Running a system update fails due to file collision between app-alternatives/ninja-1 and dev-util/ninja-1.11.1-r3. I've tried uninstalling dev-util/ninja but it does not help as app-alternatives/ninja will pull it back in anyway. Reproducible: Always Steps to Reproduce: Try running system update`emerge -uND --with-bdeps=y --keep-going=y --fail-clean=y --backtrack=30 --quiet-build world` or simply `emerge -1 app-alternatives/ninja` Actual Results: * 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 https://bugs.gentoo.org/ unless you report exactly * which two packages install the same file(s). See * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how * to solve the problem. And once again, please do NOT file a bug report * unless you have completely understood the above message. * * package app-alternatives/ninja-1 NOT merged * * Detected file collision(s): * * /usr/bin/ninja * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * None of the installed packages claim the file(s). * * Package 'app-alternatives/ninja-1' NOT merged due to file collisions. * If necessary, refer to your elog messages for the whole content of the * above message. Expected Results: It should successfully merge. >>> emerge --info Portage 3.0.51 (python 3.11.6-final-0, default/linux/amd64/17.1/no-multilib/hardened, gcc-12, glibc-2.38-r6, 6.5.5-gentoo x86_64) ================================================================= System uname: Linux-6.5.5-gentoo-x86_64-AMD_Ryzen_5_5500U_with_Radeon_Graphics-with-glibc2.38 KiB Mem: 32269456 total, 7756104 free KiB Swap: 2097148 total, 2093820 free Timestamp of repository gentoo: Mon, 23 Oct 2023 06:15:01 +0000 Head commit of repository gentoo: ae6a3fe634dd7e0aa3e40c23f4dc35d748000813 Timestamp of repository anders-larsson: Mon, 23 Oct 2023 21:31:50 +0000 Head commit of repository anders-larsson: 73bdbac235ad948d570e63b8497efa64e0c9799c Head commit of repository sinustrom: 0a2893f0b5ae3ea12e8a74b3c6ca81aea0dbfc6d sh bash 5.2_p15-r6 ld GNU ld (Gentoo 2.41 p2) 2.41.0 distcc 3.4 x86_64-pc-linux-gnu [enabled] app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p15-r6::gentoo dev-lang/perl: 5.38.0-r1::gentoo dev-lang/python: 3.11.6::gentoo, 3.12.0::gentoo dev-lang/rust: 1.72.0::gentoo dev-util/cmake: 3.27.6-r1::gentoo dev-util/meson: 1.2.1-r2::gentoo sys-apps/baselayout: 2.14::gentoo sys-apps/openrc: 0.50::gentoo sys-apps/sandbox: 2.38::gentoo sys-devel/autoconf: 2.71-r7::gentoo sys-devel/automake: 1.16.5-r1::gentoo sys-devel/binutils: 2.41-r1::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 16.0.6::gentoo, 17.0.1::gentoo sys-devel/gcc: 12.3.1_p20230825::gentoo sys-devel/gcc-config: 2.11::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/lld: 16.0.6::gentoo, 17.0.1::gentoo sys-devel/llvm: 16.0.6::gentoo, 17.0.1::gentoo sys-devel/make: 4.4.1-r1::gentoo sys-kernel/linux-headers: 6.5-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.38-r6::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://barbican.sinustrom.net/gentoo-portage priority: -1000 volatile: False sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 anders-larsson location: /var/db/repos/anders-larsson sync-type: git sync-uri: https://github.com/gentoo-mirror/anders-larsson.git masters: gentoo volatile: False sinustrom location: /var/db/repos/sinustrom sync-type: git sync-uri: https://github.com/zpuskas/sinustrom-gentoo-overlay.git masters: gentoo volatile: False ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=znver2 -madx -maes -mavx -mavx2 -mbmi -mbmi2 -mclflushopt -mclwb -mclzero -mcx16 -mf16c -mfma -mfsgsbase -mfxsr -mlzcnt -mmmx -mmovbe -mmwaitx -mpclmul -mpopcnt -mprfchw -mrdpid -mrdrnd -mrdseed -msahf -msha -msse -msse2 -msse3 -msse4.1 -msse4.2 -msse4a -mssse3 -mwbnoinvd -mxsave -mxsavec -mxsaveopt -mxsaves --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=512 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php8.2/ext-active/ /etc/php/cgi-php8.2/ext-active/ /etc/php/cli-php8.2/ext-active/ /etc/php/fpm-php8.2/ext-active/ /etc/php/phpdbg-php8.2/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=znver2 -madx -maes -mavx -mavx2 -mbmi -mbmi2 -mclflushopt -mclwb -mclzero -mcx16 -mf16c -mfma -mfsgsbase -mfxsr -mlzcnt -mmmx -mmovbe -mmwaitx -mpclmul -mpopcnt -mprfchw -mrdpid -mrdrnd -mrdseed -msahf -msha -msse -msse2 -msse3 -msse4.1 -msse4.2 -msse4a -mssse3 -mwbnoinvd -mxsave -mxsavec -mxsaveopt -mxsaves --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=512 -O2 -pipe" DISTDIR="/var/cache/portage/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME" FCFLAGS="-march=znver2 -madx -maes -mavx -mavx2 -mbmi -mbmi2 -mclflushopt -mclwb -mclzero -mcx16 -mf16c -mfma -mfsgsbase -mfxsr -mlzcnt -mmmx -mmovbe -mmwaitx -mpclmul -mpopcnt -mprfchw -mrdpid -mrdrnd -mrdseed -msahf -msha -msse -msse2 -msse3 -msse4.1 -msse4.2 -msse4a -mssse3 -mwbnoinvd -mxsave -mxsavec -mxsaveopt -mxsaves --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=512 -O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live collision-protect config-protect-if-modified distcc distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=znver2 -madx -maes -mavx -mavx2 -mbmi -mbmi2 -mclflushopt -mclwb -mclzero -mcx16 -mf16c -mfma -mfsgsbase -mfxsr -mlzcnt -mmmx -mmovbe -mmwaitx -mpclmul -mpopcnt -mprfchw -mrdpid -mrdrnd -mrdseed -msahf -msha -msse -msse2 -msse3 -msse4.1 -msse4.2 -msse4a -mssse3 -mwbnoinvd -mxsave -mxsavec -mxsaveopt -mxsaves --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=512 -O2 -pipe" GENTOO_MIRRORS="rsync://barbican.sinustrom.net/gentoo-distfiles" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LEX="flex" MAKEOPTS="-j89 -l12" PKGDIR="/var/cache/portage/binpkgs" 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" SHELL="/bin/zsh" USE="7zip acl acpi amd64 bash-completion bzip2 cet cli crypt dri fortran gdbm gmp hardened iconv ipv6 libtirpc lto lzma ncurses nls nptl opencl opengl openmp pam pcre pie posix readline seccomp smp sockets split-usr ssl ssp test-rust threads unicode usb vim-syntax xattr xtpax zlib zsh-completion zstd" ABI_X86="64" ADA_TARGET="gnat_2021" 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="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq 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" LLVM_TARGETS="AMDGPU" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" NGINX_MODULES_HTTP="access addition auth_basic autoindex browser charset empty_gif fancyindex fastcgi geo grpc gzip headers_more limit_conn limit_req map mirror proxy push_stream referer rewrite scgi ssi userid uwsgi" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" RUBY_TARGETS="ruby32" VIDEO_CARDS="amdgpu radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live collision-protect config-protect-if-modified distcc distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" See "collision-protect". Same deal as the warning in https://www.gentoo.org/support/news-items/2022-12-27-alternatives-introduction.html.
