I get "conf directory is not writable" from the dokuwiki check routine if dokuwiki/conf/ is not writable.
How did you install dokuwiki? Here's what I have on my install (USE="vhosts"): ls -la <vhost>/htdocs-secure/dokuwiki/conf/ total 112 drwxrwxr-x 2 root apache 4096 Jun 2 19:23 . drwxr-xr-x 6 root root 4096 Jun 2 19:23 .. -rw-r--r-- 1 apache apache 229 Set 12 2013 acl.auth.php -rw-r--r-- 1 root root 448 Jun 2 19:23 acl.auth.php.dist -rw-r--r-- 1 root root 2021 Jun 2 19:23 acronyms.conf -rw-r--r-- 1 root root 12161 Jun 2 19:23 dokuwiki.php -rw-r--r-- 1 root root 354 Jun 2 19:23 entities.conf -rw-r--r-- 1 root root 87 Dez 23 17:46 .htaccess -rw-r--r-- 1 root root 1623 Jun 2 19:23 interwiki.conf -rw-r--r-- 1 root root 1208 Jun 2 19:23 license.php -rw-r--r-- 1 apache apache 967 Set 20 2013 local.php -rw-r--r-- 1 apache apache 708 Set 13 2013 local.php.bak -rw-r--r-- 1 root root 462 Jun 2 19:23 local.php.dist -rw-r--r-- 1 root root 2572 Jun 2 19:23 mediameta.php -rw-r--r-- 1 root root 2170 Jun 2 19:23 mime.conf -rw-r--r-- 1 root root 11391 Jun 2 19:23 mysql.conf.php.example -rw-r--r-- 1 apache apache 242 Set 12 2013 plugins.local.php -rw-r--r-- 1 root root 173 Jun 2 19:23 plugins.php -rw-r--r-- 1 root root 552 Jun 2 19:23 plugins.required.php -rw-r--r-- 1 root root 105 Jun 2 19:23 scheme.conf -rw-r--r-- 1 root root 748 Jun 2 19:23 smileys.conf -rw-r--r-- 1 apache apache 261 Set 12 2013 users.auth.php -rw-r--r-- 1 root root 153 Jun 2 19:23 users.auth.php.dist -rw-r--r-- 1 root root 1729 Jun 2 19:23 wordblock.conf As you can see, conf is owned by root:apache and writable by group.
I have conf owned by root:apache on a fresh install... # ls -lha dokuwiki/conf total 92K drwxr-xr-x 2 root apache 4.0K Mar 28 11:06 . drwxr-xr-x 6 root root 4.0K Mar 28 11:06 .. -rw-r--r-- 1 root root 66 Mar 28 11:06 .htaccess -rw-r--r-- 1 root root 448 Mar 28 11:06 acl.auth.php.dist -rw-r--r-- 1 root root 2.0K Mar 28 11:06 acronyms.conf -rw-r--r-- 1 root root 12K Mar 28 11:06 dokuwiki.php -rw-r--r-- 1 root root 354 Mar 28 11:06 entities.conf -rw-r--r-- 1 root root 1.6K Mar 28 11:06 interwiki.conf -rw-r--r-- 1 root root 1.2K Mar 28 11:06 license.php -rw-r--r-- 1 root root 462 Mar 28 11:06 local.php.dist -rw-r--r-- 1 root root 2.6K Mar 28 11:06 mediameta.php -rw-r--r-- 1 root root 2.3K Mar 28 11:06 mime.conf -rw-r--r-- 1 root root 12K Mar 28 11:06 mysql.conf.php.example -rw-r--r-- 1 root root 173 Mar 28 11:06 plugins.php -rw-r--r-- 1 root root 552 Mar 28 11:06 plugins.required.php -rw-r--r-- 1 root root 105 Mar 28 11:06 scheme.conf -rw-r--r-- 1 root root 748 Mar 28 11:06 smileys.conf -rw-r--r-- 1 root root 153 Mar 28 11:06 users.auth.php.dist -rw-r--r-- 1 root root 1.7K Mar 28 11:06 wordblock.conf ..but get the following when I go to http://localhost/dokuwiki/install.php ... The installer found some problems, indicated below. You can not continue until you have fixed them. {DOCUMENT_ROOT}/dokuwiki/conf/ is not writable by DokuWiki. You need to fix the permission settings of this directory! I noticed also that dokuwiki/lib/plugins isn't writable (on a fresh install) for the web-process (apache2) as suggested in the documentation (https://www.dokuwiki.org/install:permissions)... # ls -lha dokuwiki/lib total 36K drwxr-xr-x 8 root root 4.0K Mar 28 11:06 . drwxr-xr-x 6 root root 4.0K Mar 28 11:06 .. drwxr-xr-x 2 root root 4.0K Mar 28 11:06 exe drwxr-xr-x 8 root root 4.0K Mar 28 11:06 images -rw-r--r-- 2 root root 241 Mar 28 07:54 index.html drwxr-xr-x 15 root root 4.0K Mar 28 11:06 plugins drwxr-xr-x 3 root root 4.0K Mar 28 11:06 scripts drwxr-xr-x 2 root root 4.0K Mar 28 11:06 styles drwxr-xr-x 3 root root 4.0K Mar 28 11:06 tpl