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stamasd

Broken emerge?

Question

I've been using Funtoo for a little while now. I have it installed on a small headless box that I use mostly to host Minecraft servers. I'm not doing scheduled updates since the CPU power of this box is so limited, I have to shutdown the Minecraft stuff to do that. So I mostly ssh into it, turn off Minecraft then do emerge --sync && emerge @world. This worked great for a month or so; then a couple of days ago I had a problem with my laptop's wifi connection and got disconnected in the middle of doing a fairly large emerge (117 packages).

 

When I reconnected and tried to update again it complained of needing to unmask a package (=sys-libs/glibc-2.20). I did that, and the emerge completed apparently succesfully.

 

The problem is, now every time I try to update, it emerges the same 115 packages over and over again. Each time it seems to complete succesfully, but if I do emerge @world again it re-downloads and re-compiles the same list of 115 packages. It seems broken to me, and am not familiar with funtoo enough to figure out what needs fixing.

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Yeah, I should have used screen, I use it for the Minecraft stuff but I was lazy... :(

 

 

Here's the output:

sudo emerge -av world
Password:

 * IMPORTANT: 3 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.


These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] app-arch/xz-utils-5.2.1  USE="nls threads -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-libs/ncurses-5.9-r4:5  USE="cxx unicode -ada -debug -doc -gpm -minimal -profile -static-libs -tinfo -trace" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] app-arch/bzip2-1.0.6-r7  USE="-static -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-devel/gnuconfig-20150308  0 kB
[ebuild   R    ] app-arch/gzip-1.6  USE="-pic -static" 0 kB
[ebuild   R    ] net-dns/openresolv-3.6.1  0 kB
[ebuild   R    ] sys-apps/which-2.21  0 kB
[ebuild   R    ] sys-kernel/linux-firmware-20150320  USE="-savedconfig" 0 kB
[ebuild   R    ] app-arch/unarj-2.65  0 kB
[ebuild   R    ] app-arch/unrar-5.2.7  0 kB
[ebuild   R    ] net-misc/netdate-1.2  0 kB
[ebuild   R    ] virtual/os-headers-0  0 kB
[ebuild   R    ] sys-devel/m4-1.4.17  USE="-examples" 0 kB
[ebuild   R    ] sys-apps/coreutils-8.23  USE="acl nls xattr -caps -gmp (-selinux) -static -vanilla" 0 kB
[ebuild   R    ] virtual/man-0  0 kB
[ebuild   R    ] sys-apps/less-475  USE="pcre unicode" 0 kB
[ebuild   R    ] virtual/ssh-0  USE="-minimal" 0 kB
[ebuild   R    ] sys-devel/patch-2.7.5  USE="xattr -static {-test}" 0 kB
[ebuild   R    ] virtual/package-manager-0  0 kB
[ebuild   R    ] sys-apps/net-tools-1.60_p20141019041918  USE="nls old-output (-selinux) -static" 0 kB
[ebuild   R    ] app-eselect/eselect-vi-1.1.9  0 kB
[ebuild   R    ] sys-apps/busybox-1.21.1  USE="ipv6 pam static -make-symlinks -math -savedconfig (-selinux) -sep-usr -syslog -systemd" 0 kB
[ebuild   R    ] sys-apps/findutils-4.5.14-r1  USE="nls -debug (-selinux) -static" 0 kB
[ebuild   R    ] sys-apps/diffutils-3.3  USE="nls -static" 0 kB
