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Bug 657964 - sci-libs/xdmf2-1.0_p141226-r2: compile failure: libXdmfCore.so: undefined reference to H5...
Summary: sci-libs/xdmf2-1.0_p141226-r2: compile failure: libXdmfCore.so: undefined ref...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal with 1 vote (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-06-12 10:48 UTC by Thomas Deutschmann
Modified: 2018-10-28 22:12 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,64.75 KB, text/plain)
2018-06-12 10:48 UTC, Thomas Deutschmann
Details

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Description Thomas Deutschmann gentoo-dev Security 2018-06-12 10:48:36 UTC
Created attachment 535694 [details]
build.log

/usr/bin/i686-pc-linux-gnu-g++  -O2 -pipe -march=pentium4m -mtune=pentium4m -std=c++14  -Wl,-O1 -Wl,--as-needed -rdynami
c CMakeFiles/TestXdmfInformation.dir/TestXdmfInformation.cpp.o  -o TestXdmfInformation -Wl,-rpath,/var/tmp/portage/sci-l
ibs/xdmf2-1.0_p141226-r2/work/xdmf2-1.0_p141226_build ../../../libXdmfCore.so -lxml2
../../../libXdmfCore.so: undefined reference to `H5Dset_extent'
../../../libXdmfCore.so: undefined reference to `H5Pcreate'
../../../libXdmfCore.so: undefined reference to `H5Fopen'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_INT_g'
../../../libXdmfCore.so: undefined reference to `H5check_version'
../../../libXdmfCore.so: undefined reference to `H5Dget_space'
../../../libXdmfCore.so: undefined reference to `H5Sget_simple_extent_npoints'
../../../libXdmfCore.so: undefined reference to `H5Eget_auto2'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_SHORT_g'
../../../libXdmfCore.so: undefined reference to `H5Dread'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_UCHAR_g'
../../../libXdmfCore.so: undefined reference to `H5Sget_simple_extent_ndims'
../../../libXdmfCore.so: undefined reference to `H5Tset_size'
../../../libXdmfCore.so: undefined reference to `H5Fis_hdf5'
../../../libXdmfCore.so: undefined reference to `H5Fcreate'
../../../libXdmfCore.so: undefined reference to `H5Pclose'
../../../libXdmfCore.so: undefined reference to `H5Screate_simple'
../../../libXdmfCore.so: undefined reference to `H5Sselect_hyperslab'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_DOUBLE_g'
../../../libXdmfCore.so: undefined reference to `H5Dvlen_reclaim'
../../../libXdmfCore.so: undefined reference to `H5T_C_S1_g'
../../../libXdmfCore.so: undefined reference to `H5Lexists'
../../../libXdmfCore.so: undefined reference to `H5Dopen2'
../../../libXdmfCore.so: undefined reference to `H5Tcopy'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_UINT_g'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_FLOAT_g'
../../../libXdmfCore.so: undefined reference to `H5Eset_auto2'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_LONG_g'
../../../libXdmfCore.so: undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
../../../libXdmfCore.so: undefined reference to `H5Sget_select_npoints'
../../../libXdmfCore.so: undefined reference to `H5Sclose'
../../../libXdmfCore.so: undefined reference to `H5open'
../../../libXdmfCore.so: undefined reference to `H5Pset_chunk'
../../../libXdmfCore.so: undefined reference to `H5Tclose'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_SCHAR_g'
../../../libXdmfCore.so: undefined reference to `H5T_NATIVE_USHORT_g'
../../../libXdmfCore.so: undefined reference to `H5Dwrite'
../../../libXdmfCore.so: undefined reference to `H5Dclose'
../../../libXdmfCore.so: undefined reference to `H5Fclose'
../../../libXdmfCore.so: undefined reference to `H5Gget_num_objs'
../../../libXdmfCore.so: undefined reference to `H5Dcreate2'
collect2: error: ld returned 1 exit status


