Sorry but I think I still miss something. What should I set? 
whups-mail-filter is found only the Application.php not.

But If I see the 
http://git.horde.org/horde-git/-/commit/330c5ace6772b6cb4e890ad3b47806fae4aac9cb git 
diff:
---
if (file_exists(dirname(__FILE__) . '/../../whups/lib/Application.php')) {
     $baseDir = dirname(__FILE__) . '/../';
} else {
---
I think it should look like:
---
if (file_exists(dirname(__FILE__) . '/../../whups/lib/Application.php')) {
     $baseDir = dirname(__FILE__) . '/../../';
} else {
---

Then you need to specify that when running the script. Read the Horde docs.

After upgrading to the 2.0.1 version I still have an error:

Command output: PHP Warning:
     require_once(/usr/share/php/www/horde/whups/lib/Application.php): 
failed to
     open stream: No such file or directory in
     /var/www/horde/pear/whups-mail-filter on line 66 PHP Fatal error:
     require_once(): Failed opening required
     '/usr/share/php/www/horde/whups/lib/Application.php'
     (include_path='/var/www/horde/pear/php') in
     /var/www/horde/pear/whups-mail-filter on line 66

Because horde isn't installed in common way but in a separate pear 
environment.

TNX.

Changes have been made in Git for this ticket:

[jan] Fix some CLI scripts if run from a PEAR installation (Bug #10839).

  6 files changed, 35 insertions(+), 4 deletions(-)
http://git.horde.org/horde-git/-/commit/330c5ace6772b6cb4e890ad3b47806fae4aac9cb

Hi All!

In whups-mail-filter I had to edit Application.php location at line 59 
because it is in
/../webmail/lib/Application.php

Horde is installed in separate pear location...