* package sci-chemistry/openbabel-python-2.2.2 NOT merged * * Detected file collision(s): * * /usr/lib/debug/usr/lib64/python2.6/site-packages/_openbabel.so.debug * /usr/lib64/python2.6/site-packages/openbabel.py * /usr/lib64/python2.6/site-packages/openbabel-1.5-py2.6.egg-info * /usr/lib64/python2.6/site-packages/openbabel.pyo * /usr/lib64/python2.6/site-packages/pybel.pyc * /usr/lib64/python2.6/site-packages/pybel.py * /usr/lib64/python2.6/site-packages/pybel.pyo * /usr/lib64/python2.6/site-packages/openbabel.pyc * /usr/lib64/python2.6/site-packages/_openbabel.so * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-chemistry/openbabel-2.2.2-r1 * /usr/lib/debug/usr/lib64/python2.6/site-packages/_openbabel.so.debug * /usr/lib64/python2.6/site-packages/_openbabel.so * /usr/lib64/python2.6/site-packages/openbabel-1.5-py2.6.egg-info * /usr/lib64/python2.6/site-packages/openbabel.py * /usr/lib64/python2.6/site-packages/openbabel.pyc * /usr/lib64/python2.6/site-packages/openbabel.pyo * /usr/lib64/python2.6/site-packages/pybel.py * /usr/lib64/python2.6/site-packages/pybel.pyc * /usr/lib64/python2.6/site-packages/pybel.pyo * * Package 'sci-chemistry/openbabel-python-2.2.2' NOT merged due to file * collisions. If necessary, refer to your elog messages for the whole * content of the above message. plaes@chi ~/code/QMForge-2.1 $ emerge --info Portage 2.2_rc44 (default/linux/amd64/2008.0/no-multilib, gcc-4.4.1, glibc-2.10.1-r0, 2.6.32-rc2-00309-g8a0382f x86_64) ================================================================= System uname: Linux-2.6.32-rc2-00309-g8a0382f-x86_64-Intel-R-_Core-TM-2_CPU_L7400_@_1.50GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 08 Oct 2009 05:00:01 +0000 distcc 3.1 x86_64-pc-linux-gnu [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.0_p33 dev-java/java-config: 1.3.7-r1, 2.1.9-r1 dev-lang/python: 2.6.3, 3.1.1-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.1 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -ggdb -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /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/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=native -ggdb -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests ccache collision-protect distlocks fixpackages multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="et_EE.UTF-8" LDFLAGS="-Wl,--as-needed" LINGUAS="en et" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" 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="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/layman/science /home/plaes/code/gentoo/gnome /home/plaes/code/gentoo/local /home/plaes/code/gentoo/tryton-overlay" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acpi adns alsa amd64 amr apache2 ares autoipd avahi berkdb blas bluetooth branding bzip2 cairo cdr cjk cli consolekit cracklib crypt cups curl daap dbus dga djvu dri dvd dvdr dvi eds empathy encode exif faac faad fam ffmpeg fftw flac fortran fuse galago gcj gd gdbm gif gimp git glib glitz gmp gnome gnome-keyring gnuplot gnutls gphoto2 gs gsl gstreamer gtk h323 hal hardened hdri iconv idn imagemagick introspection ipv6 isdnlog jingle jpeg jpeg2k kdrive kpathsea lapack laptop latex lcms libffi libnotify lzma lzo mad mmx mng moonlight mozdevelop mp3 mpeg msn mudflap music nautilus ncurses network network-cron networkmanager nls nptl nptlonly nsplugin numpy ogg openexr opengl openmp pam pch pcmcia pcre pcsc-lite pdf perl png policykit pppd pygments python qt3support raw readline reflection resolvconf samba sasl sdl session sip smartcard smp sound source spl sse sse2 ssl ssse3 startup-notification subversion svg sysfs tcpd theora tiff truetype unicode upnp usb v4l v4l2 vim-syntax vorbis webkit wps x264 xcb xinerama xml xmp xorg xulrunner xv xvid xvmc zeroconf 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 mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd 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 dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="adc65 agfa_cl20 aox barbie canon casio_qv clicksmart310 digigr8 digita dimagev dimera3500 directory enigma13 fuji gsmart300 hp215 iclick jamcam jd11 jl2005a kodak_dc120 kodak_dc210 kodak_dc240 kodak_dc3200 kodak_ez200 konica konica_qm150 largan lg_gsm mars mustek panasonic_coolshot panasonic_dc1000 panasonic_dc1580 panasonic_l859 pccam300 pccam600 polaroid_pdc320 polaroid_pdc640 polaroid_pdc700 ptp2 ricoh ricoh_g3 samsung sierra sipix_blink sipix_blink2 sipix_web2 smal sonix sony_dscf1 sony_dscf55 soundvision spca50x sq905 stv0674 stv0680 sx330z template topfield toshiba_pdrm11" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en et" USERLAND="GNU" VIDEO_CARDS="intel" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
sci-chemistry/openbabel-python is not in the main tree and it has basically the same effect as building >=sci-chemistry/openbabel-2.2.2-r1 built with USE=python, with the added bonus, that you don't need to recompile whole openbabel just to get bindings. Your openbabel already is compiled with USE=python, so you don't need to install sci-chemistry/openbabel-python to be able to use python bindings.
Aha.. openbabel-python came from gentoo-science overlay. I didn't notice that before. Maybe this bug should be assigned to the maintainer of science overlay.
Can be closed I put a blocker on openbabel[python] in the ebuild of openbabel-python.
Removed from overlay