[ebuild   R    ] virtual/modutils-0  0 kB
[ebuild   R    ] sys-devel/make-3.82-r4  USE="nls -static" 0 kB
[ebuild   R    ] virtual/libc-0  0 kB
[ebuild   R    ] app-arch/unzip-6.0-r3  USE="bzip2 unicode -natspec" 0 kB
[ebuild   R    ] app-arch/rar-5.2.1  USE="-all_sfx -static" 0 kB
[ebuild   R    ] app-portage/eix-0.30.4  USE="dep nls -debug -doc -optimization -security -sqlite -strong-optimization -strong-security -swap-remote -tools" LINGUAS="-de -ru" 0 kB
[ebuild   R    ] sys-apps/mlocate-0.26-r1  USE="nls (-selinux)" 0 kB
[ebuild   R    ] app-arch/p7zip-9.38.1-r1  USE="pch -doc -kde -rar (-static) -wxwidgets" ABI_X86="(-x32)" 0 kB
[ebuild   R    ] app-arch/lzop-1.03  0 kB
[ebuild   R    ] sys-apps/sed-4.2.2  USE="acl nls (-selinux) -static" 0 kB
[ebuild   R    ] sys-libs/readline-6.3_p8-r2  USE="-static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-devel/flex-2.5.39-r1  USE="nls -static {-test}" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] app-arch/tar-1.28-r1  USE="acl nls xattr -minimal (-selinux) -static" 0 kB
[ebuild   R    ] sys-apps/grep-2.21-r1  USE="nls pcre -static" 0 kB
[ebuild   R    ] net-misc/dhcpcd-6.8.2  USE="embedded ipv6 udev zeroconf" 0 kB
[ebuild   R    ] net-misc/iputils-20121221-r2  USE="ipv6 ssl -SECURITY_HAZARD -caps -doc -gnutls -idn -static" 0 kB
[ebuild   R    ] sys-apps/shadow-4.2.1-r1  USE="acl cracklib nls pam xattr -audit (-selinux) -skey" 0 kB
[ebuild   R    ] net-misc/rsync-3.1.1  USE="acl iconv ipv6 xattr -static" 0 kB
[ebuild   R    ] virtual/pager-0  0 kB
[ebuild   R    ] virtual/dev-manager-0  0 kB
[ebuild   R    ] sys-apps/man-pages-4.00-r1  USE="nls" LINGUAS="-da -de -fr -it -ja -nl -pl -ro -ru -zh_CN" 0 kB
[ebuild   R    ] sys-process/procps-3.3.10-r1  USE="ncurses nls unicode -modern-top (-selinux) -static-libs -systemd {-test}" 0 kB
[ebuild   R    ] app-arch/zip-3.0-r3  USE="bzip2 crypt unicode -natspec" 0 kB
[ebuild   R    ] xfce-base/xfce4-meta-4.10  USE="svg thunar -minimal -mixer -ristretto -terminal -thunar-volman -tumbler -xfburn" 0 kB
[ebuild   R    ] sys-apps/gawk-4.1.1  USE="nls readline" 0 kB
[ebuild   R    ] virtual/shadow-0  0 kB
[ebuild   R    ] sys-devel/bc-1.06.95-r1  USE="readline -libedit -static" 0 kB
[ebuild   R    ] net-wireless/wpa_supplicant-2.4-r2  USE="dbus hs2-0 readline ssl -ap -eap-sim -fasteap -gnutls -p2p (-ps3) -qt4 (-selinux) -smartcard -tdls -uncommon-eap-types -wimax -wps" 0 kB
[ebuild   R    ] xfce-extra/xfce4-mixer-4.11.0  USE="alsa keybinder -debug -oss" 0 kB
[ebuild   R    ] app-office/orage-4.10.0  USE="berkdb dbus -debug -libnotify" XFCE_PLUGINS="clock" 0 kB
[ebuild   R    ] xfce-extra/xfce4-taskmanager-1.1.0  USE="-debug -gksu -gtk3" 0 kB
[ebuild   R    ] app-arch/xarchiver-0.5.4  USE="-debug" 0 kB
[ebuild   R    ] xfce-extra/xfce4-verve-plugin-1.0.1  USE="dbus" 0 kB
[ebuild   R    ] x11-terms/xfce4-terminal-0.6.3  USE="-debug" 0 kB
[ebuild   R    ] xfce-extra/xfce4-mount-plugin-0.6.7  USE="-debug" 0 kB
[ebuild   R    ] sys-apps/baselayout-2.2.0-r6  USE="-build" 0 kB
[ebuild   R    ] sys-apps/openrc-0.12.4-r4  USE="ncurses pam unicode -debug (-selinux) -static-libs" 0 kB
