Package 'sys-apps/coreutils-7.1' NOT merged due to file collisions. Reproducible: Always Steps to Reproduce: 1.emerge --update world 2. 3. Actual Results: >>> Installing sys-apps/coreutils-7.1 * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / <filename>` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at http://bugs.gentoo.org unless you report exactly which * two packages install the same file(s). Once again, please do NOT file * a bug report unless you have completely understood the above message. * * Detected file collision(s): * * /usr/share/man/man1/timeout.1.bz2 * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * app-forensics/tct-1.18 * /usr/share/man/man1/timeout.1.bz2 * * Package 'sys-apps/coreutils-7.1' NOT merged due to file collisions. If * necessary, refer to your elog messages for the whole content of the * above message. Expected Results: Successful merge.
# emerge --info Portage 2.1.6.7 (default/linux/x86/2008.0/desktop, gcc-4.3.3, glibc-2.9_p20081201-r2, 2.6.25-gentoo-r8 i686) ================================================================= System uname: Linux-2.6.25-gentoo-r8-i686-Intel-R-_Pentium-R-_M_processor_2.00GHz-with-glibc2.0 Timestamp of tree: Sun, 22 Feb 2009 03:00:01 +0000 app-shells/bash: 3.2_p48-r1 dev-java/java-config: 1.3.7-r1, 2.1.7 dev-lang/python: 2.4.4-r15, 2.5.4-r2 dev-python/pycrypto: 2.0.1-r6 dev-util/cmake: 2.6.2-r1 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.3-r1 sys-apps/sandbox: 1.3.8 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19.1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.28-r1 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=i686 -O2 -pipe -ggdb" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /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/sandbox.d /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-march=i686 -O2 -pipe -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1" MAKEOPTS="" 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" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext X a52 aac acl acpi aiglx alsa apache2 apm arts ati audiofile avahi avi bash-completion berkdb bitmap-fonts bluetooth branding bzip2 cairo caps cardbus cdio cdr clicracklib crypt ctype cups dba dbtool dbus digitalradio diskio djvu dri dts dvd dvdr dvdreadeds emboss encode esd ethereal evo exif expat fam fastbuild ffmpeg fftw fglrx firefox foomaticdb force-cgi-redirect fortran ftp fuse gamin gd gdbm gif glib glitz glut gmp gnome gpm gstreamer gtk gtk2 gtkhtml guile hal iconv idn imlib ipv6 isdnlog ithreads jack java jpeg kde kerberos kqemu lcms ldap libclamav libg++ libnotify libwww lirc live lm_sensors lua mad madwifi matroska mdnsresponder-compat memlimit mhash midi mikmod mmx mmxext mng mono motif mozilla mp3 mpeg mudflap mysql ncurses netboot netjack networking nforce2 nls nptl nptlonly nvidia ocaml ogg oggvorbis opengl openmp oss pam pango pch pcmcia pcre pdf pdflib pear perl php pmu png portaudio posix ppds pppd pulseaudio python qt qt3 qt3support qt4 qtmt quicktime readline reflection ruby samba sasl sdl session simplexml slang sndfile snmp soap sockets spell spl sqlite sse sse2 ssl startup-notification svg sysfs tcl tcltk tcpd theora threads threadsafe tiff tk tokenizer truetype truetype-fonts type1-fonts udev unicode usb utempter vorbis webkit wifi win32codecs x86 xanim xinerama xml xmlrpc xorg xscreensaver xsl xulrunner xv 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 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" ELIBC="glibc" FOO2ZJS_DEVICES="hp2600n" INPUT_DEVICES="evdev keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="radeon ati fglrx" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
I have a similar error, with netatalk seeming to provide the package collision. sys-apps:coreutils-7.1:20090222-115629.log ERROR: preinst This package will overwrite one or more files that may belong to other packages (see list below). You can use a command such as `portageq owners / <filename>` to identify the installed package that owns a file. If portageq reports that only one package owns a file then do NOT file a bug report. A bug report is only useful if it identifies at least two or more packages that are known to install the same file(s). If a collision occurs and you can not explain where the file came from then you should simply ignore the collision since there is not enough information to determine if a real problem exists. Please do NOT file a bug report at http://bugs.gentoo.org unless you report exactly which two packages install the same file(s). Once again, please do NOT file a bug report unless you have completely understood the above message. Detected file collision(s): /usr/bin/timeout /usr/share/man/man1/timeout.1.bz2 Searching all installed packages for file