mjhjmtu

I had to reinstall PackageKit-glib2 because of errors about missing libpackagekit-glib2.so.18. rpm -q --verify says there were a couple of files missing, and even after reinstalling that package, there are some other packages I need to reinstall

missing /usr/lib64/gnome-settings-daemon-3.0/gtk-modules/pk-gtk-module.desktop
missing /usr/lib64/gtk-2.0/modules/libpk-gtk-module.so
missing /usr/lib64/gtk-3.0/modules/libpk-gtk-module.so
missing c /etc/PackageKit/CommandNotFound.conf
missing /etc/profile.d/PackageKit.sh
missing /usr/libexec/pk-command-not-found
missing /usr/libexec/pk-gstreamer-install

rpm -q --verify --all didn't find anything else either missing or corrupted.

I was quite surprised by this. Package updates replace files atomically using rename() (and should use fsync() before rename() to guarantee that the written contents are not lost in case power is interrupted).

Is there a bug in Fedora 28 which could have removed these files?

Or is it some other known issue, e.g. with hardware?

Is there a report of a similar symptom anywhere else?

The current date is 2018-05-28. etckeeper (which updates daily) suggests the files in /etc were lost by 2018-05-16 11:33:41.

I can see an offline package update just before this, but the only package it admits to upgrading is ostree.

$ journalctl --since=-1month /usr/libexec/pk-offline-update
...
May 16 11:17:03 alan-laptop pk-offline-update[773]: package updating ostree-2018.5-1.fc28.x86_64 (updates)
...
May 16 11:17:05 alan-laptop pk-offline-update[773]: package cleanup ostree-2018.3-2.fc28.x86_64 (installed)

dnf history shows

 328 | install PackageKit | 2018-05-16 11:33 | Install | 1 <
 327 | debuginfo-install glibc- | 2018-05-16 11:02 | Update | 2 > 
 326 | downgrade ostree | 2018-05-16 10:56 | Downgrade | 1 <
 325 | builddep PackageKit | 2018-05-16 10:47 | Install | 11 ><

GNOME Disks SMART information for my hard drive reports "Disk is OK", and the short SMART test succeeded with no errors.

/lost+found/ is empty.

This system is an upgrade from Fedora 27 (etc), not a fresh install.

The hardware is a Dell Lattitude E5450 - a business series laptop - with a spinning hard drive. The hard drive identifies as WDC WD5000LPLX-75ZNTT0 (01.01A01).

coredumpctl -r list /usr/libexec/packagekitd

I had some packagekit crashes two weeks before the files in /etc went missing: https://bugzilla.redhat.com/show_bug.cgi?id=1523706#c21

and according to coredumpctl, I had a couple of later crashes that were very close to the date the files went missing

TIME PID UID GID SIG COREFILE EXE
Mon 2018-05-14 18:14:01 BST 4474 0 0 11 missing /usr/libexec/packagekitd
Mon 2018-05-14 16:40:28 BST 1599 0 0 11 missing /usr/libexec/packagekitd
Wed 2018-05-02 12:10:53 BST 2174 0 0 11 missing /usr/libexec/packagekitd
Wed 2018-05-02 11:39:55 BST 27919 0 0 11 missing /usr/libexec/packagekitd
Wed 2018-05-02 10:47:53 BST 25548 0 0 6 missing /usr/libexec/packagekitd
Wed 2018-05-02 10:46:52 BST 21783 0 0 6 missing /usr/libexec/packagekitd
Wed 2018-05-02 10:42:43 BST 18529 0 0 11 missing /usr/libexec/packagekitd
Wed 2018-05-02 10:37:56 BST 12763 0 0 6 missing /usr/libexec/packagekitd
Wed 2018-05-02 10:15:49 BST 1569 0 0 6 missing /usr/libexec/packagekitd
Sat 2018-04-28 14:34:43 BST 1394 0 0 11 missing /usr/libexec/packagekitd
Tue 2018-03-06 10:54:03 GMT 1498 0 0 6 missing /usr/libexec/packagekitd
Wed 2018-02-28 10:40:55 GMT 1487 0 0 11 missing /usr/libexec/packagekitd
Fri 2018-02-23 21:01:21 GMT 1557 0 0 6 missing /usr/libexec/packagekitd
Thu 2017-11-16 10:05:46 GMT 10987 0 0 11 missing /usr/libexec/packagekitd
Tue 2017-11-14 11:04:56 GMT 1631 0 0 11 missing /usr/libexec/packagekitd
Mon 2017-10-16 16:56:48 BST 1557 0 0 11 missing /usr/libexec/packagekitd
Thu 2017-09-28 16:31:19 BST 1513 0 0 11 missing /usr/libexec/packagekitd

 328 | install PackageKit | 2018-05-16 11:33 | Install | 1 <
 327 | debuginfo-install glibc- | 2018-05-16 11:02 | Update | 2 > 
 326 | downgrade ostree | 2018-05-16 10:56 | Downgrade | 1 <
 325 | builddep PackageKit | 2018-05-16 10:47 | Install | 11 ><

This problem was caused by some testing I did.

I removed PackageKit using rpm --nodeps -e, so I could build and install a patched PackageKit.

I then used make uninstall, and dnf install PackageKit.

The problem is that the PackageKit source package is split into several different RPMs. So I had only reinstalled the main one, and not any of the sub-packages.