Seems the ebuild fails on Gentoo:Prefix via bootstrap_rap.sh (with it's own glibc). I see the library comes from gcc so I am puzzled what could be the real cause. I think my toolchain works fine. make[1]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15_p1_build/fortran' Making all in src make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15_p1_build/fortran/src' x86_64-pc-linux-gnu-gfortran -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/src -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/fortran/src -O2 -pipe -c -o H5test_kind_STORAGE_SIZE.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/fortran/src/H5test_kind_STORAGE_SIZE.f90 /scratch/mmokrejs/gentoo_rap/bin/bash ../../libtool --tag=FC --mode=link x86_64-pc-linux-gnu-gfortran -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/src -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/fortran/src -O2 -pipe -static-libgfortran -Wl,-O1 -Wl,--as-needed -Wl,-rpath,/scratch/mmokrejs/gentoo_rap/usr/lib64 -Wl,-rpath,/scratch/mmokrejs/gentoo_rap/lib64 -o H5test_kind H5test_kind_STORAGE_SIZE.o -lz -ldl -lm libtool: link: x86_64-pc-linux-gnu-gfortran -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/src -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/fortran/src -O2 -pipe -static-libgfortran -Wl,-O1 -Wl,-rpath -Wl,/scratch/mmokrejs/gentoo_rap/usr/lib64 -Wl,-rpath -Wl,/scratch/mmokrejs/gentoo_rap/lib64 -o H5test_kind H5test_kind_STORAGE_SIZE.o -Wl,--as-needed -lz -ldl -lm ./H5test_kind > H5fortran_detect.f90 ./H5test_kind: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory make[2]: *** [Makefile:1437: H5fortran_detect.f90] Error 127 make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15_p1_build/fortran/src' make[1]: *** [Makefile:750: all-recursive] Error 1 make[1]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15_p1_build/fortran' make: *** [Makefile:589: all-recursive] Error 1 ESC[31;01m*ESC[0m ERROR: sci-libs/hdf5-1.8.15_p1::gentoo failed (compile phase): ESC[31;01m*ESC[0m emake failed ESC[31;01m*ESC[0m ESC[31;01m*ESC[0m If you need support, post the output of `emerge --info '=sci-libs/hdf5-1.8.15_p1::gentoo'`, ESC[31;01m*ESC[0m the complete build log and the output of `emerge -pqv '=sci-libs/hdf5-1.8.15_p1::gentoo'`. ESC[31;01m*ESC[0m The complete build log is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/temp/build.log'. ESC[31;01m*ESC[0m The ebuild environment file is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/temp/environment'. ESC[31;01m*ESC[0m Working directory: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15_p1_build' ESC[31;01m*ESC[0m S: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1' $ emerge --info '=sci-libs/hdf5-1.8.15_p1::gentoo' Portage 2.3.0 (python 3.4.4-final-0, prefix/linux-standalone/amd64, gcc-5.4.0, unavailable, 2.6.32-573.12.1.el6.Bull.88.x86_64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-573.12.1.el6.Bull.88.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2670_0_@_2.60GHz-with-redhat-6.4-Santiago KiB Mem: 131942764 total, 10708976 free KiB Swap: 65536128 total, 64526960 free Timestamp of repository gentoo: Wed, 29 Jun 2016 12:30:01 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26) 2.26.20160125 app-shells/bash: 4.3_p46::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.11-r2::gentoo, 3.4.4::gentoo dev-util/cmake: 3.5.2-r1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.2::rap sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26::rap sys-devel/gcc: 5.4.0::gentoo sys-devel/gcc-config: 1.8_p20160608::rap sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::rap Repositories: gentoo location: /scratch/mmokrejs/gentoo_rap/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap rap location: /scratch/mmokrejs/gentoo_rap/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap science location: /scratch/mmokrejs/gentoo/var/lib/layman/science masters: gentoo priority: 0 eclass-overrides: rap haskell location: /scratch/mmokrejs/gentoo/var/lib/layman/haskell masters: gentoo priority: 1 eclass-overrides: rap x-layman location: /scratch/mmokrejs/gentoo_rap/var/lib/layman masters: gentoo priority: 2 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -O2 -pipe -march=native" DISTDIR="/scratch/mmokrejs/gentoo_rap/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged userfetch userpriv usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/scratch/mmokrejs/gentoo_rap/usr/portage/packages" PORTAGE_CONFIGROOT="/scratch/mmokrejs/gentoo_rap/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/scratch/mmokrejs/gentoo_rap/var/tmp" USE="acl amd64 berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx mmxext modules ncurses nls nptl openmp pcre prefix readline seccomp session sse sse2 ssl tcpd unicode zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 ublox 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa 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" USE_PYTHON="2.7" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Does calling EPREFIX/sbin/ldconfig manually solve this bug?
Seems you are right: $ cd /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15_p1_build/fortran/src $ /scratch/mmokrejs/gentoo_rap/sbin/ldconfig $ /scratch/mmokrejs/gentoo_rap/bin/bash ../../libtool --tag=FC --mode=link x86_64-pc-linux-gnu-gfortran -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/src -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/fortran/src -O2 -pipe -static-libgfortran -Wl,-O1 -Wl,--as-needed -Wl,-rpath,/scratch/mmokrejs/gentoo_rap/usr/lib64 -Wl,-rpath,/scratch/mmokrejs/gentoo_rap/lib64 -o H5test_kind H5test_kind_STORAGE_SIZE.o -lz -ldl -lm libtool: link: x86_64-pc-linux-gnu-gfortran -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/src -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-libs/hdf5-1.8.15_p1/work/hdf5-1.8.15-patch1/fortran/src -O2 -pipe -static-libgfortran -Wl,-O1 -Wl,-rpath -Wl,/scratch/mmokrejs/gentoo_rap/usr/lib64 -Wl,-rpath -Wl,/scratch/mmokrejs/gentoo_rap/lib64 -o H5test_kind H5test_kind_STORAGE_SIZE.o -Wl,--as-needed -lz -ldl -lm $ ls -latr H5test_kind -rwxr-xr-x 1 mmokrejs mmokrejs 215424 Jun 30 13:40 H5test_kind $ without an error.
*** This bug has been marked as a duplicate of bug 532100 ***
