Problem upgrading the system to Debian Buster and YunoHost 4.x

My YunoHost server

Hardware: Proxmox VM server
YunoHost version: 3.8.5.9 (stable)
I have access to my server : Through both SSH and the webadmin
Are you in a special context or did you perform some particular tweaking on your YunoHost instance ? : no

Description of my issue

I’m attempting to perform a pending migration and upgrade my system to Debian Buster and YunoHost 4.x. I am getting a conflic error about apache2 and do not know how to fix it.

Via the webadmin: Receive the error “Migration 0015_migrate_to_buster did not complete, aborting. Error: Your system is not fully up-to-date. Please perform a regular upgrade before running the migration to Buster.”

Via the cli: Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming. The following information may help to resolve the situation:

The following packages have unmet dependencies:
yunohost : Conflicts: apache2 but 2.4.25-3+deb9u9 is to be installed
E: Broken packages

Apache2 is not installed. I ran “sudo apt list --upgradable” but apache2 isn’t in the list:
Listing… Done
ldap-utils/oldstable 2.4.44+dfsg-5+deb9u8 amd64 [upgradable from: 2.4.44+dfsg-5+deb9u7]
libldap-2.4-2/oldstable 2.4.44+dfsg-5+deb9u8 amd64 [upgradable from: 2.4.44+dfsg-5+deb9u7]
libldap-common/oldstable 2.4.44+dfsg-5+deb9u8 all [upgradable from: 2.4.44+dfsg-5+deb9u7]
libpcre2-8-0/unknown 10.36-2+0~20210212.6+debian9~1.gbp6138a4 amd64 [upgradable from: 10.34-7+0~20191219.5+debian9~1.gbp555bb9]
libzip4/unknown 1.7.3-1+0~20210114.10+debian9~1.gbp4c125d amd64 [upgradable from: 1.5.1-4+0~20190318173229.9+stretch~1.gbp333132]
openssl/unknown 1.1.1i-1+0~20201212.21+debian9~1.gbpc1ad96 amd64 [upgradable from: 1.1.0l-1~deb9u3]
php/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php-common/unknown 2:80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 2:79+0~20201210.30+debian9~1.gbpedaf15]
php-curl/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-fpm/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-gd/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php-intl/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-ldap/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-mbstring/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-mcrypt/unknown 3:1.0.4-5+0~20210220.2+debian9~1.gbp68347e all [upgradable from: 1:7.0+49]
php-mysql/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-pear/unknown 1:1.10.12+submodules+notgz+20210212-1+0~20210220.19+debian9~1.gbpf2b98f all [upgradable from: 1:1.10.12+submodules+notgz-1+0~20201204.17+debian9~1.gbp545cab]
php-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php-tidy/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 2:7.4+79+0~20201210.30+debian9~1.gbpedaf15]
php-xml/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php-zip/unknown 2:8.0+80+0~20210220.33+debian9~1.gbp730ac0 all [upgradable from: 1:7.0+49]
php5.6-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php5.6-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php5.6-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php5.6-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php5.6-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php7.0/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 all [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php7.0-cli/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-common/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-curl/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-fpm/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-gd/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php7.0-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php7.0-intl/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-json/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-ldap/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-mbstring/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-mcrypt/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-mysql/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-opcache/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-readline/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php7.0-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php7.0-tidy/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-xml/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.0-zip/unknown 7.0.33-45+0~20210220.50+debian9~1.gbp703a20 amd64 [upgradable from: 7.0.33-37+0~20201103.43+debian9~1.gbp25a3d7]
php7.1-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php7.1-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php7.1-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php7.1-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php7.1-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php7.2-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php7.2-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php7.2-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php7.2-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php7.2-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php7.3/unknown 7.3.27-7+0~20210220.80+debian9~1.gbpccb1ab all [upgradable from: 7.3.25-1+0~20201130.73+debian9~1.gbp042074]
php7.3-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php7.3-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php7.3-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php7.3-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php7.3-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php7.4-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php7.4-cli/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-common/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-curl/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-fpm/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-gd/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php7.4-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php7.4-json/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-mbstring/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-mysql/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-opcache/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-readline/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php7.4-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
php7.4-tidy/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-xml/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php7.4-zip/unknown 7.4.15-5+0~20210220.39+debian9~1.gbpb3863c amd64 [upgradable from: 7.4.13-1+0~20201130.33+debian9~1.gbpd59941]
php8.0-apcu/unknown 5.1.19+4.0.11-7+0~20210220.21+debian9~1.gbp08eb57 amd64 [upgradable from: 5.1.19+4.0.11-2+0~20201210.18+debian9~1.gbpa95fb8]
php8.0-igbinary/unknown 3.2.1+2.0.8-2+0~20210215.22+debian9~1.gbp87adeb amd64 [upgradable from: 3.1.6+2.0.8-2+0~20201208.20+debian9~1.gbpbabaec]
php8.0-imagick/unknown 3.4.4+php8.0+3.4.4-6+0~20210220.26+debian9~1.gbp25c811 amd64 [upgradable from: 3.4.4-10+0~20201211.23+debian9~1.gbp2e170e]
php8.0-redis/unknown 5.3.2+4.3.0-2+0~20210215.31+debian9~1.gbp7bf950 amd64 [upgradable from: 5.3.2+4.3.0-1+0~20201211.30+debian9~1.gbp404a40]
php8.0-smbclient/unknown 1.0.5-5+0~20210220.15+debian9~1.gbpbd0457 amd64 [upgradable from: 1.0.0-3+0~20201211.11+debian9~1.gbp4e5196]
slapd/oldstable 2.4.44+dfsg-5+deb9u8 amd64 [upgradable from: 2.4.44+dfsg-5+deb9u7]

