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Multiple issues after update




Hello,
 
after a recent dist-upgrade on my debian 9 server I am experimenting several issues with services complaining about missing permissions.
 
There has not been any major changes on that server but since the upgrade was done apachae, postfix and apt are complaining and refusing to work as intended.
 
The apache server shows a permission denied on all webpages, the postfix server just dies after a while ("systemctl status postfix" shows the service as active after startup)
 
apt update complains about permissions too.
 
Some DBus error appears too which I have never seen before the update
 
 
Since I have an old snapshot of the server I compared the permissions on the files in question and they all match, therefore I don't know where else to look.
 
Here is some of the relevant information and log entries:
 
 
apt update
Hit:1 http://security.debian.org stretch/updates InRelease
Ign:2 http://ftp.de.debian.org/debian stretch InRelease
Hit:3 http://ftp.de.debian.org/debian stretch-updates InRelease
Hit:4 http://ftp.de.debian.org/debian stretch Release
Hit:5 https://download.docker.com/linux/debian stretch InRelease
Error: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.PackageKit was not provided by any .service files
Reading package lists... Done
Building dependency tree       
Reading state information... Done
All packages are up to date.
W: Download is performed unsandboxed as root as file '/var/lib/apt/lists/partial/ftp.de.debian.org_debian_dists_stretch_InRelease' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
ls -l /var/lib/apt/lists/partial/ftp.de.debian.org_debian
ls: cannot access '/var/lib/apt/lists/partial/ftp.de.debian.org_debian': No such file or directory
 
ls -l /var/lib/apt/lists/
total 108268
-rw-r--r-- 1 root root    39105 Mar 11 04:04 download.docker.com_linux_debian_dists_stretch_InRelease
-rw-r--r-- 1 root root    16254 Feb 28 02:52 download.docker.com_linux_debian_dists_stretch_stable_binary-amd64_Packages
-rw-r--r-- 1 root root 39116092 Mar 10 10:33 ftp.de.debian.org_debian_dists_stretch_main_binary-amd64_Packages
-rw-r--r-- 1 root root  7115196 Jun 16  2017 ftp.de.debian.org_debian_dists_stretch_main_i18n_Translation-de
-rw-r--r-- 1 root root     1347 Jun 16  2017 ftp.de.debian.org_debian_dists_stretch_main_i18n_Translation-de%5fDE
-rw-r--r-- 1 root root 26457271 Mar 10 10:33 ftp.de.debian.org_debian_dists_stretch_main_i18n_Translation-en
-rw-r--r-- 1 root root 33781328 Mar 10 10:33 ftp.de.debian.org_debian_dists_stretch_main_source_Sources
-rw-r--r-- 1 root root   117943 Mar 10 11:22 ftp.de.debian.org_debian_dists_stretch_Release
-rw-r--r-- 1 root root     2434 Mar 10 11:36 ftp.de.debian.org_debian_dists_stretch_Release.gpg
-rw-r--r-- 1 root root    91028 Mar 12 15:35 ftp.de.debian.org_debian_dists_stretch-updates_InRelease
-rw-r--r-- 1 root root    34570 Feb 11 21:45 ftp.de.debian.org_debian_dists_stretch-updates_main_binary-amd64_Packages
-rw-r--r-- 1 root root     2704 Feb 11 21:45 ftp.de.debian.org_debian_dists_stretch-updates_main_binary-amd64_Packages.diff_Index
-rw-r--r-- 1 root root    21713 Jan 29 21:29 ftp.de.debian.org_debian_dists_stretch-updates_main_i18n_Translation-en
-rw-r--r-- 1 root root     2212 Jan 29 21:29 ftp.de.debian.org_debian_dists_stretch-updates_main_i18n_Translation-en.diff_Index
-rw-r--r-- 1 root root    13564 Feb 11 21:45 ftp.de.debian.org_debian_dists_stretch-updates_main_source_Sources
-rw-r--r-- 1 root root     2704 Feb 11 21:45 ftp.de.debian.org_debian_dists_stretch-updates_main_source_Sources.diff_Index
-rw-r----- 1 root root        0 Jul 26  2016 lock
drwx------ 2 _apt root     4096 Mar 12 21:11 partial
-rw-r--r-- 1 root root    62959 Mar 11 20:01 security.debian.org_dists_stretch_updates_InRelease
-rw-r--r-- 1 root root  1868567 Mar 10 22:43 security.debian.org_dists_stretch_updates_main_binary-amd64_Packages
-rw-r--r-- 1 root root  1048251 Mar 10 22:43 security.debian.org_dists_stretch_updates_main_i18n_Translation-en
-rw-r--r-- 1 root root  1022428 Mar 10 22:43 security.debian.org_dists_stretch_updates_main_source_Sources

the partial folder is empty
 

[Mon Mar 12 20:48:22.711299 2018] [mpm_prefork:notice] [pid 1053] AH00163: Apache/2.4.25 (Debian) OpenSSL/1.0.2l configured -- resuming normal operations
[Mon Mar 12 20:48:22.791915 2018] [core:notice] [pid 1053] AH00094: Command line: '/usr/sbin/apache2'
[Mon Mar 12 20:48:38.739798 2018] [ssl:error] [pid 1113] (13)Permission denied: [client <IP_redacted>:37336] AH01972: could not resolve address of OCSP responder ocsp.int-x3.letsencrypt.org
[Mon Mar 12 20:48:38.739889 2018] [ssl:error] [pid 1113] AH01941: stapling_renew_response: responder error
[Mon Mar 12 20:48:38.778277 2018] [core:error] [pid 1113] (13)Permission denied: [client <IP_redacted>:37336] AH00035: access to / denied (filesystem path '/var') because search permissions are missing on a component of the path
[Mon Mar 12 20:48:38.881378 2018] [core:error] [pid 1113] (13)Permission denied: [client <IP_redacted>:37336] AH00035: access to /favicon.ico denied (filesystem path '/var') because search permissions are missing on a component of the path

Start-Date: 2018-03-11  13:30:41
Commandline: apt-get dist-upgrade
Upgrade: libfdisk1:amd64 (2.29.2-1, 2.29.2-1+deb9u1), libmount1:amd64 (2.29.2-1, 2.29.2-1+deb9u1), util-linux:amd64 (2.29.2-1, 2.29.2-1+deb9u1), mount:amd64 (2.29.2-1, 2.29.2-1+deb9u1), libblkid1:amd64 (2.29.2-1, 2.29.2-1+deb9u1), libuuid1:amd64 (2.29.2-1, 2.29.2-1+deb9u1), libsmartcols1:amd64 (2.29.2-1, 2.29.2-1+deb9u1), bsdutils:amd64 (1:2.29.2-1, 1:2.29.2-1+deb9u1)
End-Date: 2018-03-11  13:31:02
 
drwxr-xr-x  12 root root  4096 Aug 25  2016 var
drwxr-xr-x  6 root root   4096 Oct 18  2016 www
drwxr-xr-x  5 root root 4096 Mar 12 19:24 html

drwxr-xr-x 2 root root 4096 Oct 18  2016 css
-rw-r--r-- 1 root root  550 Oct 18  2016 subpage.html
drwxr-xr-x 2 root root 4096 Oct 18  2016 img
-rw-r--r-- 1 root root 1321 Oct 18  2016 index.html
drwxr-xr-x 2 root root 4096 Oct 18  2016 js
 
 
 
 
Can anyone give me a hint on where elso to look for this issue?
 
This all happened after debian 9.4 was released but I don't think this should be the cause.