[ebuild   R    ] virtual/service-manager-0  USE="(-prefix)" 0 kB
[ebuild   R    ] virtual/baselayout-0  0 kB
[ebuild   R    ] virtual/editor-0  0 kB
[ebuild   R    ] app-shells/bash-4.3_p30-r1  USE="net nls (readline) -afs -bashlogger -examples -mem-scramble -plugins -vanilla" 0 kB
[ebuild   R    ] sys-devel/autoconf-2.69:2.5  USE="-emacs (-multislot)" 0 kB
[ebuild   R    ] sys-devel/libtool-2.4.3-r2:2  USE="-vanilla" 0 kB
[ebuild   R    ] sys-libs/zlib-1.2.8-r1  USE="minizip -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] app-arch/cpio-2.11-r3  USE="nls" 0 kB
[ebuild   R    ] net-misc/bridge-utils-1.5  0 kB
[ebuild   R    ] sys-apps/kbd-2.0.2  USE="nls pam {-test}" 0 kB
[ebuild   R    ] sys-process/psmisc-22.21-r2  USE="X ipv6 nls (-selinux)" 0 kB
[ebuild   R    ] net-misc/networkmanager-1.0.0  USE="dhcpcd ncurses nss ppp resolvconf wifi -bluetooth -connection-sharing -consolekit -dhclient -gnutls -introspection -modemmanager -plugins_openconnect -plugins_openswan -plugins_openvpn -plugins_pptp -plugins_sstp -plugins_vpnc -policykit (-selinux) -teamd {-test} -vala -wext -zeroconf" 0 kB
[ebuild   R    ] sys-process/htop-1.0.3  USE="unicode -oom -openvz -vserver" 0 kB
[ebuild   R    ] app-arch/lha-114i-r7  0 kB
[ebuild   R    ] app-arch/arj-3.10.22-r4  0 kB
[ebuild   R    ] xfce-extra/xfce4-sensors-plugin-1.2.6  USE="acpi -debug -hddtemp -libnotify -lm_sensors" VIDEO_CARDS="-nvidia" 0 kB
[ebuild   R    ] x11-base/xorg-server-1.16.4-r1:0/1.16.1  USE="ipv6 nptl suid udev xorg -dmx -doc -glamor -kdrive -minimal (-selinux) -static-libs -systemd -tslib -unwind -wayland -xnest -xvfb" 0 kB
[ebuild   R    ] dev-lang/perl-5.20.2-r1:0/5.20  USE="berkdb gdbm -debug -doc -ithreads" 0 kB
[ebuild   R    ] sys-apps/util-linux-2.25.2  USE="cramfs ncurses nls pam python static-libs suid tty-helpers udev unicode -caps -fdformat (-selinux) -slang {-test}" ABI_X86="(64) -32 (-x32)" PYTHON_SINGLE_TARGET="python2_7 -python3_3 -python3_4" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 kB
[ebuild   R    ] sys-devel/binutils-2.24-r3  USE="cxx nls zlib (-multislot) -multitarget -static-libs {-test} -vanilla" 0 kB
[ebuild   R    ] net-misc/wget-1.16.3  USE="ipv6 nls pcre ssl zlib -debug -gnutls -idn -ntlm -static {-test} -uuid" 0 kB
[ebuild   R    ] sys-apps/usbutils-007  USE="python zlib" PYTHON_TARGETS="python2_7" 0 kB
[ebuild   R    ] sys-apps/pciutils-3.3.1  USE="kmod udev zlib -dns -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-auth/consolekit-0.4.6  USE="acl pam policykit -debug -doc (-selinux) -systemd-units {-test}" 0 kB
[ebuild   R    ] gnome-extra/nm-applet-1.0.0  USE="-bluetooth -introspection -modemmanager" 0 kB
[ebuild   R    ] games-strategy/freeciv-2.5.0  USE="ipv6 nls readline server sound -aimodules -auth -dedicated -gtk -mapimg -modpack -mysql (-qt5) -sdl -sqlite (-system-lua)" 0 kB
[ebuild   R    ] sys-devel/automake-1.14.1:1.14  0 kB
[ebuild   R    ] sys-apps/texinfo-5.2  USE="nls -static" 0 kB
[ebuild   R    ] sys-apps/gptfdisk-1.0.0  USE="ncurses -static" 0 kB
