Bug 589918 – games-action/xbomber-101-r1 : file collision with sci-biology/emboss-6.6.0

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2016-07-28 15:01:26 UTC]

 * Detected file collision(s):
 * 
 * 	/usr/bin/matcher
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * sci-biology/emboss-6.6.0:0::gentoo
 * 	/usr/bin/matcher
 * 
 * Package 'games-action/xbomber-101-r1' NOT merged due to file


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-plasma-unstable_20160710-112417) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------

  make.conf:
USE="pax_kernel xtpax -cdinstall -oci8 -bindist btrfs cgi cups -egl emacs ffmpeg gles gnomecanvas -gpg gstreamer gui gzip haptic imlib ipv6 isag -logrotate minimal -mng -mysql odbc -opencv pam pcre16 php policykit -pulseaudio rendering scrypt source ssh svg system-ffmpeg -system-icu system-jpeg system-llvm -szip timidity tools vaapi vala x265 -xkb zenmap -ziffy"

  package specific USE flags:
mail-mta/ssmtp    ssl
net-misc/wget     ssl
app-editors/emacs -dbus -svg -ssl -gtk -gtk3
net-misc/iputils -caps -filecaps
>=media-libs/mesa-12.0.1 egl
>=x11-libs/libxcb-1.12 xkb
gnome-base/librsvg -tools
media-libs/mesa -vaapi

  -----------------------------------------------------------------

Portage 2.3.0 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.4.0, glibc-2.23-r2, 4.6.4-hardened-r3 x86_64)
=================================================================
System uname: Linux-4.6.4-hardened-r3-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16156124 total,   2263296 free
KiB Swap:   16777212 total,  16667492 free
Timestamp of repository gentoo: Wed, 27 Jul 2016 22:03:28 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
distcc 3.2rc1 x86_64-pc-linux-gnu [disabled]
ccache version 3.2.7 [disabled]
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/ccache:          3.2.7::gentoo
dev-util/cmake:           3.6.1::gentoo
sys-apps/baselayout:      2.2-r1::gentoo
sys-apps/openrc:          0.21.2::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, 1.10.3-r2::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:       2.25.1-r1::gentoo, 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: 4.4::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::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 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/omega.conf /etc/stunnel/stunnel.conf /opt/openfire/resources/security/ /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /var/lib/hsqldb /var/lib/i2pd/certificates /var/lib/redmine/config /var/rancid/.cloginrc /var/yp/Makefile"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 /var/lib/redmine/config/locales /var/lib/redmine/config/settings.yml"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue 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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding btrfs bzip2 cairo cdda cdr cgi cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emacs emboss encode exif fam ffmpeg firefox flac fortran gdbm gif glamor gles gnomecanvas gpm gstreamer gtk gui gzip haptic iconv imlib ipv6 isag jpeg kde kipi lcms ldap libnotify mad minimal mmx mmxext modules mp3 mp4 mpeg multilib ncurses nls nptl odbc ogg opengl openmp pam pango pax_kernel pcre pcre16 pdf phonon php plasma png policykit ppds qml qt3support qt4 qt5 readline rendering scrypt sdl seccomp semantic-desktop session source spell sse sse2 ssh ssl startup-notification svg system-ffmpeg system-jpeg system-llvm tcpd tiff timidity tools truetype udev udisks unicode upower usb vaapi vala vorbis widgets wxwidgets x264 x265 xattr xcb xcomposite xinerama xml xscreensaver xtpax xv xvid zenmap zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" 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="amdgpu fbdev intel nouveau radeon radeonsi vesa 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

[Comment 1 Toralf Förster 2016-07-28 15:01:29 UTC]

Created attachment 441810 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2016-07-28 15:01:32 UTC]

Created attachment 441812 [details]
games-action:xbomber-101-r1:20160727-224139.log

[Comment 3 Austin English (RETIRED) 2016-07-28 21:37:57 UTC]

Fixed by
https://github.com/gentoo/gentoo/commit/38ae04afecd43fd2a719b34977d8cf660cf409c2
and
https://github.com/gentoo/gentoo/commit/dcc939b030709edc0352f2909d4ec5406abeedf6