papua ~ # emerge -vautND @world These are the packages that would be merged, in reverse order: Calculating dependencies / * A file is not listed in the Manifest: '/usr/portage/app-shells/bash/bash-4.3_p39.ebuild' | * A file is not listed in the Manifest: '/usr/portage/dev-java/maven-bin/maven-bin-3.2.3.ebuild' ... done! [ebuild UD ] app-shells/bash-4.3_p39::gentoo [4.3_p42-r1::gentoo] USE="net nls (readline) -afs -bashlogger -examples -mem-scramble -plugins -vanilla" 7,990 KiB Total: 1 package (1 downgrade), Size of downloads: 7,990 KiB Would you like to merge these packages? [Yes/No] yes >>> Verifying ebuild manifests !!! A file is not listed in the Manifest: '/usr/portage/app-shells/bash/bash-4.3_p39.ebuild' Reproducible: Always Steps to Reproduce: 1. emerge --sync && emerge -vautND @world -or- 1. emerge --sync && emerge -vautND bash Actual Results: >>> Verifying ebuild manifests !!! A file is not listed in the Manifest: '/usr/portage/app-shells/bash/bash-4.3_p39.ebuild' Expected Results: >>> Verifying ebuild manifests >>> Emerging (1 of 1) app-shells/bash-4.3_p39::gentoo papua ~ # emerge --info Portage 2.2.26 (python 2.7.10-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.21-r1, 4.1.12-gentoo x86_64) ================================================================= System uname: Linux-4.1.12-gentoo-x86_64-Intel-R-_Core-TM-_i7-4790K_CPU_@_4.00GHz-with-gentoo-2.2 KiB Mem: 2056352 total, 162488 free KiB Swap: 524284 total, 306516 free Timestamp of repository gentoo: Mon, 25 Jan 2016 16:45:01 +0000 sh bash 4.3_p42-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.3_p42-r1::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10-r1::gentoo, 3.4.3::gentoo dev-util/cmake: 3.3.1-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.19.1::gentoo sys-apps/sandbox: 2.10-r1::gentoo sys-devel/autoconf: 2.69::gentoo sys-devel/automake: 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: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.us.gentoo.org/gentoo-portage priority: -1000 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8-sse3 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=k8-sse3 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync 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://mirror.leaseweb.com/gentoo/ http://mirror.lug.udel.edu/pub/gentoo/ http://gentoo.mirrors.pair.com/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j2" 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="acl amd64 berkdb bzip2 cli cracklib crypt curl cxx daemon device-mapper dri exif faac fam fortran fpm gd gdbm geoip highlight iconv ipv6 jack mmx mmxext modules mp3 multilib mysql mysqli ncurses nls nptl ogg opengl openmp openssl pam pcntl pcre pdo php postgres python readline resolvconf rubytests sdl seccomp server session sqlite sse sse2 sse3 ssh ssl ssse3 symlink syslog tcpd theora truetype unicode unzip vdpau vorbis webinterface x264 xattr xmlrpc xvid 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="mmx mmxext sse sse2 sse3 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python3_4" 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" USE_PYTHON="2.7 3.4" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Additionally suspect: the downgrade attempt is spurious. app-shells/bash/bash-4.3_p39.ebuild should not exist; moreover, if it must, it should not assert any keywords for any architectures because... app-shells/bash/bash-4.3_p39_pre0.ebuild preexists, and asserts no arch keywords, and... app-shells/bash/bash-4.3_p42-r1.ebuild preexists, and asserts stable keywords for (almost) all architectures.
papua ~ # emerge -pv =bash-4.3_p42-r1 These are the packages that would be merged, in order: Calculating dependencies - * A file is not listed in the Manifest: '/usr/portage/app-shells/bash/bash-4.3_p39.ebuild' ... done! !!! All ebuilds that could satisfy "=bash-4.3_p42-r1" have been masked. !!! One of the following masked packages is required to complete your request: - app-shells/bash-4.3_p42-r1::gentoo (masked by: corruption)
Per conversation in irc.freenode.net/#gentoo, apparently some rsync mirrors have outdated information causing this problem. Synchronizing to a more current mirror (starling, in my case) resolved the issue for all affected ebuilds.
