I never saw anything like this before. :) I needed to reinstall kdebase-3.5.5-r1 on top of itself (same version). I watched the installation fairly closely and saw (during the uninstall old version part): <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/libkonq/html <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/libkonq <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin/lib/html <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin/lib <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin/html <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kate/html <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kate <<< dir /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs and later: <<< dir /usr/kde/3.5/share/applnk/Settings/Information Sure enough, checking the install: # equery check kdebase [ Checking kde-base/kdebase-3.5.5-r1 ] !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kate does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kate/html does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin/html does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin does not exist !!! /usr/kde/3.5/share/applnk/Settings/Information does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/libkonq does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin/lib does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/kwin/lib/html does not exist !!! /usr/kde/3.5/share/doc/HTML/en/kdebase-apidocs/libkonq/html does not exist * 4890 out of 4900 files good # emerge -p --info Portage 2.1.1-r2 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r4, 2.6.17-gentoo-r8 i686) ================================================================= System uname: 2.6.17-gentoo-r8 i686 Pentium III (Coppermine) Gentoo Base System version 1.12.6 Last Sync: Sun, 19 Nov 2006 08:30:01 +0000 app-admin/eselect-compiler: [Not Present] dev-java/java-config: 1.3.7, 2.0.30 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.60 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.13-r4 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium3 -Os -pipe -fomit-frame-pointer -mfpmath=sse" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=pentium3 -Os -pipe -fomit-frame-pointer -mfpmath=sse" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="ru_RU.UTF-8" LINGUAS="en ru" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage /usr/portage/local/layman/sunrise" SYNC="rsync://baron/gentoo-portage" USE="x86 X aac aalib acpi alsa arts audiofile berkdb bitmap-fonts bzip2 caps cdparanoia cjk cracklib crypt css cups dbus dga directfb dlloader dri elibc_glibc encode exif expat fbcon ffmpeg flac gcj ggi gif glibc-omitfp gmp gphoto2 gpm gstreamer hal i8x0 iconv idea imagemagick imap imlib input_devices_keyboard input_devices_mouse ipv6 javascript jbig joystick jpeg kde kernel_linux lcms libcaca libwww linguas_en linguas_ru live mad matroska mbox memlimit mmx mng mp3 mpeg mysql nas ncurses network nls no-old-linux nodrm nptl nptlonly ogg opengl pcre pdflib perl png ppds qt3 quicktime readline real rtc samba scanner sdl silc sndfile speex spell sse ssl sysfs tcpd theora threads tiff truetype truetype-fonts type1-fonts unicode usb userland_GNU userlocales utf8 vcd video_cards_i810 vorbis win32codecs xinerama xml xorg xv xvid zlib" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS, MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS I don't really know why portage removed those files. I can only guess something like the timestamps didn't get updated. Good luck.
Those are empty directories, it's correct they get removed.
Then why do they get created in the first place? :) Seriously (and this sounds like a portage issue - not something you deal with), something feels wrong to me when consecutive installs of the same ebuild don't produce identical results.
Reopen to dupe.
*** This bug has been marked as a duplicate of 16162 ***
