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Currently, vzctl creates a few empty directories when it is installed.  These
directories are removed upon re-installation of vzctl.

The ones I have found are:
/vz/template/cache
/vz/template
/vz/lock
/vz/dump
/var/lib/vzctl/veip
/var/lib/vzctl
/usr/lib/vzctl/modules

Reproducible: Always

Steps to Reproduce:
1. Install vzctl
2. Immediately re-install vzctl
Actual Results:  
Removes empty directories belonging to vzctl package.

Expected Results:  
Should keep directories belonging to it.

No. It works correctly with newer Portage. Please post the output of:
emerge --info

Portage 2.1.2.11 (hardened/amd64, gcc-3.4.6, glibc-2.5-r4, 2.6.18-028stab027
x86_64)
=================================================================
System uname: 2.6.18-028stab027 x86_64 Dual-Core AMD Opteron(tm) Processor 8212
Gentoo Base System release 1.12.9
Timestamp of tree: Fri, 03 Aug 2007 13:30:01 +0000
ccache version 2.4 [enabled]
dev-lang/python:     2.4.4-r4
dev-python/pycrypto: 2.0.1-r6
dev-util/ccache:     2.4-r7
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.61
sys-devel/automake:  1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.16
sys-devel/libtool:   1.5.23b
virtual/os-headers:  2.6.21
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=opteron -msse3 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-march=opteron -msse3 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache distlocks metadata-transfer parallel-fetch sandbox sfperms
strict"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
MAKEOPTS="-j9"
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
--filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 apache2 bash-completion berkdb cracklib crypt hardened justify midi
nls nptl nptlonly pam pic readline sse sse2 ssl tcpd urandom xorg zlib"
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="mouse keyboard" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses
text" USERLAND="GNU"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS,
PORTDIR_OVERLAY

(In reply to comment #2)
> Portage 2.1.2.11 (hardened/amd64, gcc-3.4.6, glibc-2.5-r4, 2.6.18-028stab027
> x86_64)

Update GCC to 4.1.2. Try with Portage 2.1.3.3. It works correctly.

(In reply to comment #0)
> Currently, vzctl creates a few empty directories when it is installed.  These
> directories are removed upon re-installation of vzctl.
> 
> The ones I have found are:
> /vz/template/cache
> /vz/template
> /vz/lock
> /vz/dump
> /var/lib/vzctl/veip
> /var/lib/vzctl
> /usr/lib/vzctl/modules

Which version of vzctl is that exactly ?

Should be fixed in vzctl-3.0.18-r1 (hopefully).