| Summary: | sci-physics/root-6.04.06 - /usr/lib64/libicuuc.so.58: undefined reference to `operator delete(void*, unsigned long)@CXXABI_1.3.9' | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | Current packages | Assignee: | Andrew Savchenko <bircoph> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | jstein, sci-physics |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
This looks like an upstream bug to me. Can you report this to upstream and link the ticket here? Is there a patch available, that can be used for gentoo? /usr/lib64/libicuuc.so.58: undefined reference to `operator delete(void*, unsigned long)@CXXABI_1.3.9' ^^^ This bothers me. Looks like you have C++ ABI mismatch. Have you updated your gcc recently? Try to rebuild dev-libs/icu first (or run system-wide rebuild of @preserved-rebuild and run revdep-rebuild afterwards) with the same compiler version as used for root. Please note that after icu rebuild you may have similar failures with other libraries, so they should be all rebuild with the same version of gcc. Also please note that >=gcc-5 is not supported for >=root-6, so you'll have to build most of your C++ libs with gcc-4.x or downgrade to root-5. Looks like root-6.08 has this issue fixed: https://sft.its.cern.ch/jira/browse/ROOT-7947 at least for C++11, they still have trouble with C++14: https://sft.its.cern.ch/jira/browse/ROOT-8270 Considering enormous complexity of ROOT these days it will take some serious time to add 6.08 to the tree. *** This bug has been marked as a duplicate of bug 596290 *** The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=819d5014a7859a590292287d76e5a708daf230c0 commit 819d5014a7859a590292287d76e5a708daf230c0 Author: Guilherme Amadio <amadio@gentoo.org> AuthorDate: 2017-12-14 16:05:56 +0000 Commit: Guilherme Amadio <amadio@gentoo.org> CommitDate: 2017-12-15 11:56:09 +0000 sci-physics/root: version bump to 6.12.04 Closes: https://bugs.gentoo.org/622034 Closes: https://bugs.gentoo.org/617160 Closes: https://bugs.gentoo.org/599274 Closes: https://bugs.gentoo.org/596290 Package-Manager: Portage-2.3.18, Repoman-2.3.6 sci-physics/root/Manifest | 1 + sci-physics/root/files/root-6.11.02-hsimple.patch | 34 +++ sci-physics/root/metadata.xml | 32 +- sci-physics/root/root-6.12.04.ebuild | 345 ++++++++++++++++++++++ 4 files changed, 403 insertions(+), 9 deletions(-) |
'emerge -v1 root' fails with: ... x86_64-pc-linux-gnu-g++ -m64 -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--no-undefined -Wl,--as-needed -o bin/hist2workspace roofit/histfactory/src/MakeModelAndMeasurements.o roofit/histfactory/src/hist2workspace.o \ -Llib -lRIO -lHist -lGraf -lGraf3d -lGpad -lTree -lMatrix -lNet -lThread -lMathCore -lCore -lRint -Llib -lRooFit -lRooFitCore -lTree -lRIO -lMatrix -lHist -lMathCore -lGraf -lGpad -lMinuit -lFoam -lRooStats -lXMLParser -lHistFactory -lMathMore -lgsl -lgslcblas \ -lm -ldl -pthread -rdynamic /usr/lib64/libicuuc.so.58: undefined reference to `operator delete(void*, unsigned long)@CXXABI_1.3.9' collect2: error: ld returned 1 exit status make: *** [/var/tmp/portage/sci-physics/root-6.04.06/work/root-6.04.06/roofit/histfactory/Module.mk:123: bin/hist2workspace] Error 1 lynx ~ # emerge --info '=sci-physics/root-6.04.06::local' Portage 2.3.2 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.23-r2, 4.8.6-rt-rt5 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.8.6-rt-rt5-x86_64-Intel-R-_Core-TM-_i7-3630QM_CPU_@_2.40GHz-with-gentoo-2.3 KiB Mem: 15202184 total, 5427236 free KiB Swap: 50331644 total, 49777952 free Timestamp of repository gentoo: Wed, 09 Nov 2016 07:30:01 +0000 sh bash 4.4-r1 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 distcc[18484] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Oct 2 2016 20:49:06 [disabled] app-shells/bash: 4.4-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r2::gentoo dev-lang/python: 2.7.12-r100::sage-on-gentoo, 3.4.5::gentoo, 3.5.2::gentoo dev-util/cmake: 3.6.3::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.22.3::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 4.9.3::gentoo, 5.4.0::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage_lynx sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 local location: /usr/local/portage masters: gentoo priority: 0 g-cpan location: /var/lib/cpan masters: gentoo priority: 1 g-octave location: /var/lib/g-octave masters: gentoo priority: 2 activehome location: /var/lib/layman/activehome masters: gentoo priority: 50 ago location: /var/lib/layman/ago masters: gentoo priority: 50 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo masters: gentoo science priority: 50 science location: /var/lib/layman/science masters: gentoo priority: 50 sunrise location: /var/lib/layman/sunrise masters: gentoo priority: 50 tlp location: /var/lib/layman/tlp masters: gentoo priority: 50 x11 location: /var/lib/layman/x11 masters: gentoo priority: 50 Installed sets: @system ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news noclean nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j9" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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="/var/tmp" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile aufs automap automount barcode bash-completion berkdb blas blast bluetooth bluray boost branding btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cilk cli cmake collada consolekit contrib cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia digitalradio djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples excel exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse gcj gd gdal gdbm gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jadetex java jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate lirc live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg opencl opencv openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python q16 q32 qemu qhull qml qt3support qt4 qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tbb tcl tcpd tex tex4ht theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video vim-syntax virt-network virtualbox visio vorbis vpx vtk wav wayland webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zsh-completion zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="nss" DVB_CARDS="usb-wt220u dvb_usb_rtl28xxu" ELIBC="glibc" GPSD_PROTOCOLS="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 navcom ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf superstar2 tnt tripmate tsip ublox nmea0183 nmea2000 passthrough" GRUB_PLATFORMS="emu efi-64 pc xen" INPUT_DEVICES="keyboard mouse evdev synaptics void" KERNEL="linux" L10N="de en fr ru" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en fr ru" LIRC_DEVICES="devinput" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="nouveau intel i965 displaylink" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-physics/root-6.04.06::local was built with the following: USE="R X doc emacs examples fftw fits graphviz http kerberos ldap math memstat mpi mysql odbc opengl postgres python qt4 sqlite ssl tiff xml -afs -avahi -gdml -geocad -openmp -oracle (-prefix) -pythia6 -pythia8 -shadow -table -xinetd -xrootd" ABI_X86="64" PYTHON_TARGETS="python2_7" lynx ~ # emerge -pqv '=sci-physics/root-6.04.06::local' [ebuild R ] sci-physics/root-6.04.06 USE="R X doc emacs examples fftw fits graphviz http kerberos ldap math memstat mpi mysql odbc opengl postgres python qt4 sqlite ssl tiff xml -afs -avahi -gdml The local root-6.04.06.ebuild contains the gsl-2.patch: root@lynx:/usr/local/portage/sci-physics/root(151)# diff root-6.04.06.ebuild root-6.04.06.ebuild_orig 244,245c244 < "${FILESDIR}"/${P}-prop-flags.patch \ < "${FILESDIR}"/${P}_gsl-2.patch --- > "${FILESDIR}"/${P}-prop-flags.patch