[ebuild   R    ] dev-vcs/git-2.4.0  USE="blksha1 curl gpg iconv nls pcre perl python threads webdav -cgi -cvs -doc -emacs -gnome-keyring -gtk -highlight -mediawiki (-ppcsha1) -subversion {-test} -tk -xinetd" PYTHON_TARGETS="python2_7" 0 kB
[ebuild   R    ] sys-fs/xfsprogs-3.2.2  USE="nls readline -libedit -static -static-libs" 0 kB
[ebuild   R    ] xfce-base/thunar-1.6.7  USE="dbus pcre udisks -debug -exif -libnotify {-test}" XFCE_PLUGINS="trash" 0 kB
[ebuild   R    ] app-text/wgetpaste-2.25-r3  0 kB
[ebuild   R    ] www-client/firefox-37.0.2  USE="dbus gmp-autoupdate gstreamer startup-notification -bindist -custom-cflags -custom-optimization -debug -hardened -minimal (-pgo) -pulseaudio (-selinux) -system-cairo -system-icu -system-jpeg -system-libvpx -system-sqlite {-test} -wifi" LINGUAS="-af -ar -as -ast -be -bg -bn_BD -bn_IN -br -bs -ca -cs -cy -da -de -el -en_GB -en_ZA -eo -es_AR -es_CL -es_ES -es_MX -et -eu -fa -fi -fr -fy_NL -ga_IE -gd -gl -gu_IN -he -hi_IN -hr -hu -hy_AM -id -is -it -ja -kk -km -kn -ko -lt -lv -mai -mk -ml -mr -nb_NO -nl -nn_NO -or -pa_IN -pl -pt_BR -pt_PT -rm -ro -ru -si -sk -sl -son -sq -sr -sv_SE -ta -te -th -tr -uk -vi -xh -zh_CN -zh_TW" 0 kB
[ebuild   R    ] net-irc/irssi-0.8.17  USE="ipv6 perl proxy ssl (-selinux) -socks5" 0 kB
[ebuild   R    ] app-editors/mousepad-0.4.0  USE="dbus -debug -gtk3" 0 kB
[ebuild   R    ] dev-lang/python-3.3.6-r1000:3.3  USE="gdbm ipv6 ncurses readline sqlite ssl (threads) xml -build -doc -examples -tk -wininst" 0 kB
[ebuild   R    ] sys-devel/bison-3.0.4-r1  USE="nls -examples -static {-test}" 0 kB
[ebuild   R    ] sys-fs/e2fsprogs-1.42.12  USE="nls -static-libs" 0 kB
[ebuild   R    ] xfce-extra/tumbler-0.1.31  USE="gstreamer jpeg -curl -debug -ffmpeg -odf -pdf -raw" 0 kB
[ebuild   R    ] xfce-extra/thunar-volman-0.8.1  USE="-debug -libnotify" 0 kB
[ebuild   R    ] app-misc/screen-4.2.1-r2  USE="pam -debug -multiuser -nethack (-selinux)" 0 kB
[ebuild   R    ] xfce-extra/thunar-archive-plugin-0.3.1  USE="-debug" 0 kB
[ebuild   R    ] sys-devel/gcc-4.8.4:4.8  USE="cxx fortran (multilib) nls openmp (-altivec) -doc -go (-hardened) (-libssp) (-multislot) -objc -objc++ -vanilla" 0 kB
[ebuild   R    ] sys-apps/file-5.22-r1000  USE="python zlib -static-libs" ABI_X86="(64) -32 (-x32)" PYTHON_ABIS="2.7 3.3 -2.6 -2.7-pypy -3.1 -3.2 -3.2-pypy -3.4 (-3.5)" 0 kB
[ebuild   R    ] sys-apps/iproute2-3.16.0  USE="berkdb iptables ipv6 -atm -minimal (-selinux)" 0 kB
[ebuild   R    ] app-portage/gentoolkit-0.3.0.9-r1003  PYTHON_ABIS="2.7 3.3 -2.6 -2.7-pypy -3.1 -3.2 -3.2-pypy -3.4 (-3.5)" 0 kB
[ebuild   R    ] app-admin/ego-0.9.5  0 kB
[ebuild   R    ] sys-boot/boot-update-1.7.3  PYTHON_ABIS="2.7 3.3 -2.6 -3.2 -3.4 (-3.5)" 0 kB
[ebuild   R    ] app-misc/mc-4.8.14  USE="X edit nls slang xdg -gpm -mclib -samba -sftp -spell {-test}" 0 kB
[ebuild   R    ] app-admin/sudo-1.8.13  USE="nls pam sendmail -ldap -offensive (-selinux) -skey" 0 kB
[ebuild   R    ] app-editors/nano-2.3.6  USE="magic ncurses nls spell unicode -debug -justify -minimal -slang" 0 kB
[ebuild   R    ] net-misc/ifenslave-1.1.0-r6  0 kB
[ebuild   R    ] dev-java/icedtea-bin-7.2.5.5:7  USE="X alsa -cjk -cups -doc -examples -nsplugin -pulseaudio (-selinux) -source -webstart" 0 kB