collisions... Press Ctrl-C to Stop net-fs/netatalk-2.0.3-r3 /usr/bin/timeout /usr/share/man/man1/timeout.1.bz2 Package 'sys-apps/coreutils-7.1' NOT merged due to file collisions. If necessary, refer to your elog messages for the whole content of the above message. =============== # emerge --info Portage 2.2_rc23 (default/linux/x86/2008.0/desktop, gcc-4.3.3, glibc-2.9_p20081201-r2, 2.6.28-gentoo-r2 i686) ================================================================= System uname: Linux-2.6.28-gentoo-r2-i686-Intel-R-_Core-TM-2_CPU_4400_@_2.00GHz-with-glibc2.0 Timestamp of tree: Sun, 22 Feb 2009 11:15:01 +0000 app-shells/bash: 3.2_p48-r1 dev-java/java-config: 1.3.7-r1, 2.1.7 dev-lang/python: 2.5.4-r2 dev-util/cmake: 2.6.2-r1 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.3-r1 sys-apps/sandbox: 1.3.8 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.5, 1.7.9-r1, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19.1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.28-r1 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=prescott -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -march=prescott -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US" LC_ALL="en_US" LDFLAGS="-Wl,-O1" LINGUAS="en" 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" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="X a52 aac aalib acl acpi alsa artworkextra automount avahi bash-completion beagle berkdb bluetooth branding bzip2 cairo cdda cddb cdr cjk cleartype cli cracklib crypt cups curl dbus device-mapper dri dvd dvdr dvdread eds emboss encode epiphany esd exif fam ffmpeg flac fortran gd gdbm gif gnome gnome-keyring gnomecd gpm gs gstreamer gtk gtkhtml guile hal iconv inotify ipv6 isdnlog java jpeg keyring ldap libnotify loop-aes lzma lzo mad mdnsresponder-compat midi mikmod mmx mono mp3 mpeg mudflap nautilus ncurses networking nls nptlonly nsplugin offensive ogg opengl openmp pam pcre pdf perl png ppds pppd profile python quicktime readline reflection reiserfs rtc sdl session sound spell spl sse sse2 ssl startup-notification svg symlink sysfs tcpd threads tiff truetype unicode usb utils vorbis win32codecs x86 xattr xml xmp xorg xulrunner xv xvid zlib" ALSA_CARDS="hda-intel" 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" USERLAND="GNU" VIDEO_CARDS="intel" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
the packages providing the timeout program should be updated to not provide it anymore. that means netatalk and tct.
*** Bug 259988 has been marked as a duplicate of this bug. ***
*** Bug 260034 has been marked as a duplicate of this bug. ***
Created attachment 182974 [details] tct-1.18-r1 ebuild Fixed app-forensics/tct-1.18 conflict, since I submitted the 1.18 ebuild anyway.
RedHat has the same problem: https://bugzilla.redhat.com/show_bug.cgi?id=473186 Could inspire a solution :-)
There are another 2 collisions with sci-chemistry/ccp4-6.0.2: /usr/bin/truncate /usr/share/man/man1/truncate.1.bz2 Unfortunately, truncate from ccp4 is completely unrelated to the truncate utility shipped with coreutils.
then file a new bug please
ive added blockers to coreutils. when the other packages get fixed, the committer should update the blocker in the coreutils dep so it only blocks older versions.
(In reply to comment #6) > Created an attachment (id=182974) [edit] > tct-1.18-r1 ebuild > > Fixed app-forensics/tct-1.18 conflict, since I submitted the 1.18 ebuild > anyway. > Will it appear in portage and fix the blocker noted in comment #10?
That's up to the Gentoo devs; forensics@ has been a pretty dead herd for the past year, but Patrick has recently picked up a lot of the slack in recent weeks. I'm just a power user with my own local repo where I fix things and submit them upstream.
Created attachment 185115 [details] new netatalk ebuild that fixes coreutils-7.1 file collisions Here's my attempt at fixing the netatalk ebuild so that /usr/bin/timeout and /usr/share/man/man1/timeout.1.bz2 are no longer supplied by netatalk. From the coreutils documentation, the coreutils version of /usr/bin/timeout provides all the functionality of netatalk's timeout, plus more. Testing on my system, the only way I could upgrade from coreutils-6.* and netatalk-2.0.3-r3 was to unmerge netatalk-2.0.3-r3, upgrade coreutils to 7.1, and then reemerge netatalk-2.0.3-r4. The only way I can see around this so that everything happens automagically is if the coreutils ebuild was written so that it overwrites /usr/bin/timeout and the timeout man page from netatalk, but this is probably not desirable.
in the future, please post diffs of files, not entirely new files ive committed new versions of tct/netatalk because i doubt the maintainers of said packages will be able to get around to it any time soon thanks for the ebuilds
