For now I use squashed portage tree. When at least one node (overlay) was mounted without read-access (for example 750 portage:portage and user not into portage group) execution of equery utility fails with output trace: $ equery u net-fs/nfs-utils Traceback (most recent call last): File "/usr/lib64/python3.4/site-packages/portage/eclass_cache.py", line 119, in update_eclasses eclass_filenames = os.listdir(x) File "/usr/lib64/python3.4/site-packages/portage/__init__.py", line 259, in __call__ rval = self._func(*wrapped_args, **wrapped_kwargs) PermissionError: [Errno 13] Permission denied: b'/usr/portage/local/eclass' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python-exec/python3.4/equery", line 38, in <module> equery.main(sys.argv) File "/usr/lib64/python3.4/site-packages/gentoolkit/equery/__init__.py", line 355, in main expanded_module_name, globals(), locals(), [], 1 File "/usr/lib64/python3.4/site-packages/gentoolkit/equery/uses.py", line 30, in <module> from gentoolkit.query import Query File "/usr/lib64/python3.4/site-packages/gentoolkit/query.py", line 32, in <module> from gentoolkit.package import Package File "/usr/lib64/python3.4/site-packages/gentoolkit/package.py", line 68, in <module> default_settings = _NewPortageConfig(local_config=True) File "/usr/lib64/python3.4/site-packages/gentoolkit/package.py", line 65, in _NewPortageConfig target_root=os.environ.get('ROOT', None)) File "/usr/lib64/python3.4/site-packages/portage/proxy/objectproxy.py", line 31, in __call__ return result(*args, **kwargs) File "/usr/lib64/python3.4/site-packages/portage/package/ebuild/config.py", line 528, in __init__ self.repositories = load_repository_config(self) File "/usr/lib64/python3.4/site-packages/portage/repository/config.py", line 999, in load_repository_config return RepoConfigLoader(repoconfigpaths, settings) File "/usr/lib64/python3.4/site-packages/portage/repository/config.py", line 851, in __init__ tree_db = eclass_cache.cache(eclass_location) File "/usr/lib64/python3.4/site-packages/portage/eclass_cache.py", line 79, in __init__ self.update_eclasses() File "/usr/lib64/python3.4/site-packages/portage/eclass_cache.py", line 125, in update_eclasses raise PermissionDenied(x) portage.exception.PermissionDenied: /usr/portage/local/eclass I expect equery perform a check and output some more readable error message. # equery u =app-portage/gentoolkit-0.3.0.9-r2 * Found these USE flags for app-portage/gentoolkit-0.3.0.9-r2: U I + + python_targets_python2_7 : Build with Python 2.7 - - python_targets_python3_3 : Build with Python 3.3 + + python_targets_python3_4 : Build with Python 3.4 # einfo Portage 2.2.28 (python 3.4.3-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.22-r4, 4.1.12-aufs x86_64) ================================================================= System uname: Linux-4.1.12-aufs-x86_64-AMD_Athlon-tm-_II_X2_250_Processor-with-gentoo-2.2 KiB Mem: 1793492 total, 94428 free KiB Swap: 8000364 total, 7690052 free Timestamp of repository gentoo: Mon, 20 Jun 2016 00:45:01 +0000 sh bash 4.3_p42-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.3_p42-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo dev-util/cmake: 3.3.1-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.19.1::gentoo sys-apps/sandbox: 2.10-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.22-r4::gentoo Repositories: gentoo location: /usr/portage/gentoo sync-type: webrsync priority: -1000 local location: /usr/portage/local masters: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/env.d /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--ask --verbose --autounmask=n" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildsyspkg config-protect-if-modified distlocks downgrade-backup ebuild-locks fixlafiles merge-sync metadata-transfer news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles/ ftp://mirror.yandex.ru/gentoo-distfiles/ http://ftp.corbina.net/pub/Linux/gentoo/ ftp://ftp.corbina.net/pub/Linux/gentoo/" LANG="ru_RU.utf8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--exclude-from=/etc/portage/rsync_excludes" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="X a52 ac3 acl alsa amd64 avi berkdb bold bzip2 cdr cli consolekit cracklib crypt cups cxx dbus djvu dri dvd flac fortran gdbm gif gtk iconv inotify jpeg jpeg2k lock mmx mmxext modules mp3 multilib ncurses nls nptl ogg openmp pam pcre pdf png policykit qt3support readline seccomp session sse sse2 ssl tcpd thunar tiff udev udisks unicode utf8 vorbis xattr xcb xulrunner zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext popcnt sse sse2 sse3 sse4a" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="ru ru_RU" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20" USERLAND="GNU" VIDEO_CARDS="radeon" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, USE_PYTHON
Probably similiar issue with the same version of app-portage/gentoolkit, see bug #550862