Total: 115 packages (115 reinstalls), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] n

Quitting.

So it looks that all of these 115 packages are still marked for reinstall, even though they have just been reinstalled. Don't know what to do about it.

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It also seems that any new package that I emerge independently is automatically set to reinstall. I emerged chrony, and immediately after that it was already set to reinstall:

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] sys-libs/ncurses-5.9-r4:5  USE="cxx unicode -ada -debug -doc -gpm -minimal -profile -static-libs -tinfo -trace" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] app-arch/xz-utils-5.2.1  USE="nls threads -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] app-arch/bzip2-1.0.6-r7  USE="-static -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-devel/gnuconfig-20150308  0 kB
[ebuild   R    ] app-arch/gzip-1.6  USE="-pic -static" 0 kB
[ebuild   R    ] net-dns/openresolv-3.6.1  0 kB
[ebuild   R    ] sys-apps/which-2.21  0 kB
[ebuild   R    ] net-misc/netdate-1.2  0 kB
[ebuild   R    ] app-arch/unrar-5.2.7  0 kB
[ebuild   R    ] app-arch/unarj-2.65  0 kB
[ebuild   R    ] sys-kernel/linux-firmware-20150320  USE="-savedconfig" 0 kB
[ebuild   R    ] sys-devel/m4-1.4.17  USE="-examples" 0 kB
[ebuild   R    ] virtual/os-headers-0  0 kB
[ebuild   R    ] sys-devel/patch-2.7.5  USE="xattr -static {-test}" 0 kB
[ebuild   R    ] sys-apps/net-tools-1.60_p20141019041918  USE="nls old-output (-selinux) -static" 0 kB
[ebuild   R    ] app-arch/unzip-6.0-r3  USE="bzip2 unicode -natspec" 0 kB
[ebuild   R    ] app-arch/lzop-1.03  0 kB
[ebuild   R    ] sys-libs/readline-6.3_p8-r2  USE="-static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-apps/coreutils-8.23  USE="acl nls xattr -caps -gmp (-selinux) -static -vanilla" 0 kB
[ebuild   R    ] virtual/libc-0  0 kB
[ebuild   R    ] sys-process/procps-3.3.10-r1  USE="ncurses nls unicode -modern-top (-selinux) -static-libs -systemd {-test}" 0 kB
[ebuild   R    ] app-arch/zip-3.0-r3  USE="bzip2 crypt unicode -natspec" 0 kB
[ebuild   R    ] app-arch/rar-5.2.1  USE="-all_sfx -static" 0 kB
[ebuild   R    ] app-arch/p7zip-9.38.1-r1  USE="pch -doc -kde -rar (-static) -wxwidgets" ABI_X86="(-x32)" 0 kB
[ebuild   R    ] net-misc/rsync-3.1.1  USE="acl iconv ipv6 xattr -static" 0 kB
[ebuild   R    ] sys-apps/baselayout-2.2.0-r6  USE="-build" 0 kB
[ebuild   R    ] sys-apps/sed-4.2.2  USE="acl nls (-selinux) -static" 0 kB
[ebuild   R    ] sys-devel/flex-2.5.39-r1  USE="nls -static {-test}" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] app-arch/tar-1.28-r1  USE="acl nls xattr -minimal (-selinux) -static" 0 kB
[ebuild   R    ] sys-apps/gawk-4.1.1  USE="nls readline" 0 kB
[ebuild   R    ] sys-apps/findutils-4.5.14-r1  USE="nls -debug (-selinux) -static" 0 kB
[ebuild   R    ] sys-devel/make-3.82-r4  USE="nls -static" 0 kB
[ebuild   R    ] sys-apps/diffutils-3.3  USE="nls -static" 0 kB
[ebuild   R    ] app-portage/eix-0.30.4  USE="dep nls -debug -doc -optimization -security -sqlite -strong-optimization -strong-security -swap-remote -tools" LINGUAS="-de -ru" 0 kB
