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  • [gentoo-user] Segfaults during and especially after emerging packages

    From Erik Geiger@21:1/5 to All on Wed Jun 4 17:40:01 2025
    Hello,

    I'm having at least 2 VMs that show segfaults in the log files during, and especially after compiling.

    First I thought it's a hardware issue. But now the hardware is replaced
    and they still show up.

    So if I try to rebuild pkgconf, which showed segfaults when trying to install/build some other packages, I already get error messages during installation:

    emerge -va1 pkgconf

    ~~~~~
    Completed installing dev-util/pkgconf-2.4.3 into /var/tmp/portage/dev-util/pkgconf-2.4.3/image

    * Final size of build directory: 3065 KiB (2.9 MiB)
    * Final size of installed tree: 170 KiB

    /usr/lib/portage/python3.12/install-qa-check.d/60pkgconfig: line 8: 9360 Segmentation fault pkg-config --maximum-traverse-depth=1 --with-path="${ED}"/usr/{lib*,share}/pkgconfig --validate "${files[@
    ]}"
    * QA Notice: pkg-config files which fail validation found!
    * Run 'pkg-config --validate ...' for more information /usr/lib/portage/python3.12/install-qa-check.d/60systemd: line 3: 9392 Segmentation fault pkg-config --exists systemd

    * QA Notice: The following shared libraries lack a SONAME
    * /usr/lib64/libpkgconf.so.6.0.0

    x86_64-pc-linux-gnu-nm: warning: /var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/lib64/libpkgconf.so.6.0.0 has a corrupt string table index
    x86_64-pc-linux-gnu-nm: /var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/lib64/libpkgconf.so.6.0.0: no symbols


    * QA Notice: Pre-stripped files found:
    * /usr/lib64/libpkgconf.so.6.0.0
    * /usr/bin/x86_64-pc-linux-gnu-pkgconf
    * /usr/bin/bomtool
    strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version
    /usr/bin/x86_64-pc-linux-gnu-pkgconf
    /usr/lib64/libpkgconf.so.6.0.0
    /usr/bin/bomtool
    x86_64-pc-linux-gnu-strip: x86_64-pc-linux-gnu-strip: warning: /var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/lib64/libpkgconf.so.6.0.0 has a corrupt string table index
    x86_64-pc-linux-gnu-strip: unable to modify '/var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/lib64/libpkgconf.so.6.0.0' due to errors
    warning: /var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/bin/x86_64-pc-linux-gnu-pkgconf has a corrupt string table index
    x86_64-pc-linux-gnu-strip: unable to modify '/var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/bin/x86_64-pc-linux-gnu-pkgconf' due to errors
    x86_64-pc-linux-gnu-strip: warning: /var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/bin/bomtool has a corrupt string table index
    x86_64-pc-linux-gnu-strip: unable to modify '/var/tmp/portage/dev-util/pkgconf-2.4.3/image/usr/bin/bomtool' due to errors
    ~~~~~

    And I can see segfaults in the log:

    ~~~~~
    [626700.291462] pkg-config[9339]: segfault at 8 ip 00007fee83e3e4f5 sp 00007ffecafe4660 error 4 in ld-linux-x86-64.so.2[1f4f5,7fee83e20000+27000] likely on CPU 1 (core 0, socket 1)
    [626700.291474] Code: 81 39 52 e5 74 64 0f 84 7a 06 00 00 48 85 c0 75 e4 48 83 3d 3c 6a 01 00 00 0f 85 89 06 00 00 49 8b 55 68 49 8b 85 a0 02 00 00 <48> 8b 5a 08 41 f6 85 56 03 00 00 20 0f 84 3c 06 00 00 49 03 5d 00
    [626700.443884] pkg-config[9360]: segfault at 8 ip 00007fd46928f4f5 sp 00007ffc3bd03420 error 4 in ld-linux-x86-64.so.2[1f4f5,7fd469271000+27000] likely on CPU 0 (core 0, socket 0)
    [626700.443893] Code: 81 39 52 e5 74 64 0f 84 7a 06 00 00 48 85 c0 75 e4 48 83 3d 3c 6a 01 00 00 0f 85 89 06 00 00 49 8b 55 68 49 8b 85 a0 02 00 00 <48> 8b 5a 08 41 f6 85 56 03 00 00 20 0f 84 3c 06 00 00 49 03 5d 00
    [626700.760173] pkg-config[9392]: segfault at 8 ip 00007fcd6a7de4f5 sp 00007fffed53f240 error 4 in ld-linux-x86-64.so.2[1f4f5,7fcd6a7c0000+27000] likely on CPU 0 (core 0, socket 0)
    [626700.760183] Code: 81 39 52 e5 74 64 0f 84 7a 06 00 00 48 85 c0 75 e4 48 83 3d 3c 6a 01 00 00 0f 85 89 06 00 00 49 8b 55 68 49 8b 85 a0 02 00 00 <48> 8b 5a 08 41 f6 85 56 03 00 00 20 0f 84 3c 06 00 00 49 03 5d 00
    ~~~~~

    If I reinstall libffi for example, I can't even call "emerge" any more,
    without receiving segfaults. So I had to manually unpack a binary
    package and overwrite libraries to get at least the emerge command back.

    I'm not aware of any change to CHOST variable or anything like that. So
    no idea where this is coming from.

    I'm using libvirt/kvm/qemu for virtualisation. Right now this is
    happening to 2 VMs I tried to update (the last one was somewhen in
    March). I didn't dare to test this on other VMs after I discovered the
    issues. I just used another VM (without syncing) to build binpkgs to at
    least fix some things (like gcc not able to compile any packages at all
    any more).

    Any idea what might be causing this or how to fix this?

    Kind regards,

    Erik

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