after a major system upgrade (new glibc, new gcc, new binutils), performing an "emerge -ve world" avogadro fails to merge
emerge --info Portage 2.2_rc1 (default/linux/amd64/2008.0, gcc-4.3.1, glibc-2.8_p20080602-r0, 2.6.25-gentoo-r6 x86_64) ================================================================= System uname: Linux-2.6.25-gentoo-r6-x86_64-AMD_Athlon-tm-_64_Processor_3200+-with-glibc2.2.5 Timestamp of tree: Tue, 08 Jul 2008 05:33:01 +0000 app-shells/bash: 3.2_p39 dev-java/java-config: 1.3.7, 2.1.6-r1 dev-lang/python: 2.5.2-r5 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.2.5 sys-apps/sandbox: 1.2.18.1-r3 sys-devel/autoconf: 2.13, 2.62-r1 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.4 virtual/os-headers: 2.6.25-r4 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/4.0/env /usr/kde/4.0/share/config /usr/kde/4.0/shutdown /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=k8 -O2 -pipe" DISTDIR="/var/distfiles" FEATURES="distlocks fixpackages metadata-transfer parallel-fetch preserve-libs sandbox sfperms strict unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="it_IT.UTF-8" LDFLAGS="" LINGUAS="it en fr" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" 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="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/layman/science /usr/local/portage/layman/java-overlay /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 7zip X Xaw3d a52 aac aalib acl acpi adns alsa amd64 amr amrnb amrwb ao apache2 apm audiofile bcmath berkdb bidi bzip2 cairo caps cdda cddb cdparanoia cgraph chm cjk cli clisp cracklib crypt css cups curl cvs daap dbus divx djbfft djvu dts dv dvb dvd dvdr dvdread dynamic enca encode epydoc exif expat extra extrafilters fame faxonly ffmpeg fftw flac flash fltk fontconfig foomaticdb fortran fpx freetds ftp fuse games gcj gcrypt gd gdbm gif gimp ginac glib glitz gmedia gmp gnome gnuplot gnutls gpm graphics graphviz gs gtk hal hdri heterogeneous hfs howl-compat hpn html iconv id3 id3tag idn imagemagick imlib inotify iproute2 ipv6 isc isdnlog jack jadetex java java6 javascript jbig jpeg jpeg2k kerberos kpathsea ladspa lame lapack latex lcms libcaca libffi libsamplerate libwww live loop-aes lua lzo mad matroska md5sum mdnsresponder-compat metric midi mikmod mjpeg mmap mmx mmxext mng modplug motif mozsha1 mp2 mp3 mp4 mpeg mpeg2 mplayer msn mudflap multilib musepack musicbrainz mysql ncurses nemesi nethack network network-cron nls nodrm nptl nptlonly nsplugin nss ntfs nuv objc octave odbc offensive ogg ogm openal openexr opengl openmp oss paste64 pcap pch pcre pdf perl php physfs plotutils plugins png pnm portaudio postgres postscript ppds pppd pstricks pth publishers python q32 q8 qhull qt3support qt4 quicktime rar react readline realmedia reflection reiserfs rle romio rtc rtsp samba sasl scanner science sdl sdl-image session sftp slang slp smux sndfile snmp socks5 soundtouch sox sparse speex spell spl spoof-source sqlite sqlite3 srt sse sse2 ssl stream subversion svg tcl teletext tetex tex4ht tftp tga theora threads threadsafe tidy tiff timidity tk tools tordns truetype twolame unicode urandom usb utempter v4l v4l2 vamp vcd vdr vim-syntax vim-with-x vorbis wavpack webdav wmf wmp wxwindows x264 xanim xcb xetex xforms xft xml xmlrpc xmp xorg xpm xscreensaver xsl xulrunner xv xvid xvmc yv12 zip 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="it en fr" USERLAND="GNU" VIDEO_CARDS="nvidia v4l" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS logfiles attached
Created attachment 159876 [details] emerge log
found a (partial) solution... maybe the bug name should be changed. avogadro builds fine against openbabel-2.2.0_beta5, and fails against openbabel-2.2.0
(In reply to comment #3) > found a (partial) solution... maybe the bug name should be changed. > > avogadro builds fine against openbabel-2.2.0_beta5, and fails against > openbabel-2.2.0 > Thanks for the note! I'll have a look at this. Best, Markus
The problem was an API change in the final openbabel release which broke avogadro. I've just bumped avogadro to version 0.8.1 with a fix for this issue. Thanks, Markus
