I had both 2.4.4 and 2.5.1 of dev-python/python-docs installed, and I unmerged the 2.4.4 version. However this removed the /etc/env.d/50python-docs file for the newer version. Reproducible: Always Steps to Reproduce: 1. emerge =dev-python/python-docs-2.4.4 2. emerge =dev-python/python-docs-2.5.1 3. emerge -C =dev-python/python-docs-2.4.4 4. equery check dev-python/python-docs Actual Results: # equery check dev-python/python-docs [ Checking dev-python/python-docs-2.5.1 ] !!! /etc/env.d/50python-docs does not exist * 1623 out of 1624 files good Expected Results: The file should not have been deleted when removing the older version. # emerge --info Portage 2.1.4.4 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.25-gentoo-r6 x86_64) ================================================================= System uname: 2.6.25-gentoo-r6 x86_64 AMD Sempron(tm) Processor 3300+ Timestamp of tree: Mon, 21 Jul 2008 06:36:01 +0000 ccache version 2.4 [disabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r13, 2.5.2-r5 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r2 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -pipe -O2" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/bind /var/gopher/gophermap" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=k8 -pipe -O2" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="http://trumpetti.atm.tut.fi/gentoo/ http://ftp.linux.ee/pub/gentoo/distfiles/ http://mirror.muntinternet.net/pub/gentoo/ http://mirror.gentoo.no/" LINGUAS="en en_GB sv sv_SE" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/crossdev-overlay /usr/local/portage/cpan-overlay /usr/local/portage/nethack-overlay /usr/local/portage/generic-overlay" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext X acl acpi alsa amd64 audiofile bash-completion berkdb bzip2 cairo caps ccache cdb cdr cli cracklib crypt cups curl dbus dri dvd dvdr dvdread emacs emboss encode evo exif expat fam fastcgi fbcon firefox flac fontconfig foomaticdb fortran gd gdbm geoip gif glep gmp gnutls gpm gstreamer gtk iconv idea idn ieee1394 imlib iproute2 ipv6 isdnlog javascript joystick jpeg jpeg2k kde kdeenablefinal kdehiddenvisibility kqemu lcms lm_sensors logrotate loop-aes lyx mad mbox midi mikmod mmx mmxext mng mono mozdevelop mp3 mpeg mudflap mysql mysqli ncurses nls nodrm nptl nptlonly nsplugin objc ogg openexr opengl openmp pam pcre pdf perl php physfs pic png ppds pppd python qt3 qt3support qt4 quicktime readline reflection rle scanner sdl session sndfile spell spl sqlite sse sse2 ssl svg tcl tcpd tetex tiff tk truetype unicode usb utempter vorbis xcomposite xorg xpm xv zlib zsh-completion" ALSA_CARDS="emu10k1 loopback seq-dummy dummy" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse joystick evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_GB sv sv_SE" USERLAND="GNU" VIDEO_CARDS="ati radeon vesa fbdev r128 nv nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
/etc/env.d/50python-docs is installed in pkg_preinst(), so it doesn't belong to any version of dev-python/python-docs.
I misinterpreted this bug.
Fixed.