[ebuild   R    ] sys-apps/mlocate-0.26-r1  USE="nls (-selinux)" 0 kB
[ebuild   R    ] sys-devel/bc-1.06.95-r1  USE="readline -libedit -static" 0 kB
[ebuild   R    ] net-misc/iputils-20121221-r2  USE="ipv6 ssl -SECURITY_HAZARD -caps -doc -gnutls -idn -static" 0 kB
[ebuild   R    ] net-misc/dhcpcd-6.8.2  USE="embedded ipv6 udev zeroconf" 0 kB
[ebuild   R    ] virtual/dev-manager-0  0 kB
[ebuild   R    ] x11-apps/xauth-1.0.9-r2  USE="ipv6" 0 kB
[ebuild     U  ] sys-apps/less-476 [475] USE="pcre unicode" 309 kB
[ebuild   R    ] sys-apps/grep-2.21-r1  USE="nls pcre -static" 0 kB
[ebuild   R    ] virtual/pager-0  0 kB
[ebuild   R    ] app-eselect/eselect-vi-1.1.9  0 kB
[ebuild   R    ] sys-apps/openrc-0.12.4-r4  USE="ncurses pam unicode -debug (-selinux) -static-libs" 0 kB
[ebuild   R    ] virtual/service-manager-0  USE="(-prefix)" 0 kB
[ebuild   R    ] virtual/baselayout-0  0 kB
[ebuild   R    ] sys-apps/busybox-1.21.1  USE="ipv6 pam static -make-symlinks -math -savedconfig (-selinux) -sep-usr -syslog -systemd" 0 kB
[ebuild   R    ] virtual/package-manager-0  0 kB
[ebuild   R    ] virtual/modutils-0  0 kB
[ebuild   R    ] virtual/man-0  0 kB
[ebuild   R    ] sys-apps/man-pages-4.00-r1  USE="nls" LINGUAS="-da -de -fr -it -ja -nl -pl -ro -ru -zh_CN" 0 kB
[ebuild   R    ] sys-apps/shadow-4.2.1-r1  USE="acl cracklib nls pam xattr -audit (-selinux) -skey" 0 kB
[ebuild   R    ] virtual/shadow-0  0 kB
[ebuild   R    ] virtual/ssh-0  USE="-minimal" 0 kB
[ebuild   R    ] virtual/editor-0  0 kB
[ebuild   R    ] xfce-extra/xfce4-taskmanager-1.1.0  USE="-debug -gksu -gtk3" 0 kB
[ebuild   R    ] app-arch/xarchiver-0.5.4  USE="-debug" 0 kB
[ebuild   R    ] app-office/orage-4.10.0  USE="berkdb dbus -debug -libnotify" XFCE_PLUGINS="clock" 0 kB
[ebuild   R    ] xfce-extra/xfce4-mount-plugin-0.6.7  USE="-debug" 0 kB
[ebuild   R    ] xfce-extra/xfce4-verve-plugin-1.0.1  USE="dbus" 0 kB
[ebuild   R    ] net-wireless/wpa_supplicant-2.4-r2  USE="dbus hs2-0 readline ssl -ap -eap-sim -fasteap -gnutls -p2p (-ps3) -qt4 (-selinux) -smartcard -tdls -uncommon-eap-types -wimax -wps" 0 kB
[ebuild   R    ] app-shells/bash-4.3_p30-r1  USE="net nls (readline) -afs -bashlogger -examples -mem-scramble -plugins -vanilla" 0 kB
[ebuild   R    ] x11-terms/xfce4-terminal-0.6.3  USE="-debug" 0 kB
[ebuild   R    ] xfce-extra/xfce4-mixer-4.11.0  USE="alsa keybinder -debug -oss" 0 kB
[ebuild   R    ] xfce-base/xfce4-meta-4.10  USE="svg thunar -minimal -mixer -ristretto -terminal -thunar-volman -tumbler -xfburn" 0 kB
[ebuild   R    ] dev-lang/perl-5.20.2-r1:0/5.20  USE="berkdb gdbm -debug -doc -ithreads" 0 kB
[ebuild   R    ] sys-devel/autoconf-2.69:2.5  USE="-emacs (-multislot)" 0 kB
[ebuild   R    ] sys-apps/texinfo-5.2  USE="nls -static" 0 kB
[ebuild   R    ] xfce-base/thunar-1.6.7  USE="dbus pcre udisks -debug -exif -libnotify {-test}" XFCE_PLUGINS="trash" 0 kB
[ebuild   R    ] net-irc/irssi-0.8.17  USE="ipv6 perl proxy ssl (-selinux) -socks5" 0 kB
[ebuild   R    ] app-editors/mousepad-0.4.0  USE="dbus -debug -gtk3" 0 kB
[ebuild   R    ] sys-devel/automake-1.14.1:1.14  0 kB
