Portage 2.1.9.30 (default/linux/x86/10.0, gcc-4.5.2-asneeded, glibc-2.12.2-r0, 2.6.37 i686) ================================================================= System uname: Linux-2.6.37-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-gentoo-2.0.1 Timestamp of tree: Sun, 09 Jan 2011 16:30:01 +0000 ccache version 3.1.3 [disabled] app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.4.6, 2.6.6-r1, 2.7.1, 3.1.3 dev-util/ccache: 3.1.3 dev-util/cmake: 2.8.3-r1 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.6.8 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="*" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /opt/openjms/config /usr/lib/tomoyo/conf /usr/share/bufrtables /usr/share/config /usr/share/maven-bin-2.2/conf /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /usr/share/qpsmtpd/plugins /var/bind /var/lib/hsqldb /var/lib/redmine/config /var/phxd /var/vpopmail/etc /var/yp/Makefile" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/games/angband/edit/ /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/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="-O2 -pipe" DISTDIR="/var/cache/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms split-log strict test test-fail-continue unknown-features-warn unmerge-orphans userfetch userpriv usersandbox" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://gentoo.wheel.sk/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" MAKEOPTS="-j14" PKGDIR="/var/spool/portage/packages" PORTAGE_COMPRESS="" 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="/var/cache/portage/tree" SYNC="rsync://yamato.home.flameeyes.eu/gentoo-portage" USE="acl berkdb bzip2 cli cracklib crypt cups cxx dri fortran gdbm gpm iconv ipv6 java5 java6 modules mudflap mysql ncurses nls nostatic nptl nptlonly openmp pam pcre pcsc-lite perl postgres pppd python qt3support readline ruby session ssl sysfs tcpd unicode vhosts x86 xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 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 auth_digest cgi" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18 jruby ruby19 ree18" USERLAND="GNU" VIDEO_CARDS="intel radeon nouveau vmware" 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"
Created attachment 259398 [details] Build log
Parallel make issue, Diego?
I think it looks more like a broken link line with --as-needed: /usr/bin/i686-pc-linux-gnu-g++ -fPIC -O2 -pipe -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security -fno-exceptions -fno-check-new -fno-common -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security -fno-exceptions -DQT_NO_EXCEPTIONS -fno-check-new -fno-common -Woverloaded-virtual -fno-threadsafe-statics -fvisibility=hidden -fvisibility-inlines-hidden -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -shared -Wl,-soname,libmolsketch.so -o ../../lib/libmolsketch.so CMakeFiles/molsketch_LIB.dir/molecule.o CMakeFiles/molsketch_LIB.dir/atom.o CMakeFiles/molsketch_LIB.dir/mollibitem.o CMakeFiles/molsketch_LIB.dir/bond.o CMakeFiles/molsketch_LIB.dir/element.o CMakeFiles/molsketch_LIB.dir/molview.o CMakeFiles/molsketch_LIB.dir/molscene.o CMakeFiles/molsketch_LIB.dir/commands.o CMakeFiles/molsketch_LIB.dir/fileio.o CMakeFiles/molsketch_LIB.dir/minimise.o CMakeFiles/molsketch_LIB.dir/TextInputItem.o CMakeFiles/molsketch_LIB.dir/osra.o CMakeFiles/molsketch_LIB.dir/electronsystem.o CMakeFiles/molsketch_LIB.dir/residue.o CMakeFiles/molsketch_LIB.dir/itemplugin.o