https://paste.yunohost.org/raw/cujagopamu
The app was restored to the way it was before the failed upgrade.
there were 7 instances of dokuwiki running only 1 was preserved all the others are gone
restore dont work
Php is failing every app which need php will fail.
Show :
$ service php7.0-fpm status$ service php7.0-fpm status
-bash: service: command not found
What yunohost version are you on?
Other apps are working?
If you are on yunohost 3.xx try installing php.
$ sudo apt install php7.0 php7.0-cli php7.0-common php7.0-curl php7.0-mbstring php7.0-mysql php7.0-xml
Show the services you are running if any of other service is failing.
$ yunohost service status
YunoHost 3.2.2 (stable)
i tested nextcloud and looks ok no idea about others
sudo apt install php7.0 php7.0-cli php7.0-common php7.0-curl php7.0-mbstring php7.0-mysql php7.0-xml
Reading package lists... Done
Building dependency tree
Reading state information... Done
php7.0-cli is already the newest version (7.0.30-0+deb9u1).
php7.0-cli set to manually installed.
php7.0-common is already the newest version (7.0.30-0+deb9u1).
php7.0-common set to manually installed.
php7.0-curl is already the newest version (7.0.30-0+deb9u1).
php7.0-curl set to manually installed.
php7.0-mbstring is already the newest version (7.0.30-0+deb9u1).
php7.0-mbstring set to manually installed.
php7.0-mysql is already the newest version (7.0.30-0+deb9u1).
php7.0-mysql set to manually installed.
php7.0-xml is already the newest version (7.0.30-0+deb9u1).
php7.0-xml set to manually installed.
**The following NEW packages will be installed:**
** php7.0**
yunohost service status
avahi-daemon:
active: active
active_at:
human: 2018-11-16 10:55:02
timestamp: 1542365702405332
description: allows to reach your server using yunohost.local on your local network
loaded: enabled
service_file_path: /lib/systemd/system/avahi-daemon.service
status: running
dnsmasq:
active: active
active_at:
human: 2018-11-16 11:21:22
timestamp: 1542367282586375
description: handles domain name resolution (DNS)
loaded: enabled
service_file_path: /lib/systemd/system/dnsmasq.service
status: running
dovecot:
active: active
active_at:
human: 2018-11-16 11:01:22
timestamp: 1542366082022254
description: allows e-mail client to access/fetch email (via IMAP and POP3)
loaded: enabled
service_file_path: /lib/systemd/system/dovecot.service
status: running
fail2ban:
active: active
active_at:
human: 2018-11-16 11:01:28
timestamp: 1542366088280879
description: protects against bruteforce and other kind of attacks from the Internet
loaded: enabled
service_file_path: /lib/systemd/system/fail2ban.service
status: running
glances:
active: active
active_at:
human: 2018-11-16 10:57:17
timestamp: 1542365837658638
description: monitors system information on your server
loaded: enabled
service_file_path: /run/systemd/generator.late/glances.service
status: running
metronome:
active: active
active_at:
human: 2018-11-16 10:56:32
timestamp: 1542365792236184
description: manage XMPP instant messaging accounts
loaded: enabled
service_file_path: /run/systemd/generator.late/metronome.service
status: running
mysql:
active: active
active_at:
human: 2018-11-16 10:56:46
timestamp: 1542365806777122
description: stores applications data (SQL database)
loaded: enabled
service_file_path: /lib/systemd/system/mariadb.service
status: running
nginx:
active: active
active_at:
human: 2018-11-16 11:01:02
timestamp: 1542366062798980
description: serves or provides access to all the websites hosted on your server
loaded: enabled
service_file_path: /lib/systemd/system/nginx.service
status: running
nslcd:
active: active
active_at:
human: 2018-11-16 10:54:52
timestamp: 1542365692332181
description: handles YunoHost user shell connection
loaded: enabled
service_file_path: /run/systemd/generator.late/nslcd.service
status: running
php7.0-fpm:
active: failed
active_at:
human: 2018-11-16 11:05:26