Portage 2.3.40 (python 3.5.5-final-0, default/linux/x86/17.0, gcc-6.4.0, glibc-2.26-r7, 4.9.95-gentoo i686)
=================================================================
System uname: Linux-4.9.95-gentoo-i686-Intel-R-_Core-TM-_i7-3770K_CPU_@_3.50GHz-with-gentoo-2.4.1
KiB Mem:     3108308 total,   1720260 free
KiB Swap:     488276 total,    488276 free
Timestamp of repository gentoo: Tue, 12 Jun 2018 10:06:38 +0000
Head commit of repository gentoo: 6161b7216da22b4aeeeecd0cd61cc78750a7c2a0

sh bash 4.4_p12
ld GNU ld (Gentoo 2.30 p2) 2.30.0
app-shells/bash:          4.4_p12::gentoo
dev-lang/perl:            5.24.3-r1::gentoo
dev-lang/python:          2.7.14-r1::gentoo, 3.5.5::gentoo
dev-util/cmake:           3.9.6::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.4.1-r2::gentoo
sys-apps/openrc:          0.34.11::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.15.1-r2::gentoo
sys-devel/binutils:       2.29.1-r1::gentoo, 2.30-r2::gentoo
sys-devel/gcc:            6.4.0-r1::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers)
sys-libs/glibc:           2.26-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gentoo.git
    priority: -1000

ABI="x86"
ABI_X86="32"
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA"
ACCEPT_PROPERTIES="*"
ACCEPT_RESTRICT="*"
ARCH="x86"
BROOT=""
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=pentium4m -mtune=pentium4m"
CHOST="i686-pc-linux-gnu"
CHOST_x86="i686-pc-linux-gnu"
COLLISION_IGNORE="/lib/modules/* *.py[co] *$py.class */dropin.cache"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CPU_FLAGS_X86="mmx mmxext sse sse2"
CXXFLAGS="-O2 -pipe -march=pentium4m -mtune=pentium4m"
DEFAULT_ABI="x86"
EDITOR="/usr/bin/mcedit"
ELIBC="glibc"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
EPREFIX=""
EROOT="/"
ESYSROOT="/"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs cgroup config-protect-if-modified distlocks downgrade-backup ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=i686 -pipe"
GCC_SPECS=""
GRUB_PLATFORMS="efi-32 pc"
GSETTINGS_BACKEND="dconf"
HOME="/root"
INFOPATH="/usr/share/gcc-data/i686-pc-linux-gnu/6.4.0/info:/usr/share/binutils-data/i686-pc-linux-gnu/2.30/info:/usr/share/info:/usr/share/info/emacs-25"
INPUT_DEVICES="libinput keyboard mouse"
IUSE_IMPLICIT="abi_x86_32 prefix prefix-chain prefix-guest"
KERNEL="linux"
L10N="en en-US de de-DE"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
LC_MESSAGES="C"
LC_PAPER="de_DE.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LIBDIR_x86="lib"
LINGUAS="en de"
LOGNAME="root"
MAIL="/var/mail/root"
MAKEOPTS="--jobs 5 --load-average 7.95"
MULTILIB_ABIS="x86"
NOCOLOR="true"
OFFICE_IMPLEMENTATION="libreoffice"
OLDPWD="/root"
OPENCL_PROFILE="mesa"
OPENGL_PROFILE="xorg-x11"
PAGER="/usr/bin/less"
PATH="/usr/i686-pc-linux-gnu/gcc-bin/6.4.0:/usr/lib/llvm/5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin"
PHP_TARGETS="php5-6 php7-0"
POSTGRES_TARGETS="postgres9_5"
PWD="/etc/portage/patches"
PYTHONDONTWRITEBYTECODE="1"
PYTHON_SINGLE_TARGET="python3_5"
PYTHON_TARGETS="python2_7 python3_5"
QT_GRAPHICSSYSTEM="raster"
ROOT="/"
ROOTPATH="/usr/i686-pc-linux-gnu/gcc-bin/6.4.0:/usr/lib/llvm/5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin"
RUBY_TARGETS="ruby22 ruby23"
SHELL="/bin/bash"
SHLVL="2"
SSH_TTY="/dev/pts/0"
SYSROOT="/"
TERM="tmux-256color"
TMUX="/tmp/tmux-0/default,4926,0"
TMUX_PANE="%2"
TWISTED_DISABLE_WRITING_OF_PLUGIN_CACHE="1"
USER="root"
USERLAND="GNU"
VIDEO_CARDS="vmware"
XDG_CONFIG_DIRS="/etc/xdg"
XDG_DATA_DIRS="/usr/local/share:/usr/share"
Comment 1 Daniel M. Weeks 2018-10-08 21:28:05 UTC
The stable version of this package is broken (bug 630728) and this is blocking the fix (bug 657938).