Hi, I wonder if this is actually an emerge suboptimally interpreting the slots: # emerge -uN system --verbose-conflicts Calculating dependencies... done! [ebuild U ] app-arch/bzip2-1.0.6-r9 [1.0.6-r8] [ebuild U ] sys-devel/gnuconfig-20170101 [20161104] [ebuild U ] sys-devel/patch-2.7.6-r1 [2.7.5] [ebuild U ] sys-libs/readline-7.0_p3 [6.3_p8-r3] [ebuild U ] net-misc/rsync-3.1.3 [3.1.2-r2] [ebuild U ] app-shells/bash-4.4_p12 [4.3_p48-r1] [ebuild U ] virtual/editor-0-r1 [0] [ebuild U ] virtual/package-manager-1 [0] [ebuild U ] sys-apps/busybox-1.28.0 [1.25.1] [ebuild U ] sys-apps/kbd-2.0.4 [2.0.3] [ebuild U ] sys-apps/util-linux-2.30.2-r1 [2.30.2] [ebuild U ] sys-libs/e2fsprogs-libs-1.43.9 [1.43.6] [ebuild U ] virtual/dev-manager-0-r1 [0] [ebuild U ] net-misc/wget-1.19.5 [1.19.1-r2] [ebuild U ] sys-fs/e2fsprogs-1.43.9 [1.43.6] [ebuild U ] sys-apps/man-pages-4.14 [4.13] !!! Multiple package instances within a single package slot have been pulled !!! into the dependency graph, resulting in a slot conflict: sys-libs/readline:0 (sys-libs/readline-7.0_p3:0/7::gentoo, ebuild scheduled for merge) pulled in by >=sys-libs/readline-7.0:0= required by (app-shells/bash-4.4_p12:0/0::gentoo, ebuild scheduled for merge) ^^ ^^^^^^ (sys-libs/readline-6.3_p8-r3:0/0::gentoo, installed) pulled in by >=sys-libs/readline-4.1:0/0= required by (dev-lang/python-3.4.5:3.4/3.4m::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (dev-lang/R-3.2.2:0/0::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (dev-libs/libpcre-8.39:3/3::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (net-fs/samba-4.5.10-r1:0/0::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (x11-wm/fvwm-2.6.5-r1:0/0::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (sci-biology/mrbayes-3.1.2-r2:0/0::gentoo, installed) ^^^^^ >=sys-libs/readline-4.1:0/0= required by (dev-lang/python-3.5.4-r1:3.5/3.5m::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (dev-libs/libxml2-2.9.4-r1:2/2::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (sys-apps/gawk-4.1.4:0/0::gentoo, installed) ^^^^^ >=sys-libs/readline-4.1:0/0= required by (dev-lang/python-2.7.12:2.7/2.7::gentoo, installed) ^^^^^ sys-libs/readline:0/0= required by (app-crypt/gnupg-2.2.4-r2:0/0::gentoo, installed) ^^^^^ sys-libs/readline:0/0=[abi_x86_32(-),abi_x86_64(-)] required by (dev-db/sqlite-3.16.2:3/3::gentoo, installed) ^^^^^ !!! The slot conflict(s) shown above involve package(s) which may need to !!! be rebuilt in order to solve the conflict(s). However, the following !!! package(s) cannot be rebuilt for the reason(s) shown: (dev-lang/python-2.7.12:2.7/2.7::gentoo, installed): ebuild is masked or unavailable (x11-wm/fvwm-2.6.5-r1:0/0::gentoo, installed): ebuild is masked or unavailable (net-fs/samba-4.5.10-r1:0/0::gentoo, installed): ebuild is masked or unavailable (dev-libs/libpcre-8.39:3/3::gentoo, installed): ebuild is masked or unavailable (dev-libs/libxml2-2.9.4-r1:2/2::gentoo, installed): ebuild is masked or unavailable (dev-db/sqlite-3.16.2:3/3::gentoo, installed): ebuild is masked or unavailable (dev-lang/python-3.4.5:3.4/3.4m::gentoo, installed): ebuild is masked or unavailable It may be possible to solve this problem by using package.mask to prevent one of those packages from being selected. However, it is also possible that conflicting dependencies exist such that they are impossible to satisfy simultaneously. If such a conflict exists in the dependencies of two different packages, then those packages can not be installed simultaneously. You may want to try a larger value of the --backtrack option, such as --backtrack=30, in order to see if that will solve this conflict automatically. For more information, see MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook. # emerge --info WARNING: One or more