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unattended-upgrades downloaded package information only from the sources in sources.list.d directory ignoring sources.list file

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  unattended-upgrades downloaded package information only from the  sources in sources.list.d directory ignoring sources.list file Martin T <m4rtntns@gmail.com> - 2019-06-05 11:50 +0200
    Re: unattended-upgrades downloaded package information only from the  sources in sources.list.d directory ignoring sources.list file Martin T <m4rtntns@gmail.com> - 2019-06-06 11:10 +0200
      Re: unattended-upgrades downloaded package information only from the  sources in sources.list.d directory ignoring sources.list file Martin T <m4rtntns@gmail.com> - 2019-06-08 10:30 +0200
        Re: unattended-upgrades downloaded package information only from the  sources in sources.list.d directory ignoring sources.list file Martin T <m4rtntns@gmail.com> - 2019-06-09 15:10 +0200

#209628 — unattended-upgrades downloaded package information only from the sources in sources.list.d directory ignoring sources.list file

Hi,

in order to test unattended-upgrades I downgraded yesterday(4.06)
packages iceweasel, qemu-utils and thunderbird:

# # "apt list --upgradable" command below was executed on 4.06
# apt list --upgradable
Listing... Done
iceweasel/stable 60.7.0esr-1~deb9u1 all [upgradable from: 52.9.0esr-1~deb9u1]
qemu-utils/stable 1:2.8+dfsg-6+deb9u6 amd64 [upgradable from:
1:2.8+dfsg-6+deb9u5]
thunderbird/stable 1:60.7.0-1~deb9u1 amd64 [upgradable from: 1:60.6.1-1~deb9u1]
#

As expected, the unattended-upgrades ran today(5.06) morning, but it
reported, that "No packages found that can be upgraded unattended and
no pending auto-removals". Indeed, when I checked for example "apt
policy iceweasel", then the apt saw the installed version as the
latest one:

$ sudo apt policy iceweasel
iceweasel:
  Installed: 52.9.0esr-1~deb9u1
  Candidate: 52.9.0esr-1~deb9u1
  Version table:
 *** 52.9.0esr-1~deb9u1 100
        100 /var/lib/dpkg/status
$

"apt policy" listed only the repository configured in
/etc/apt/sources.list.d/digitalocean-agent.list while ignoring the
ones in sources.list:

# apt policy
Package files:
 100 /var/lib/dpkg/status
     release a=now
 500 https://repos.insights.digitalocean.com/apt/do-agent main/main
amd64 Packages
     release o=. main,a=main,n=main,l=. main,c=main,b=amd64
     origin repos.insights.digitalocean.com
Pinned packages:
#

After executing "apt update", the rest of the repositories were again
seen in the output of "apt policy" and for example, the iceweasel was
again upgradable to 60.7.0esr-1~deb9u1:

$ sudo apt policy iceweasel
iceweasel:
  Installed: 52.9.0esr-1~deb9u1
  Candidate: 60.7.0esr-1~deb9u1
/* output removed for brevity */
$

Looks like the "apt update" or equivalent ran by unattended-upgrades
ignored the /etc/apt/sources.list file and used only
/etc/apt/sources.list.d/digitalocean-agent.list as a source for
repositories.
What might cause this behavior?


thanks,
Martin

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#209678

> Looks like the "apt update" or equivalent ran by unattended-upgrades
> ignored the /etc/apt/sources.list file and used only
> /etc/apt/sources.list.d/digitalocean-agent.list as a source for
> repositories.
> What might cause this behavior?

I did some further debugging and it is the
/usr/lib/apt/apt.systemd.daily script executed by apt-daily systemd
service unit which updates the package index from the sources:

    # update package lists
    UPDATED=0
    UPDATE_STAMP=/var/lib/apt/periodic/update-stamp
    if check_stamp $UPDATE_STAMP $UpdateInterval; then
        if eval apt-get $XAPTOPT -y update $XSTDERR; then
        /* output removed fro brevity */


Now I set the APT::Periodic::Verbose value to "2":

$ apt-config dump APT::Periodic::Verbose
APT::Periodic::Verbose "2";
$

..and actually the entries in /etc/apt/sources.list file are not ignored:

