Emerge broken [solved]

Message

eemax · Post by **eemax** » Mon Dec 08, 2025 4:12 pm

Emerge seems to be broken on my system:

# emerge =dev-lang/python-3.13.5_p1
Traceback (most recent call last):
  File "/usr/lib/python3.13/site-packages/portage/util/locale.py", line 103, in _set_and_check_locale
    ret = _check_locale(silent)
  File "/usr/lib/python3.13/site-packages/portage/util/locale.py", line 52, in _check_locale
    rlc = [libc.tolower(c) for c in uc]
           ~~~~~~~~~~~~^^^
RuntimeError: ffi_prep_cif failed
Calculating dependencies... done!
Dependency resolution took 4.52 s (backtrack: 0/20).


>>> Verifying ebuild manifests

>>> Running pre-merge checks for dev-lang/python-3.13.5_p1
Traceback (most recent call last):
  File "/usr/lib/python3.13/site-packages/portage/util/locale.py", line 103, in _set_and_check_locale
    ret = _check_locale(silent)
  File "/usr/lib/python3.13/site-packages/portage/util/locale.py", line 52, in _check_locale
    rlc = [libc.tolower(c) for c in uc]
           ~~~~~~~~~~~~^^^
RuntimeError: ffi_prep_cif failed
Process Process-5:
Traceback (most recent call last):
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 1288, in __call__
    return self._results[flags]
           ~~~~~~~~~~~~~^^^^^^^
KeyError: 1812070400

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/multiprocessing/process.py", line 313, in _bootstrap
    self.run()
    ~~~~~~~~^^
  File "/usr/lib/python3.13/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
    ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 1338, in _run_subproc
    subproc_pipe.send(target(*args, **kwargs))
                      ~~~~~~^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 1358, in _validate_subproc
    return 0 if libc.unshare(flags) == 0 else ctypes.get_errno()
                ~~~~~~~~~~~~^^^^^^^
RuntimeError: ffi_prep_cif failed
[ERROR] Exception in callback AsynchronousTask._exit_listener_cb()
handle: <Handle AsynchronousTask._exit_listener_cb()>
Traceback (most recent call last):
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 1288, in __call__
    return self._results[flags]
           ~~~~~~~~~~~~~^^^^^^^
KeyError: 1812070400

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/asyncio/events.py", line 89, in _run
    self._context.run(self._callback, *self._args)
    ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/_emerge/AsynchronousTask.py", line 209, in _exit_listener_cb
    listener(self)
    ~~~~~~~~^^^^^^
  File "/usr/lib/python3.13/site-packages/_emerge/EbuildPhase.py", line 272, in _async_start_exit
    self._start_lock()
    ~~~~~~~~~~~~~~~~^^
  File "/usr/lib/python3.13/site-packages/_emerge/EbuildPhase.py", line 295, in _start_lock
    self._start_ebuild()
    ~~~~~~~~~~~~~~~~~~^^
  File "/usr/lib/python3.13/site-packages/_emerge/EbuildPhase.py", line 352, in _start_ebuild
    self._start_task(ebuild_process, self._ebuild_exit)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/_emerge/CompositeTask.py", line 117, in _start_task
    task.start()
    ~~~~~~~~~~^^
  File "/usr/lib/python3.13/site-packages/_emerge/AsynchronousTask.py", line 34, in start
    self._start()
    ~~~~~~~~~~~^^
  File "/usr/lib/python3.13/site-packages/_emerge/AbstractEbuildProcess.py", line 120, in _start
    self._start_post_builddir_lock(start_ipc_daemon=start_ipc_daemon)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/_emerge/AbstractEbuildProcess.py", line 153, in _start_post_builddir_lock
    SpawnProcess._start(self)
    ~~~~~~~~~~~~~~~~~~~^^^^^^
  File "/usr/lib/python3.13/site-packages/_emerge/SpawnProcess.py", line 140, in _start
    self._proc = self._spawn(self.args, **kwargs)
                 ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/_emerge/EbuildProcess.py", line 24, in _spawn
    return _doebuild_spawn(
        self.phase, self.settings, actionmap=actionmap, **kwargs
    )
  File "/usr/lib/python3.13/site-packages/portage/package/ebuild/doebuild.py", line 300, in _doebuild_spawn
    return spawn(cmd, settings, **kwargs)
  File "/usr/lib/python3.13/site-packages/portage/package/ebuild/doebuild.py", line 2262, in spawn
    return spawn_func(mystring, env=env, **keywords)
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 167, in spawn_bash
    return spawn(args, opt_name=opt_name, **keywords)
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 724, in spawn
    _unshare_validate(unshare_flags)
    ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 1290, in __call__
    result = self._results[flags] = self._validate(flags)
                                    ~~~~~~~~~~~~~~^^^^^^^
  File "/usr/lib/python3.13/site-packages/portage/process.py", line 1318, in _validate
    result = parent_pipe.recv()
  File "/usr/lib/python3.13/multiprocessing/connection.py", line 250, in recv
    buf = self._recv_bytes()
  File "/usr/lib/python3.13/multiprocessing/connection.py", line 430, in _recv_bytes
    buf = self._recv(4)
  File "/usr/lib/python3.13/multiprocessing/connection.py", line 399, in _recv
    raise EOFError
EOFError
Terminated                 emerge =dev-lang/python-3.13.5_p1