CMakeFiles/molsketch_LIB.dir/molinputitem.o CMakeFiles/molsketch_LIB.dir/mimemolecule.o CMakeFiles/molsketch_LIB.dir/reactionarrow.o CMakeFiles/molsketch_LIB.dir/mechanismarrow.o CMakeFiles/molsketch_LIB.dir/smilesitem.o CMakeFiles/molsketch_LIB.dir/atomnumberitem.o CMakeFiles/molsketch_LIB.dir/stereocenteritem.o CMakeFiles/molsketch_LIB.dir/reactionarrowdialog.o CMakeFiles/molsketch_LIB.dir/mechanismarrowdialog.o CMakeFiles/molsketch_LIB.dir/graphsymitem.o CMakeFiles/molsketch_LIB.dir/tool.o CMakeFiles/molsketch_LIB.dir/toolgroup.o CMakeFiles/molsketch_LIB.dir/tools/drawtool.o CMakeFiles/molsketch_LIB.dir/tools/movetool.o CMakeFiles/molsketch_LIB.dir/tools/lassotool.o CMakeFiles/molsketch_LIB.dir/tools/rotatetool.o CMakeFiles/molsketch_LIB.dir/tools/minimizetool.o CMakeFiles/molsketch_LIB.dir/tools/connecttool.o CMakeFiles/molsketch_LIB.dir/tools/chargetool.o CMakeFiles/molsketch_LIB.dir/tools/hydrogentool.o CMakeFiles/molsketch_LIB.dir/tools/electrontool.o CMakeFiles/molsketch_LIB.dir/tools/reactionarrowtool.o CMakeFiles/molsketch_LIB.dir/tools/mechanismarrowtool.o CMakeFiles/molsketch_LIB.dir/qrc_toolicons.o CMakeFiles/molsketch_LIB.dir/moc_atom.o CMakeFiles/molsketch_LIB.dir/moc_bond.o CMakeFiles/molsketch_LIB.dir/moc_element.o CMakeFiles/molsketch_LIB.dir/moc_itemplugin.o CMakeFiles/molsketch_LIB.dir/moc_fileio.o CMakeFiles/molsketch_LIB.dir/moc_graphicsitemtypes.o CMakeFiles/molsketch_LIB.dir/moc_reactionarrowdialog.o CMakeFiles/molsketch_LIB.dir/moc_mechanismarrowdialog.o CMakeFiles/molsketch_LIB.dir/moc_molecule.o CMakeFiles/molsketch_LIB.dir/moc_mollibitem.o CMakeFiles/molsketch_LIB.dir/moc_molscene.o CMakeFiles/molsketch_LIB.dir/moc_molinputitem.o CMakeFiles/molsketch_LIB.dir/moc_molview.o CMakeFiles/molsketch_LIB.dir/moc_osra.o CMakeFiles/molsketch_LIB.dir/moc_residue.o CMakeFiles/molsketch_LIB.dir/moc_smilesitem.o CMakeFiles/molsketch_LIB.dir/moc_tool.o CMakeFiles/molsketch_LIB.dir/moc_toolgroup.o CMakeFiles/molsketch_LIB.dir/tools/moc_drawtool.o CMakeFiles/molsketch_LIB.dir/tools/moc_movetool.o CMakeFiles/molsketch_LIB.dir/tools/moc_lassotool.o CMakeFiles/molsketch_LIB.dir/tools/moc_rotatetool.o CMakeFiles/molsketch_LIB.dir/tools/moc_minimizetool.o CMakeFiles/molsketch_LIB.dir/tools/moc_connecttool.o CMakeFiles/molsketch_LIB.dir/tools/moc_chargetool.o CMakeFiles/molsketch_LIB.dir/tools/moc_hydrogentool.o CMakeFiles/molsketch_LIB.dir/tools/moc_electrontool.o CMakeFiles/molsketch_LIB.dir/tools/moc_reactionarrowtool.o CMakeFiles/molsketch_LIB.dir/tools/moc_mechanismarrowtool.o /usr/lib/qt4/libQtAssistantClient.so /usr/lib/qt4/libQtSvg.so /usr/lib/qt4/libQtGui.so /usr/lib/qt4/libQtTest.so /usr/lib/qt4/libQtXml.so /usr/lib/qt4/libQtCore.so -lpthread -lopenbabel -Wl,-rpath,/usr/lib/qt4: the generated lib has very few symbols in it: 00036bd0 W std::_Deque_base<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::_M_initialize_map(unsigned int) 00036b70 W std::_Deque_base<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::~_Deque_base() 00036b70 W std::_Deque_base<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::~_Deque_base() 00036c80 W std::deque<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::_M_pop_front_aux() 00036e70 W std::deque<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::_M_push_back_aux(Molsketch::FFAtom* const&) 00036cd0 W std::deque<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::_M_reallocate_map(unsigned int, bool) 