В данном случае, проблемным пакетом может быть Kopete. У меня система обновилась без проблем, но сейчас я попробовал сделать emerge -pv kopete, и получил:
emerge -pv kopete
Local copy of remote index is up-to-date and will be used.
These are the packages that would be merged, in order:
Calculating dependencies... done!
[binary N ] dev-libs/qjson-0.8.1-r1::gentoo USE="-debug -doc {-test}" ABI_X86="(64) -32 (-x32)" 105 KiB
[binary N ] media-libs/qimageblitz-0.0.6-r1::gentoo USE="(-altivec) -debug" CPU_FLAGS_X86="3dnow mmx sse sse2" 110 KiB
[ebuild NS ] kde-apps/akonadi-1.13.1_pre20160203-r1:4::gentoo [16.12.0:5::gentoo] USE="postgres -mysql -sqlite {-test}" 376 KiB
[ebuild N ] kde-apps/kdepimlibs-4.14.11_pre20160211-r2:4/4.14::gentoo USE="handbook (-aqua) -debug -ldap -prison {-test}" 4200 KiB
[ebuild N ] kde-apps/kopete-16.12.0:4/16.12::gentoo USE="addbookmarks autoreplace contactnotes handbook highlight history nowlistening oscar pipes privacy ssl statistics texteffect translator urlpicpreview v4l xmpp (-aqua) -debug -gadu -groupwise -jingle -latex -meanwhile -otr -skype -testbed -webpresence -winpopup -yahoo -zeroconf" 6193 KiB
[blocks B ] kde-apps/kdepimlibs:4 ("kde-apps/kdepimlibs:4" is blocking kde-apps/kmailtransport-16.12.0, kde-apps/akonadi-mime-16.12.0, app-crypt/gpgme-1.8.0-r2)
[blocks B ] kde-apps/akonadi:4 ("kde-apps/akonadi:4" is blocking kde-apps/akonadi-16.12.0)
[blocks B ] kde-apps/kdepimlibs ("kde-apps/kdepimlibs" is blocking kde-apps/akonadi-16.12.0)
Total: 5 packages (4 new, 1 in new slot, 2 binaries), Size of downloads: 10982 KiB
Conflict: 3 blocks (3 unsatisfied)
* Error: The above package list contains packages which cannot be
* installed at the same time on the same system.
(kde-apps/kdepimlibs-4.14.11_pre20160211-r2:4/4.14::gentoo, ebuild scheduled for merge) pulled in by
>=kde-apps/kdepimlibs-4.14.3:4[aqua=] (>=kde-apps/kdepimlibs-4.14.3:4[-aqua]) required by (kde-apps/kopete-16.12.0:4/16.12::gentoo, ebuild scheduled for merge)
(kde-apps/kmailtransport-16.12.0:5/5::gentoo, installed) pulled in by
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/incidenceeditor-16.12.0:5/5::gentoo, installed)
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/mailcommon-16.12.0:5/5::gentoo, installed)
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/korganizer-16.12.0-r1:5/5::gentoo, installed)
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/kdepim-runtime-16.12.0-r1:5/5::gentoo, installed)
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/kmail-account-wizard-16.12.0:5/5::gentoo, installed)
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/messagelib-16.12.0:5/5::gentoo, installed)
>=kde-apps/kmailtransport-16.12.0:5 required by (kde-apps/akonadi-calendar-16.12.0:5/5::gentoo, installed)
(app-crypt/gpgme-1.8.0-r2:1/11::gentoo, installed) pulled in by
>=app-crypt/gpgme-1.7.1[cxx,qt5] required by (kde-apps/libkleo-16.12.0:5/5::gentoo, installed)
>=app-crypt/gpgme-1.7.1[cxx,qt5] required by (kde-apps/messagelib-16.12.0:5/5::gentoo, installed)
>=app-crypt/gpgme-1.1.6 required by (kde-apps/kdepimlibs-4.14.11_pre20160211-r2:4/4.14::gentoo, ebuild scheduled for merge)
(kde-apps/akonadi-mime-16.12.0:5/5::gentoo, installed) pulled in by
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/mailcommon-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/korganizer-16.12.0-r1:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/calendarsupport-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/kdepim-runtime-16.12.0-r1:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/akonadi-contacts-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/pimcommon-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/akonadi-calendar-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/messagelib-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/akonadi-search-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/mailimporter-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/incidenceeditor-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-mime-16.12.0:5 required by (kde-apps/kmailtransport-16.12.0:5/5::gentoo, installed)
(kde-apps/akonadi-16.12.0:5/5::gentoo, installed) pulled in by
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/mailimporter-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/libkdepim-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/incidenceeditor-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/mailcommon-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/kdepim-apps-libs-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/korganizer-16.12.0-r1:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/kdepim-runtime-16.12.0-r1:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/akonadi-contacts-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/kmail-account-wizard-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/messagelib-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/kontact-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/eventviews-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/kalarmcal-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/akonadi-notes-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/calendarsupport-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/pimcommon-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/akonadi-calendar-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/akonadi-search-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/akonadi-mime-16.12.0:5/5::gentoo, installed)
>=kde-apps/akonadi-16.12.0:5 required by (kde-apps/kmailtransport-16.12.0:5/5::gentoo, installed)
For more information about Blocked Packages, please refer to the following
section of the Gentoo Linux x86 Handbook (architecture is irrelevant):
https://wiki.gentoo.org/wiki/Handbook:X86/Working/Portage#Blocked_packages
Как видим, kopete хочет старый пакет akonadi, что и тянет за собой чреду конфликтов.