Yes, apt list --upgradable only shows the packages with upgrade available …

What does dpkg --list | grep apache2 shows …

Do you have any idea why apache2 could be installed …

dpkg --list | grep apache2 shows nothing. I reviewed the full list of installed packages (dpkg --list). Apache2 is not installed.

Then let’s look at the full log of the migration attempt that ended with yunohost : Conflicts: apache2 but 2.4.25-3+deb9u9 is to be installed

I ran cat /var/log/apt/history.log | grep apache2 but nothing is listed. I’m not sure where else to look. I’ve been reading on updating stretch to buster and realized I haven’t updated my apt sources.list file (i.e. replace all instances of stretch with buster in the sources.list file). Perhaps it’s that simple of a fix?

No, this is not “server administration by hand”, this is Yunohost, and Yunohost will take care of doing this for you because nobody should have to edit 392 configuration file and launch a hundred commands manually to manage a server or keeping it up to date …

Share the full log of the attempted migration by going in Tools > Logs > … finding the corresponding log … > click Share with Yunopaste

Here is the attempted migration log: https://paste.yunohost.org/raw/gunokaqemu

Alrighty then let’s upgrade the system (in the Upgrade section of the webadmin) and see what the log tells exactly …

I must have messed something up last night while troubleshooting. When I click on System update in the webadmin, it errors with:

Fetching available upgrades for system packages…

E: The repository ‘http://mirrors.bloomu.edu/debian stretch-updates Release’ does no longer have a Release file.

E: The repository ‘http://mirrors.bloomu.edu/debian stretch Release’ does no longer have a Release file.

Could not to update the cache of APT (Debian’s package manager). Here is a dump of the sources.list lines, which might help identify problematic lines:
sources.list:deb Index of /debian stretch main
sources.list:deb-src Index of /debian stretch main
sources.list:deb http://security.debian.org/debian-security stretch/updates main
sources.list:deb-src http://security.debian.org/debian-security stretch/updates main
sources.list:deb Index of /debian stretch-updates main
sources.list:deb-src Index of /debian stretch-updates main
sources.list.d/extra_php_version.list:deb Index of /php/ buster main
sources.list.d/yunohost.list:deb Index of /debian/ buster stable

I tried to upgrade again via the webadmin and, although it failed, I have a log of the errors: https://paste.yunohost.org/raw/hikutayuzo

Wokay then let’s try to:

apt install php7.3 php7.3-fpm

yunohost:~$ sudo apt install php7.3 php7.3-fpm
Reading package lists… Done
Building dependency tree
Reading state information… Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
nextcloud-ynh-deps : Depends: php7.3-imap but it is not going to be installed
php7.3-fpm : Depends: php7.3-common (= 7.3.27-7+0~20210220.80+debian10~1.gbpccb1ab) but 7.3.27-7+0~20210220.80+debian9~1.gbpccb1ab is to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

Hmokay yeah … going back to a few post before, it’s puzzling that only two files among the sources.list contains buster instead of stretch …

Sooo I guess you can try to naively run

sed -i 's/stretch/buster/g' /etc/apt/sources.list

Then

apt update

and then try to re-run the upgrade (and if you get exactly the same issue, try to run again apt install php7.3 php7.3-fpm to understand what’s going on)

Well … the upgrade was running for a while and then hit a 500 server error. Webmin was inaccessible. I was also connected via ssh so I ran sudo update and then sudo upgrade to hopefully finish the upgrade. Thankfully, it did. I rebooted and logged back into the webadmin, now at 4.1.7.2 (testing). All system packages are up to date. I ran lsb_release -a and am running Buster. There are some pending migrations so I went to Tools > Migrations and tried to run them. The migrations failed; here is the log:

2021-02-21 20:12:06,830: INFO - Running migration 0015_migrate_to_buster…
2021-02-21 20:12:06,843: ERROR - Migration 0015_migrate_to_buster did not complete, aborting. Error: The current Debian distribution is not Stretch!
Traceback (most recent call last):
File “/usr/lib/moulinette/yunohost/tools.py”, line 897, in tools_migrations_migrate
migration.run()
File “/usr/lib/moulinette/yunohost/data_migrations/0015_migrate_to_buster.py”, line 28, in run
self.check_assertions()
File “/usr/lib/moulinette/yunohost/data_migrations/0015_migrate_to_buster.py”, line 116, in check_assertions
raise YunohostError(“migration_0015_not_stretch”)
YunohostError: The current Debian distribution is not Stretch!

Then you can skip the migration if it completed…

I skipped the Stretch to Buster migration and the next three migrations completed without error. Thanks for all your help Aleks!

1 Like