$ sudo journalctl --since today --no-pager -u apt-daily
-- Logs begin at Mon 2019-05-13 19:38:07 UTC, end at Thu 2019-06-06
08:40:31 UTC. --
Jun 06 00:49:10 vps systemd[1]: Starting Daily apt download activities...
Jun 06 00:49:10 vps apt.systemd.daily[31062]: verbose level 2
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Reading package lists...
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Building dependency tree...
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Reading state information...
Jun 06 00:49:10 vps apt.systemd.daily[31062]: check_stamp:
interval=86400, now=1559779200, stamp=1559692800, delta=86400 (sec)
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Get:1
http://security.debian.org stretch/updates InRelease [94.3 kB]
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Ign:2
http://mirrors.digitalocean.com/debian stretch InRelease
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Get:3
http://mirrors.digitalocean.com/debian stretch-updates InRelease [91.0
kB]
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Hit:4
http://mirrors.digitalocean.com/debian stretch Release
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Get:5
http://security.debian.org stretch/updates/main Sources [205 kB]
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Get:6
http://security.debian.org stretch/updates/main amd64 Packages [492
kB]
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Get:7
https://repos.insights.digitalocean.com/apt/do-agent main InRelease
[5,132 B]
Jun 06 00:49:10 vps apt.systemd.daily[31062]: Fetched 888 kB in 0s (1,643 kB/s)
Jun 06 00:49:11 vps apt.systemd.daily[31062]: Reading package lists...
Jun 06 00:49:11 vps apt.systemd.daily[31062]: download updated
metadata (success).
Jun 06 00:49:11 vps apt.systemd.daily[31062]: send dbus signal (success)
Jun 06 00:49:11 vps apt.systemd.daily[31062]: check_stamp: interval=0
Jun 06 00:49:11 vps apt.systemd.daily[31062]: download upgradable (not run)
Jun 06 00:49:11 vps apt.systemd.daily[31062]: unattended-upgrade -d (not run)
Jun 06 00:49:11 vps systemd[1]: Started Daily apt download activities.
$

However, again, at the morning "apt policy" listed only the repository
in /etc/apt/sources.list.d/digitalocean-agent.list file:

$ apt policy
Package files:
 100 /var/lib/dpkg/status
     release a=now
 500 https://repos.insights.digitalocean.com/apt/do-agent main/main
amd64 Packages
     release o=. main,a=main,n=main,l=. main,c=main,b=amd64
     origin repos.insights.digitalocean.com
Pinned packages:
$

After running manually the "sudo apt update" command, the apt
downloaded >50MiB of packages data and output of "apt policy" listed
all the repositories.
Log files in /var/log/apt/ directory have not been updated.

What could cause such behavior? How to debug this further?


thanks,
Martin

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#209751

> I did some further debugging and it is the
> /usr/lib/apt/apt.systemd.daily script executed by apt-daily systemd
> service unit which updates the package index from the sources:

I configured cron with one minute interval to log the output of "apt
policy" with a timestamp into a log file in order to understand when
exactly the repository list is messed up. Turns out, that
/usr/lib/apt/apt.systemd.daily script executed by apt-daily systemd
service unit does not mess up the repository list. It happened between
"Sat Jun  8 06:25:01 UTC 2019" and "Sat Jun  8 06:26:01 UTC 2019".
When I check the logs for 06:00 to 06:30 time-period, then following
was logged:

$ sudo journalctl --since "2019-06-08 06:00:00" --until "2019-06-08 06:30:00"
-- Logs begin at Mon 2019-05-13 19:38:07 UTC, end at Sat 2019-06-08
08:11:24 UTC. --
Jun 08 06:25:04 vps systemd[1]: Reloading The Apache HTTP Server.
Jun 08 06:25:05 vps systemd[1]: Reloaded The Apache HTTP Server.
Jun 08 06:25:05 vps liblogging-stdlog[556]:  [origin
software="rsyslogd" swVersion="8.24.0" x-pid="556"
x-info="http://www.rsyslog.com"] rsyslogd was HUPed
$

What and why is sending those signals to processes? Could it somehow
affect the repository list..?


thanks,
Martin

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#209774

Hi,

looks like the culprit is a /etc/cron.daily/do-agent cron-job which
executes the /opt/digitalocean/do-agent/scripts/update.sh script which
includes following if statement:

        if command -v apt-get 2&>/dev/null; then
                apt-get -qq update -o
Dir::Etc::sourcelist="sources.list.d/digitalocean-agent.list" -o
Dir::Etc::sourceparts="-" -o APT::Get::List-Cleanup="1"
                apt-get -qq install -y --only-upgrade do-agent
                /* output removed for brevity */

'-o APT::Get::List-Cleanup="1"' flushes other repositories..


Martin

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