timestamp: 1542366326868844
description: runs applications written in PHP with nginx
loaded: enabled
service_file_path: /lib/systemd/system/php7.0-fpm.service
status: failed
postfix:
active: active
active_at:
human: 2018-11-16 11:01:21
timestamp: 1542366081297338
description: used to send and receive emails
loaded: enabled
service_file_path: /lib/systemd/system/postfix.service
status: exited
redis-server:
active: active
active_at:
human: 2018-11-16 10:56:25
timestamp: 1542365785811909
description: a specialized database used for rapid data access, task queue and communication between programs
loaded: enabled
service_file_path: /lib/systemd/system/redis-server.service
status: running
rspamd:
active: active
active_at:
human: 2018-11-16 11:01:23
timestamp: 1542366083449319
description: filters spam, and other email-related features
loaded: enabled
service_file_path: /lib/systemd/system/rspamd.service
status: running
slapd:
active: active
active_at:
human: 2018-11-16 10:53:32
timestamp: 1542365612336845
description: stores users, domains and related information
loaded: enabled
service_file_path: /run/systemd/generator.late/slapd.service
status: running
ssh:
active: active
active_at:
human: 2018-11-16 10:54:04
timestamp: 1542365644207611
description: allows you to connect remotely to your server via a terminal (SSH protocol)
loaded: enabled
service_file_path: /lib/systemd/system/ssh.service
status: running
yunohost-api:
active: active
active_at:
human: 2018-11-16 11:21:26
timestamp: 1542367286751110
description: manages interactions between the YunoHost web interface and the system
loaded: enabled
service_file_path: /lib/systemd/system/yunohost-api.service
status: running
yunohost-firewall:
active: active
active_at:
human: 2018-11-16 09:40:09
timestamp: 1542361209361110
description: manages open and close connexion ports to services
loaded: enabled
service_file_path: /lib/systemd/system/yunohost-firewall.service
status: exited
Php is still failing. I don’t know how nextcloud is running without php.
$ service php7.0-fpm restart
service php7.0-fpm restart
-bash: service: command not found
$ apt-get install sysvinit-utils
$ PATH=$PATH:/usr/sbin
$ service php7.0-fpm restart
sudo is required for all those, the update still fails
2018-11-16 12:22:23,428: WARNING - /var/www/dokuwiki__2 will not be saved, because backup_core_only is set. 2018-11-16 12:22:26,784: WARNING - 2018-11-16 12:22:26 URL:https://download.dokuwiki.org/src/dokuwiki/dokuwiki-2018-04-22a.tgz [3749191/3749191] -> “app.tar.gz” [1] 2018-11-16 12:22:32,134: WARNING - php7.0-fpm.service is not active, cannot reload. 2018-11-16 12:22:32,137: WARNING - !! 2018-11-16 12:22:32,139: WARNING - dokuwiki__2’s script has encountered an error. Its execution was cancelled. 2018-11-16 12:22:32,140: WARNING - !! 2018-11-16 12:22:32,142: WARNING - Upgrade failed. 2018-11-16 12:22:34,218: WARNING - php7.0-fpm.service is not active, cannot reload. 2018-11-16 12:22:34,325: WARNING - Remove the user dokuwiki__2 2018-11-16 12:22:37,321: WARNING - ‘yunohost app checkurl’ is deprecated and will be removed in the future 2018-11-16 12:22:37,425: WARNING - Packagers /!\ : ‘app checkurl’ is deprecated ! Please use the helper ‘ynh_webpath_register’ instead ! 2018-11-16 12:22:40,942: WARNING - cp: cannot stat ‘./sources’: No such file or directory 2018-11-16 12:22:41,043: WARNING - Unable to restore the app ‘dokuwiki__2’ 2018-11-16 12:22:41,885: WARNING - php7.0-fpm.service is not active, cannot reload. 2018-11-16 12:22:41,987: WARNING - Remove the user dokuwiki__2 2018-11-16 12:22:42,095: WARNING - Nothing has been restored 2018-11-16 12:22:42,197: WARNING - The app was restored to the way it was before the failed upgrade. 2018-11-16 12:22:42,352: ERROR - Unable to upgrade dokuwiki__2
This looks messed up. I would let someone more experience to help you out. I am afraid of breaking your system by my advise. 
/bump