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Dbus fails to start - maybe conda install responsible

asked 2018-12-17 02:27:15 -0600

HPCJohn gravatar image

Fedora 29 Workstation running on an HP Spectre laptop. Updated using dnf very recently. I installed conda in order to experiment with some Python plotting modules under Julia. Now the laptop will not boot - it hangs at the F logo display. I boot to rescue mode and run journalctl -b -1 The first failure is that /usr/sbin/firewalld fails with a permissions error Then the next is that the dbus service fails to start with a permissions error

I find that there is no /run/dbus directory. I create /run/dbus with permissions 4750. Reboot and the boot still fails at the F logo. Has anyone seen this problem?

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That /run/dbus will disappear again when rebooting, as it lives on a ram-disk file system and not on a disk unit. /run/dbus will be created by the dbus daemon when it starts.

villykruse gravatar imagevillykruse ( 2018-12-17 10:19:14 -0600 )edit

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answered 2018-12-17 23:41:01 -0600

HPCJohn gravatar image

Before anyone says it - WTF was I thinking running conda install under sudo. Lesson learned... Off to lick my wounds here and re-install all packages I Can find which were affected. Duh.

ps. Is there a way to erase this thread... OR maybe I can just get leave town and get plastic surgery to disguise my identity...

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It might work better to install conda from the fedora repository.

dnf install conda
villykruse gravatar imagevillykruse ( 2018-12-18 02:43:29 -0600 )edit
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answered 2018-12-17 23:27:46 -0600

HPCJohn gravatar image

Sure enough conda is the problem here. It has hosed my system. In rescue mode, I see that that /usr/bin/dbus-daemon is provided by dbus-daemon-1.12.10-1.fc29.x86_64 When I run /usr/bin/dbus-daemon --version D-Bus Message Bus Daemon 1.13.2

rpm --verify dbus-daemon fails with checksum and size errors on all /usr/bin files which it provides. Danger Will Robinson! Danger!

There is a file called /var/cache/conda/pkgs/dbus-1.13.2-h714fa37-1/bin/dbus-daemon I run that file and it reports version 1.13.2 Strangely enough the md5sum of that files does NOT match /usr/bin/dbus-daemon

Any advice on how to remove conda from my system and clean up? Just to add to the fun, in rescue mode, running dnf gives this error:

Module Not Found Error: No module named 'libdnf'

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Potentially you could try to boot from installation usb key, chroot into you broken Fedora (there are plenty of how-tos about chrooting into you install), then wget https://mirror.yandex.ru/fedora/linux/releases/29/Everything/x86_64/os/Packages/d/dbus-daemon-1.12.10-1.fc29.x86_64.rpm (or use any other mirror you like) and install it with dnf if it works or with rpm -i <path to="" downloaded="" rpm="">.

It could work if there's several packages that were broken. If there're plenty, I think i would just reinstall.

Night Romantic gravatar imageNight Romantic ( 2018-12-18 03:38:48 -0600 )edit
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answered 2018-12-17 23:03:43 -0600

HPCJohn gravatar image

I think I have a smoking gun here. Set selinux to permissive. Boot - fails to boot. Then boot into rescue mode and I see this logged

dbus-daemon[1341] Faile dto start message bus: dbus was compiled without system support

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answered 2018-12-17 04:29:27 -0600

HPCJohn gravatar image

Thankyou. I have booted into rescue mode and the / and /home filesystems mount OK, so they dont need an fsck

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Quite unexpected. What about firewall? If the issue persists, file a bug to bugzilla.redhat.com .

ed209 gravatar imageed209 ( 2018-12-17 05:22:32 -0600 )edit
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answered 2018-12-17 04:15:10 -0600

ed209 gravatar image

First disable firewalld and try again. What happens? Then check out your drive. You don't have to do anything special to boot, let alone create /run/dbus . And I doubt that conda is responsible for anything at all.

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Asked: 2018-12-17 02:27:15 -0600

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Last updated: Dec 17 '18