Calculating dependencies - * A file is not listed in the Manifest: '/portage/app-shells/bash/bash-4.3_p33.ebuild' ... done! [ebuild UD ] app-shells/bash-4.3_p39::gentoo [4.3_p42-r1::gentoo] USE="net nls (readline) -afs -bashlogger -examples -mem-scramble -plugins -vanilla" 0 KiB [ebuild U ] dev-python/numpy-1.10.4::gentoo [1.9.2::gentoo] USE="-doc -lapack {-test}" PYTHON_TARGETS="python2_7 python3_4 -python3_3 (-python3_5)" 0 KiB Total: 2 packages (1 upgrade, 1 downgrade), Size of downloads: 0 KiB >>> Fetching (1 of 2) app-shells/bash-4.3_p39::gentoo !!! A file is not listed in the Manifest: '/portage/app-shells/bash/bash-4.3_p33.ebuild' >>> Failed to emerge app-shells/bash-4.3_p39
Same here, but not just bash. - * A file is not listed in the Manifest: '/usr/portage/app-shells/bash/bash-4.3_p33-r1.ebuild' / * A file is not listed in the Manifest: '/usr/portage/app-crypt/gnupg/gnupg-2.0.27.ebuild' / * A file is not listed in the Manifest: '/usr/portage/dev-python/pip/pip-8.0.2.ebuild'
This what paludis is showing: Resolving: 16 stepscave@1453856237: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/app-admin/logrotate-3.9.2': No such file or directory Resolving: 61 stepscave@1453856238: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/app-crypt/gnupg-2.1.11': No such file or directory Resolving: 83 stepscave@1453856239: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-editors/vim-core-7.4.769' Resolving: 88 stepscave@1453856239: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-emulation/qemu-2.5.0-r1' Resolving: 116 stepscave@1453856239: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/app-eselect/eselect-pinentry-0.7': No such file or directory cave@1453856239: [QA e.ebuild.cache.no_usable] No usable cache entry for 'app-eselect/eselect-pinentry-0.7::gentoo Resolving: 156 steps, 1 metadata (1 gentoo) cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-2.05b_p13' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-3.0_p22' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-3.1_p23' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-3.2_p57' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-4.0_p44' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-4.1_p17' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-4.2_p53' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-4.3_p39_pre0' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-4.3_p42-r1' cave@1453856240: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-shells/bash-4.4_beta' Resolving: 247 steps, 1 metadata (1 gentoo) cave@1453856241: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-db/mysql-5.5.47': No such file or directory Resolving: 250 steps, 1 metadata (1 gentoo) cave@1453856241: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-db/redis-3.0.6': No such file or directory Resolving: 350 steps, 1 metadata (1 gentoo) cave@1453856242: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-libs/libinput-1.1.5': No such file or directory Resolving: 522 steps, 1 metadata (1 gentoo) cave@1453856243: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-python/numpy-1.10.4' cave@1453856243: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-python/numpy-9999' Resolving: 523 steps, 1 metadata (1 gentoo) cave@1453856243: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-python/packaging-16.0' Resolving: 564 steps, 1 metadata (1 gentoo) cave@1453856243: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-python/setuptools-19.6': No such file or directory cave@1453856243: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-python/setuptools-9999' Resolving: 586 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-qt/qtchooser-0_p20151008' Resolving: 607 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/actionpack-3.2.22.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/actionpack-4.1.14.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/actionpack-4.2.5.1': No such file or directory Resolving: 608 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/actionview-4.1.14.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/actionview-4.2.5.1': No such file or directory Resolving: 609 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activemodel-3.2.22.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activemodel-4.1.14.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activemodel-4.2.5.1': No such file or directory Resolving: 610 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activerecord-3.2.22.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activerecord-4.1.14.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activerecord-4.2.5.1': No such file or directory Resolving: 612 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activesupport-3.2.22.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activesupport-4.1.14.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/activesupport-4.2.5.1': No such file or directory Resolving: 631 steps, 1 metadata (1 gentoo) cave@1453856244: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-ruby/metasploit-payloads-1.0.15' cave@1453856244: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-ruby/metasploit-payloads-1.0.19' cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/metasploit-payloads-1.0.21': No such file or directory cave@1453856244: [QA e.ebuild.cache.no_usable] No usable cache entry for 'dev-ruby/metasploit-payloads-1.0.21::gentoo Resolving: 631 steps, 2 metadata (2 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/metasploit-payloads-1.0.22': No such file or directory Resolving: 632 steps, 2 metadata (2 gentoo) cave@1453856244: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/dev-ruby/metasploit_data_models-1.2.9' cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/metasploit_data_models-1.2.10': No such file or directory Resolving: 651 steps, 2 metadata (2 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/rails-html-sanitizer-1.0.3': No such file or directory Resolving: 652 steps, 2 metadata (2 gentoo) cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/railties-3.2.22.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/railties-4.1.14.1': No such file or directory cave@1453856244: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-ruby/railties-4.2.5.1': No such file or directory Deciding: 1 restarts, 5522 steps, 2 metadata (2 gentoo) cave@1453856319: [WARNING e.cache.stale] Stale cache file at '/usr/portage/metadata/md5-cache/app-editors/uemacs-pk-4.0.15_p20141208' cave@1453856319: [QA e.ebuild.cache.no_usable] No usable cache entry for 'app-editors/uemacs-pk-4.0.15_p20141208::gentoo Deciding: 1 restarts, 5527 steps, 3 metadata (3 gentoo) cave@1453856320: [WARNING e.cache.failure] Couldn't use the cache file at '/usr/portage/metadata/md5-cache/dev-lang/ekopath-6.0.661_p20160124': No such file or directory
I think it might help if you guys can tell which exact rsync mirrors you've pulled from
I am syncing from : rsync://rsync11.us.gentoo.org/gentoo-portage
Both French mirrors rsync1.fr and rsync2.fr have the problem
rsync.de.g.o rotation is affected, too. Apparently it also stopped updating entirely.
I'm using rsync.cz.gentoo.org which resolves to supp.name, but I've also tried rsync.at.gentoo.org which resolves to gentoo.lagis.at.
We currently don't need any further reports to triage this, thanks for the posts so far.
Well this shows clearly something is wrong... https://mirrorstats.gentoo.org/rsync/ Everything with mirror age 1.8days (currently) is wrong.
*** Bug 573108 has been marked as a duplicate of this bug. ***
Issue is resolved, mirrors are catching up. Leaving this open for affected people to find.
Hello everyone, I still have a question about this issue: How does this issue affect snapshots too? Aren't those generated by another process than rsync-ing the content of the main Portage tree? “20160125 and 20160126 snapshots were not found.” (I use snapshots for the digital signature verification)
