgcc_s.so.1: version `GCC_4.3.0' not found (required by ./H5test_kind) make[2]: *** [H5fortran_detect.f90] Error 1 Let me know if you'd prefer I open another bug.
+ 07 Jun 2012; Kacper Kowalik <xarthisius@gentoo.org> hdf5-1.8.9-r1.ebuild: + Add explicit rpath for prefix wrt #419677 by William Throwe <wtt6@cornell.edu> Try now, I've tested it with gcc-4.5 having gcc-4.6 installed, I couldn't reproduce the error from c#5
Seems to fix both remaining problems (libz and the build failure). Thanks!