[ebuild   R    ] xfce-extra/thunar-volman-0.8.1  USE="-debug -libnotify" 0 kB
[ebuild   R    ] xfce-extra/tumbler-0.1.31  USE="gstreamer jpeg -curl -debug -ffmpeg -odf -pdf -raw" 0 kB
[ebuild   R    ] xfce-extra/thunar-archive-plugin-0.3.1  USE="-debug" 0 kB
[ebuild   R    ] net-misc/chrony-2.0  USE="adns cmdmon ipv6 ntp phc pps readline refclock rtc -caps -libedit (-selinux)" 0 kB
[ebuild   R    ] sys-devel/libtool-2.4.3-r2:2  USE="-vanilla" 0 kB
[ebuild   R    ] sys-libs/zlib-1.2.8-r1  USE="minizip -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-devel/bison-3.0.4-r1  USE="nls -examples -static {-test}" 0 kB
[ebuild   R    ] app-arch/cpio-2.11-r3  USE="nls" 0 kB
[ebuild   R    ] net-misc/bridge-utils-1.5  0 kB
[ebuild   R    ] sys-apps/kbd-2.0.2  USE="nls pam {-test}" 0 kB
[ebuild   R    ] sys-process/psmisc-22.21-r2  USE="X ipv6 nls (-selinux)" 0 kB
[ebuild   R    ] x11-base/xorg-server-1.16.4-r1:0/1.16.1  USE="ipv6 nptl suid udev xorg -dmx -doc -glamor -kdrive -minimal (-selinux) -static-libs -systemd -tslib -unwind -wayland -xnest -xvfb" 0 kB
[ebuild   R    ] net-misc/networkmanager-1.0.0  USE="dhcpcd ncurses nss ppp resolvconf wifi -bluetooth -connection-sharing -consolekit -dhclient -gnutls -introspection -modemmanager -plugins_openconnect -plugins_openswan -plugins_openvpn -plugins_pptp -plugins_sstp -plugins_vpnc -policykit (-selinux) -teamd {-test} -vala -wext -zeroconf" 0 kB
[ebuild   R    ] app-arch/arj-3.10.22-r4  0 kB
[ebuild   R    ] app-arch/lha-114i-r7  0 kB
[ebuild   R    ] sys-process/htop-1.0.3  USE="unicode -oom -openvz -vserver" 0 kB
[ebuild   R    ] app-misc/screen-4.2.1-r2  USE="pam -debug -multiuser -nethack (-selinux)" 0 kB
[ebuild   R    ] xfce-extra/xfce4-sensors-plugin-1.2.6  USE="acpi -debug -hddtemp -libnotify -lm_sensors" VIDEO_CARDS="-nvidia" 0 kB
[ebuild   R    ] dev-lang/python-3.3.6-r1000:3.3  USE="gdbm ipv6 ncurses readline sqlite ssl (threads) xml -build -doc -examples -tk -wininst" 0 kB
[ebuild   R    ] sys-apps/util-linux-2.25.2  USE="cramfs ncurses nls pam python static-libs suid tty-helpers udev unicode -caps -fdformat (-selinux) -slang {-test}" ABI_X86="(64) -32 (-x32)" PYTHON_SINGLE_TARGET="python2_7 -python3_3 -python3_4" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 kB
[ebuild   R    ] sys-devel/binutils-2.24-r3  USE="cxx nls zlib (-multislot) -multitarget -static-libs {-test} -vanilla" 0 kB
[ebuild   R    ] net-misc/wget-1.16.3  USE="ipv6 nls pcre ssl zlib -debug -gnutls -idn -ntlm -static {-test} -uuid" 0 kB
[ebuild   R    ] sys-apps/pciutils-3.3.1  USE="kmod udev zlib -dns -static-libs" ABI_X86="(64) -32 (-x32)" 0 kB
[ebuild   R    ] sys-apps/iproute2-3.16.0  USE="berkdb iptables ipv6 -atm -minimal (-selinux)" 0 kB
[ebuild   R    ] dev-vcs/git-2.4.0  USE="blksha1 curl gpg iconv nls pcre perl python threads webdav -cgi -cvs -doc -emacs -gnome-keyring -gtk -highlight -mediawiki (-ppcsha1) -subversion {-test} -tk -xinetd" PYTHON_TARGETS="python2_7" 0 kB
[ebuild   R    ] sys-apps/usbutils-007  USE="python zlib" PYTHON_TARGETS="python2_7" 0 kB
[ebuild   R    ] sys-auth/consolekit-0.4.6  USE="acl pam policykit -debug -doc (-selinux) -systemd-units {-test}" 0 kB
