I have kde-frameworks/kxmlgui 5.48.0 and kde-frameworks/kio 5.48.0 installed. 5.49.0 is available for both packages, but when I try to update, emerge stops before doing anything and prints the messages: >>> Verifying ebuild manifests !!! A file is not listed in the Manifest: '/usr/portage/kde-frameworks/kxmlgui/files/kxmlgui-5.48.0-kmainwindow.patch' !!! A file is not listed in the Manifest: '/usr/portage/kde-frameworks/kio/files/kio-5.48.0-memleak.patch' I have synced a few times this week, and the problem has persisted. Reproducible: Always Steps to Reproduce: 1. emerge --sync 2. emerge -uNDv world Actual Results: >>> Verifying ebuild manifests !!! A file is not listed in the Manifest: '/usr/portage/kde-frameworks/kxmlgui/files/kxmlgui-5.48.0-kmainwindow.patch' !!! A file is not listed in the Manifest: '/usr/portage/kde-frameworks/kio/files/kio-5.48.0-memleak.patch' Expected Results: Packages are updated.
emerge --info: Portage 2.3.46 (python 3.6.6-final-0, default/linux/amd64/17.0/desktop/gnome/systemd, gcc-7.3.0, glibc-2.27-r6, 4.16.2-gentoo x86_64) ================================================================= System uname: Linux-4.16.2-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_920_@_2.67GHz-with-gentoo-2.6 KiB Mem: 24671648 total, 18144992 free KiB Swap: 4194300 total, 4194300 free Timestamp of repository gentoo: Thu, 16 Aug 2018 00:30:01 +0000 Head commit of repository gentoo: a9a2d6463641b2c60b82521bf2e33be87fcefdd2 sh bash 4.4_p23 ld GNU ld (Gentoo 2.30 p3) 2.30.0 app-shells/bash: 4.4_p23::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.15::gentoo, 3.6.6::gentoo, 3.7.0::gentoo dev-util/cmake: 3.12.1::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.16.1-r1::gentoo sys-devel/binutils: 2.30-r3::gentoo, 2.31.1::gentoo sys-devel/gcc: 7.3.0-r3::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r5::gentoo sys-devel/make: 4.2.1-r3::gentoo sys-kernel/linux-headers: 4.17::gentoo (virtual/os-headers) sys-libs/glibc: 2.27-r6::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 steam-overlay location: /var/lib/layman/steam-overlay masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=core2 -msse4 -msse4.1 -msse4.2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" 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" CXXFLAGS="-O2 -march=core2 -msse4 -msse4.1 -msse4.2 -pipe" DISTDIR="/usr/portage/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict 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://gentoo.cites.uiuc.edu/pub/gentoo rsync://mirrors.rit.edu/gentoo" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en" MAKEOPTS="-j9" 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="/tmp" USE="X a52 aac acpi alsa amd64 bash-completion berkdb branding bzip2 cairo caps cdda cdr cli colord crypt cups cxx dbus device-mapper dri dts dvb dvd dvdr emacs emboss encode evo exif fam ffmpeg flac fontconfig fortran fuse gd gdbm gif glamor gmp gnome gnome-keyring gnome-online-accounts gnutls gpm gstreamer gtk guile iconv introspection ipv6 jack java jpeg lame latex lcms ldap libnotify libsecret libtirpc mad mng modules mp3 mp4 mpeg multilib nautilus ncurses networking nls nptl nsplugin ogg opengl openmp pam pango pcre pdf png policykit postscript ppds pulseaudio readline sasl sdl seccomp smp spell sqlite ssl startup-notification svg systemd tcpd theora threads tiff tk tracker truetype udev udisks unicode upower usb v4l v4l2 vorbis wxwidgets x264 xattr xcb xinerama xml xv xvid zlib" ABI_X86="64" ALSA_CARDS="emu10k1x" 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 plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse" KERNEL="linux" L10N="en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python3_6" RUBY_TARGETS="ruby24" USERLAND="GNU" VIDEO_CARDS="nvidia" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Same problem here and been trying to dig in a bit. Seems to maybe coincide with the --link-dest change in portage. In the case of kio, /usr/portage/kde-frameworks/kio/files/ and below is owned by root:root but /usr/portage/kde-frameworks/kio/ and the stuff directly in it (ebuilds, Manifest, and metadata.xml) are owned by portage:portage. Seems like the files folder was deleted in ae142dde6d94e5e1f19658db8550dedebe9e13ca but recent syncs haven't been able to delete it because it somehow became owned by root.
*** This bug has been marked as a duplicate of bug 661834 ***
