I know this is a REALLY old thread, but I found the solution to this. I had to manually change my permission settings for the .qpkg/DokuWiki/web/ and allow the update. Here's the steps I used on my TS-251+:
I logged in to the NAS using PuTTY and performed the following commands
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[/share/CE_CACHEDEV1_DATA/.qpkg/DokuWiki] # ls -la
total 164
drwxr-xr-x 3 admin administ 4096 Oct 20 09:22 ./
drwxrwxrwx 34 admin administ 4096 Oct 20 09:22 ../
-rw-r--r-- 1 admin administ 145380 Oct 20 09:22 .list
-rwxr-xr-x 1 admin administ 800 Oct 20 09:22 .uninstall.sh*
-rwxr-xr-x 1 admin administ 1672 Jul 20 2014 DokuWiki.sh*
drwxr-xr-x 7 admin administ 4096 Jul 20 2014 web/
web/ needs to be changed to 777
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[/share/CE_CACHEDEV1_DATA/.qpkg/DokuWiki] # chmod -R 777 web
[/share/CE_CACHEDEV1_DATA/.qpkg/DokuWiki] # ls -la
total 164
drwxr-xr-x 3 admin administ 4096 Oct 20 09:22 ./
drwxrwxrwx 34 admin administ 4096 Oct 20 09:22 ../
-rw-r--r-- 1 admin administ 145380 Oct 20 09:22 .list
-rwxr-xr-x 1 admin administ 800 Oct 20 09:22 .uninstall.sh*
-rwxr-xr-x 1 admin administ 1672 Jul 20 2014 DokuWiki.sh*
drwxrwxrwx 7 admin administ 4096 Jul 20 2014 web/
Install the DokiWiki upgrade plugin from within the DokuWiki page using the url from the plugin's main page "
https://github.com/splitbrain/dokuwiki- ... all/master" and perform the DokuWiki upgrade. I then had to stop and re-start my QNAP DokuWiki instance. The page formatting was very messed up on the wiki but restarting it seemed to fix it. (Note: I did NOT use the default admin account. I made a new admin login account and deleted that old one. So not sure if that made a difference or not)
When you're done don't forget to set the web folder permissions back to the default:
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[/share/CE_CACHEDEV1_DATA/.qpkg/DokuWiki] # chmod -R 755 web
[/share/CE_CACHEDEV1_DATA/.qpkg/DokuWiki] # ls -la
total 164
drwxr-xr-x 3 admin administ 4096 Oct 20 09:22 ./
drwxrwxrwx 34 admin administ 4096 Oct 20 09:22 ../
-rw-r--r-- 1 admin administ 145380 Oct 20 09:22 .list
-rwxr-xr-x 1 admin administ 800 Oct 20 09:22 .uninstall.sh*
-rwxr-xr-x 1 admin administ 1672 Jul 20 2014 DokuWiki.sh*
drwxr-xr-x 8 admin administ 4096 Oct 20 09:39 web/
I'm assuming you'll have to continue these steps every time you attempt to install a plugin. So it's probably better to install most of the plugins you'll need all at once.
Hope this helps someone else out.