Code: Select all

# emerge --info
Portage 3.0.69 (python 3.13.5-final-0, default/linux/amd64/23.0/split-usr/desktop, gcc-14, glibc-2.42-r2, 6.18.0-gentoo x86_64)
=================================================================
System uname: Linux-6.18.0-gentoo-x86_64-AMD_Ryzen_7_1700X_Eight-Core_Processor-with-glibc2.42
KiB Mem:    65800864 total,  28847528 free
KiB Swap:   67108860 total,  67108860 free
Timestamp of repository gentoo: Sun, 07 Dec 2025 11:30:55 +0000
Head commit of repository gentoo: c8e082fb1267a567d0f8aef3ec2ff93e04453512

Timestamp of repository guru: Sun, 07 Dec 2025 11:31:05 +0000
Head commit of repository guru: 409992238683701c4b02ff00097fc026c60ed99c

sh bash 5.3_p8
ld GNU ld (Gentoo 2.45.1 p1) 2.45.1
app-misc/pax-utils:        1.3.10::gentoo
app-shells/bash:           5.3_p8::gentoo
dev-build/autoconf:        2.72-r5::gentoo
dev-build/automake:        1.18.1::gentoo
dev-build/cmake:           4.1.3::gentoo
dev-build/libtool:         2.5.4::gentoo
dev-build/make:            4.4.1-r102::gentoo
dev-build/meson:           1.9.2::gentoo
dev-java/java-config:      2.3.4::gentoo
dev-lang/perl:             5.42.0-r1::gentoo
dev-lang/python:           3.13.5_p1::gentoo, 3.14.2::gentoo
dev-lang/rust-bin:         1.90.0::gentoo, 1.91.0::gentoo
llvm-core/clang:           20.1.8::gentoo, 21.1.7::gentoo
llvm-core/lld:             20.1.8::gentoo
llvm-core/llvm:            20.1.8::gentoo, 21.1.7::gentoo
sys-apps/baselayout:       2.18::gentoo
sys-apps/openrc:           0.63::gentoo
sys-apps/sandbox:          2.46::gentoo
sys-devel/binutils:        2.45.1::gentoo
sys-devel/binutils-config: 5.6::gentoo
sys-devel/gcc:             14.3.1_p20251017::gentoo, 15.2.1_p20251122::gentoo
sys-devel/gcc-config:      2.12.2::gentoo
sys-kernel/linux-headers:  6.17-r1::gentoo (virtual/os-headers)
sys-libs/glibc:            2.42-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gentoo.git
    priority: -1000
    volatile: True
    sync-git-verify-commit-signature: yes

guru
    location: /var/db/repos/guru
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/guru.git
    masters: gentoo
    volatile: False

local
    location: /usr/local/portage/local
    masters: gentoo
    priority: 100
    volatile: True