[ebuild   R    ] gnome-extra/nm-applet-1.0.0  USE="-bluetooth -introspection -modemmanager" 0 kB
[ebuild   R    ] app-admin/sudo-1.8.13  USE="nls pam sendmail -ldap -offensive (-selinux) -skey" 0 kB
[ebuild   R    ] games-strategy/freeciv-2.5.0  USE="ipv6 nls readline server sound -aimodules -auth -dedicated -gtk -mapimg -modpack -mysql (-qt5) -sdl -sqlite (-system-lua)" 0 kB
[ebuild   R    ] sys-apps/file-5.22-r1000  USE="python zlib -static-libs" ABI_X86="(64) -32 (-x32)" PYTHON_ABIS="2.7 3.3 -2.6 -2.7-pypy -3.1 -3.2 -3.2-pypy -3.4 (-3.5)" 0 kB
[ebuild   R    ] sys-fs/e2fsprogs-1.42.12  USE="nls -static-libs" 0 kB
[ebuild   R    ] sys-devel/gcc-4.8.4:4.8  USE="cxx fortran (multilib) nls openmp (-altivec) -doc -go (-hardened) (-libssp) (-multislot) -objc -objc++ -vanilla" 0 kB
[ebuild   R    ] sys-apps/gptfdisk-1.0.0  USE="ncurses -static" 0 kB
[ebuild   R    ] app-portage/gentoolkit-0.3.0.9-r1003  PYTHON_ABIS="2.7 3.3 -2.6 -2.7-pypy -3.1 -3.2 -3.2-pypy -3.4 (-3.5)" 0 kB
[ebuild   R    ] app-admin/ego-0.9.5  0 kB
[ebuild   R    ] sys-fs/xfsprogs-3.2.2  USE="nls readline -libedit -static -static-libs" 0 kB
[ebuild   R    ] sys-boot/boot-update-1.7.3  PYTHON_ABIS="2.7 3.3 -2.6 -3.2 -3.4 (-3.5)" 0 kB
[ebuild   R    ] app-text/wgetpaste-2.25-r3  0 kB
[ebuild   R    ] www-client/firefox-37.0.2  USE="dbus gmp-autoupdate gstreamer startup-notification -bindist -custom-cflags -custom-optimization -debug -hardened -minimal (-pgo) -pulseaudio (-selinux) -system-cairo -system-icu -system-jpeg -system-libvpx -system-sqlite {-test} -wifi" LINGUAS="-af -ar -as -ast -be -bg -bn_BD -bn_IN -br -bs -ca -cs -cy -da -de -el -en_GB -en_ZA -eo -es_AR -es_CL -es_ES -es_MX -et -eu -fa -fi -fr -fy_NL -ga_IE -gd -gl -gu_IN -he -hi_IN -hr -hu -hy_AM -id -is -it -ja -kk -km -kn -ko -lt -lv -mai -mk -ml -mr -nb_NO -nl -nn_NO -or -pa_IN -pl -pt_BR -pt_PT -rm -ro -ru -si -sk -sl -son -sq -sr -sv_SE -ta -te -th -tr -uk -vi -xh -zh_CN -zh_TW" 0 kB
[ebuild   R    ] app-editors/nano-2.3.6  USE="magic ncurses nls spell unicode -debug -justify -minimal -slang" 0 kB
[ebuild   R    ] net-misc/ifenslave-1.1.0-r6  0 kB
[ebuild   R    ] app-misc/mc-4.8.14  USE="X edit nls slang xdg -gpm -mclib -samba -sftp -spell {-test}" 0 kB
[ebuild   R    ] dev-java/icedtea-bin-7.2.5.5:7  USE="X alsa -cjk -cups -doc -examples -nsplugin -pulseaudio (-selinux) -source -webstart" 0 kB

Total: 117 packages (1 upgrade, 116 reinstalls), Size of downloads: 309 kB

Would you like to merge these packages? [Yes/No]

I'm confused as to why this happens, and how to fix it. Any help appreciated.

 

At this point I can't update my system effectively since an emerge world takes about 6 hours for all of these 117 packages on this low-power system.

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I really don't have a clue, like most package managers, there is bookkeeping stuff in /var/cache, but the easy way out may be to emerge -1 portage, since it's obviously out of kilter.  Worth a shot.  Oh and you might try revdep-rebuild, same philosophy.

I have a Dockstar and a Pogoplug, I feel your pain.

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