repositories have missing repo_name entries: /var/lib/layman/profiles/repo_name NOTE: Each repo_name entry should be a plain text file containing a unique name for the repository on the first line. Portage 2.3.40 (python 2.7.12-final-0, default/linux/amd64/17.0, gcc-6.4.0, glibc-2.25-r9, 4.14.13-default x86_64) ================================================================= System uname: Linux-4.14.13-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.4.1 KiB Mem: 16404100 total, 5623472 free KiB Swap: 15647296 total, 15647296 free Timestamp of repository gentoo: Wed, 30 May 2018 08:00:01 +0000 Head commit of repository gentoo: 188a922820296d301fe8227b96c46f266b6e2356 sh bash 4.3_p48-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.3_p48-r1::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.24.3-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo, 3.5.4-r1::gentoo dev-util/cmake: 3.9.6::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.26.3::gentoo sys-apps/sandbox: 2.10-r4::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.4_p6-r1::gentoo, 1.9.6-r3::gentoo, 1.10.3::gentoo, 1.11.6::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15.1-r2::gentoo sys-devel/binutils: 2.25.1-r1::gentoo, 2.28-r2::gentoo, 2.29.1-r1::gentoo sys-devel/gcc: 6.4.0-r1::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.4::gentoo (virtual/os-headers) sys-libs/glibc: 2.25-r9::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 science location: /var/lib/layman/science masters: gentoo priority: 0 haskell location: /var/lib/layman/haskell masters: gentoo priority: 1 x-layman location: /var/lib/layman masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf /var/bind /var/lib/hsqldb" 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 -pipe -march=native" 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 nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="rsync://ftp.fi.muni.cz/pub/linux/gentoo/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en cs cz" MAKEOPTS="-j5" 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 accessibility alsa amd64 amr apache apache2 berkdb bzip2 cairo cgi cli cracklib crypt cups cxx dbus device-mapper dri encode ffmpeg flac fontconfig fortran gd gdbm geoip gnutls hal iconv id3tag innodb java jce jpeg jpg ladspa laptop mad maildir mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly ogg opengl openmp openssl pam pcre perl php png policykit postfix procmail python readline seccomp server session sndfile spf sse sse2 ssl suexec svg syslog tcpd threads tiff truetype unicode usb wavpack xattr xml xorg xvfb zlib" ABI_X86="64 32" 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="karbon plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 sse4_1 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="libinput keyboard mouse" 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="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby23" USERLAND="GNU" VIDEO_CARDS="vesa" 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, LANG, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
For >=sys-libs/readline-7 we have SLOT="0/7" which means things built against sys-libs/readline:0/0= will have to be rebuilt. For upgrades like this, it's best to do a deep @world update, like: emerge --update --deep @world If you don't want to do a deep world update, then it's easiest to use the --ignore-built-slot-operator-deps=y option and later use emerge @preserved-rebuild to perform the necessary rebuilds. Related info: https://wiki.gentoo.org/wiki/Project:Portage/FAQ#What_should_I_do_when_emerge_reports_a_lot_of_dependency_conflicts_involving_built_slot-operator_.28foo.2Fbar:X.2FY.3D.29_dependencies.3F https://wiki.gentoo.org/wiki/Project:Portage/FAQ/Built_Slot_Operator_Dependency_Conflicts