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.9/conf /usr/share/themes/oxygen-gtk/gtk-2.0"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php8.5/ext-active/ /etc/php/cgi-php8.5/ext-active/ /etc/php/cli-php8.5/ext-active/ /etc/php/fpm-php8.5/ext-active/ /etc/php/phpdbg-php8.5/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"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME"
FCFLAGS="-march=native -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news nostrip parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="        https://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/      rsync://mirror.eu.oneandone.net/gentoo/       ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo          ftp://mirror.netcologne.de/gentoo/    https://mirror.netcologne.de/gentoo/    rsync://mirror.netcologne.de/gentoo/    https://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/   https://ftp.halifax.rwth-aachen.de/gentoo/      ftp://ftp.halifax.rwth-aachen.de/gentoo/      rsync://ftp.halifax.rwth-aachen.de/gentoo/      https://ftp.fau.de/gentoo    ftp://ftp.fau.de/gentoo          rsync://ftp.fau.de/gentoo       https://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/          ftp://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/      rsync://ftp-stud.hs-esslingen.de/gentoo/      https://distfiles.gentoo.org"
INSTALL_MASK=" /usr/share/locale        -usr/share/locale/de    -usr/share/locale/de_DE         -usr/share/locale/en  -usr/share/locale/en_GB         -usr/share/locale/en_IE         -usr/share/locale/en_US /usr/share/help       -/usr/share/help/C      -/usr/share/help/de     -/usr/share/help/de_DE  -/usr/share/help/en     -/usr/share/help/en_GB        -/usr/share/help/en_IE  -/usr/share/help/en_US "
LANG="en_IE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs"
LEX="flex"
LINGUAS="en_IE en_GB en_US en de_DE de"
MAKEOPTS="-j8"
PKGDIR="/var/cache/binpkgs"
PORTAGE_COMPRESS="bzip2"
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"
SHELL="/bin/bash"
USE="X a52 aac acl acpi alsa amd64 amr apache2 avif bluetooth bluray boost bzip2 cairo cdda cddb cdr cet crypt css cups curl dbus dga djvu dri dts dv dvb dvd dvdr egl elogind encode exif ffmpeg fftw flac fluidsynth fontconfig gdbm gif git gles2 gmp gphoto2 gpm graphviz gstreamer gtk gui hardened iconv icu id3tag imagemagick imap ipv6 jack jbig jpeg jpeg2k jpegxl kde lame lash latex lcms libnotify libsamplerate libtirpc lv2 lzma lzo mad mbox mms mng modplug mp3 mp4 mpeg mtp multilib musepack musicbrainz mysql ncurses nls ntfs ogg openal openexr opengl openmp opus pam pango pcre pdf pipewire plasma png policykit postscript ppds pulseaudio python qml qt5 qt6 raw readline rubberband scanner sdl seccomp sndfile sound sox spacenav speex spell split-usr sqlite ssl startup-notification subversion svg taglib test-rust theora threads tiff truetype twolame udev udisks unicode usb v4l vaapi vorbis vpx vulkan wavpack wayland webp widgets wmf wxwidgets x264 xattr xcb xcomposite xft xine xinerama xml xmp xpm xv xvid zeroconf zlib" ABI_X86="64 32" ADA_TARGET="gcc_15" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" GRUB_PLATFORMS="emu efi-64 pc" GUILE_SINGLE_TARGET="3-0" GUILE_TARGETS="3-0" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en-IE en-GB en-US en de" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LLVM_TARGETS="X86" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-3" POSTGRES_TARGETS="postgres17" PYTHON_SINGLE_TARGET="python3_13" PYTHON_TARGETS="python3_13" RUBY_TARGETS="ruby32 ruby33" SANE_BACKENDS="pixma canon_lide70" VIDEO_CARDS="svga vesa vga radeon radeonsi amdgpu" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

I can temporarily fix the problem by restoring a backup of /usr/lib/python3.13, but as soon as python is re-emerged the problem returns.

Code: Select all

/usr/lib # mv python3.13 bython3.13-bak
[restore backup:]
/usr/lib # cp -av /mnt/usr/lib/python3.13 .
[now emerge works:]
/usr/lib # emerge =dev-lang/python-3.13.5_p1
[emerges without error]
/usr/lib # emerge =dev-lang/python-3.13.5_p1
[emerge fails with the error message above]

How can I fix this?

eemax · Post by **eemax** » Tue Dec 09, 2025 12:50 pm

This turned out to be a configuration problem.

PKG_CONFIG_PATH was set to "/usr/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/share/pkgconfig" and pkg-config was returning the wrong include and library files for libffi (/usr/lib instead of /usr/lib64).

The fix was to remove PKG_CONFIG_PATH and replace /usr/lib/python3.13/lib-dynload/_ctypes.cpython-313-x86_64-linux-gnu.so with a backup version. Then re-emerge python.