000369b0 W std::vector<Molsketch::FFInteraction*, std::allocator<Molsketch::FFInteraction*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Molsketch::FFInteraction**, std::vector<Molsketch::FFInteraction*, std::allocator<Molsketch::FFInteraction*> > >, Molsketch::FFInteraction* const&) 0002af90 W std::vector<Molsketch::Atom*, std::allocator<Molsketch::Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Molsketch::Atom**, std::vector<Molsketch::Atom*, std::allocator<Molsketch::Atom*> > >, Molsketch::Atom* const&) 0002b150 W std::vector<Molsketch::Bond*, std::allocator<Molsketch::Bond*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Molsketch::Bond**, std::vector<Molsketch::Bond*, std::allocator<Molsketch::Bond*> > >, Molsketch::Bond* const&) 00036640 W std::vector<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Molsketch::FFAtom**, std::vector<Molsketch::FFAtom*, std::allocator<Molsketch::FFAtom*> > >, Molsketch::FFAtom* const&) 000367f0 W std::vector<Molsketch::FFBond*, std::allocator<Molsketch::FFBond*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Molsketch::FFBond**, std::vector<Molsketch::FFBond*, std::allocator<Molsketch::FFBond*> > >, Molsketch::FFBond* const&) 00064740 A __bss_start 00064740 A _edata 000647c8 A _end 00053568 T _fini 0000dd78 T _init
I was afraid of that! An parallel make issue is easier to solve. On the other hand, I am using forced-as-needed and didn't have that problem.
Then now that's a strange situation, which ld version? That might matter.
GNU ld (GNU Binutils) 2.21
Which USE for openbabel are you using?
Absolutely the same situation for me. I have latest version of openbabel and all dependent packages. But i have x86_64 architecture. I've downloaded tarball for molsketch-0.2.0 and compile it by hand and i've got the same error message at link stage. I've downloaded molsketch-0.1.1 deuterium and it is compiled successfully! While you don't fix the error in 0.2 molsketch, may be it's good to add previous version to the repository?
Created attachment 267071 [details] molsketch-0.2.0 zeld build log Also i've problem while compiling molsketch, in linking library phase. I Attached my build log. Thanks zeld
issue still persists, even had to comment #set(QT_MIN_VERSION "4.5.0") # we need at least version 4.5 of Qt from CMakeLists.txt but that is rather a cmake issue. I would suggest to remove this package completely, since it seems impossible to compile, no matter what flags you use. There are numerous bug-reports about this on the web and it seems to be the same issue on other distros (confirmed on openSUSE). The project seems to be abandoned as well.
seems its not that abandoned http://molsketch.git.sourceforge.net/git/gitweb.cgi?p=molsketch/molsketch;a=summary btw. today i was able to compile it. I got no clue why. Some fixed cmake regression maybe?
Given your proxy has given up (*mutters something about proxy maintainers reassigning bugs to wranglers without saying anything*) care about removing this altogether?
I don't know, why he did this. Normally he is very fast and accurate in his actions. This bug is the next on my list.
I backported changes from upstream git which lets me build this prog, please test and reopen if still broken. + 24 Jun 2012; Justin Lecher <jlec@gentoo.org> molsketch-0.2.0-r1.ebuild, + +files/molsketch-0.2.0-openbabel-231.patch, metadata.xml: + Backport changes in order to fix some unknown build failure, #351232 +
