This is a duplicate of bug 504610 for newer git-annex ebuilds. The git-annex-2016* ebuilds are missing a dependency on sys-process/lsof when USE=assistant is set. Trying to run the assistant results in: % git annex webapp git-annex: The lsof command is needed for watch mode to be safe, and is not in PATH. To override lsof checks to ensure that files are not open for writing when added to the annex, you can use --force Be warned: This can corrupt data in the annex, and make fsck complain. Just looks like we lost the dependency again sometime between the last bug and now. % emerge --info Portage 2.2.28 (python 2.7.10-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.9.3, glibc-2.22-r4, 4.4.6-gentoo x86_64) ================================================================= System uname: Linux-4.4.6-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_L_640_@_2.13GHz-with-gentoo-2.2 KiB Mem: 7965044 total, 4768512 free KiB Swap: 4194300 total, 4194300 free Timestamp of repository gentoo: Sat, 13 Aug 2016 14:00:01 +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 sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sabayon location: /var/lib/layman/sabayon masters: gentoo priority: 0 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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/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="-O2 -pipe -march=native -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync 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://mirrors.rit.edu/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord cracklib crypt cups cxx dbus dri dts dvd dvdr eds emacs emboss encode evo exif fam firefox flac fortran gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk iconv introspection ipv6 jpeg lcms ldap libnotify libsecret mad mmx mmxext mng modules mp3 mp4 mpeg multilib nautilus ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt3support qt4 readline sdl seccomp session spell sse sse2 ssl startup-notification svg systemd tcpd tiff tracker truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xml xv xvid zlib zsh zsh-completion" 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="krita" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 synaptics wacom" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Good catch! Added as: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e1259af6a27a3de4460ca6068a0dc802c4d5ed8d Ans to the overlay where we copy thing from: https://github.com/gentoo-haskell/gentoo-haskell/commit/f2d2a6202e4222cd040d2efeb9feb7525203edf9 Thanks!
