* Detected file collision(s): * * /usr/lib64/python2.7/site-packages/pmg_tk/startup/apbs_tools.py * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-chemistry/pymol-apbs-plugin-2.1_p26-r1:0::gentoo * /usr/lib64/python2.7/site-packages/pmg_tk/startup/apbs_tools.py * * Package 'sci-chemistry/pymol-1.7.6.0' NOT merged due to file $ cat ./info.txt ----------------------------------------------------------------- This is an stable amd64 chroot image (named amd64-gnome-stable_20151031-154847) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- Portage 2.2.20.1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/gnome, gcc-4.9.3, glibc-2.21-r1, 4.1.7-hardened-r1 x86_64) ================================================================= System uname: Linux-4.1.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16164644 total, 2855136 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 12 Nov 2015 11:22:07 +0000 sh bash 4.3_p39 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.3_p39::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10::gentoo, 3.4.3::gentoo dev-util/cmake: 3.3.1-r1::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.17::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: 1 local location: /usr/local/portage masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/grs/systems.conf /etc/stunnel/stunnel.conf /opt/openfire/resources/security/ /usr/lib64/fax /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb /var/spool/fax/etc /var/yp/Makefile" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/games/angband/edit/ /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/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="/var/tmp/distfiles" EMERGE_DEFAULT_OPTS="--deep --color=n --nospinner --tree --quiet-build --accept-properties=-interactive --accept-restrict=-fetch" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" 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" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acl acpi adns alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdb cdda cdr cli colord consolekit cracklib crypt cups cxx dbus dnssec dri dts dvd dvdr eds emboss encode evo exif extraengine fam firefox flac fortran freetds ftp gd gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpg gpm gstreamer gtk iconv inifile introspection ipv6 isag jadetex jpeg lapack lcms ldap libnotify libsecret libvirtd mad mbox mmx mmxext mng modules mp3 mp4 mpeg multilib mysqli nautilus ncurses nls nptl objc odbc ogg opencv opengl openmp pam pango pax_kernel pcre pdf pdo pkcs11 png policykit postscript ppds pulseaudio qt3support qt4 readline scrypt sdl seccomp session sockets spell spice sqlite3 sse sse2 sse4_1 ssh-askpass ssl ssse3 startup-notification svg system-libvpx tcpd thinkpad tiff tk tracker truetype udev udisks unicode upower usb usbredir uxa vorbis vpx wxwidgets x264 xattr xcb xkb xml xmp xscreensaver xv xvfb xvid xz zenmap zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 416782 [details] emerge-history.txt
Created attachment 416784 [details] sci-chemistry:pymol-1.7.6.0:20151112-144334.log
commit 01222e4f46e52148f0c9e200129a6420d6b3f8fb Author: Justin Lecher <jlec@gentoo.org> Date: Thu Nov 12 17:20:32 2015 +0100 sci-chemistry/pymol: Always use included apbs plugin Correctly block files collisions Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=565600 Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org> https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01222e4f46e52148f0c9e200129a6420d6b3f8fb commit 094cc9cd2add1bbd98bb5f4c1bcb2c0d6a039437 Author: Justin Lecher <jlec@gentoo.org> Date: Thu Nov 12 17:14:43 2015 +0100 profiles: Last rite sci-chemistry/pymol-apbs-plugin Signed-off-by: Justin Lecher <jlec@gentoo.org> https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=094cc9cd2add1bbd98bb5f4c1bcb2c0d6a039437
