CPA scikits.learn deprecated


I have a problem with the CP Analyst software. When I try to open a property file I always get an error message (“See the logfile …/cpa.exe.log for details”). This logfile contains the following information:

D:\Kristin\CellProfiler Analyst\\scikits\ UserWarning: scikits.learn namespace is deprecated, please use sklearn instead
Traceback (most recent call last):
File “”, line 529, in
File “wx_core.pyc”, line 7981, in init
File “wx_core.pyc”, line 7555, in _BootstrapApp
File “”, line 447, in OnInit
File “guiutils.pyc”, line 814, in show_load_dialog
File “properties.pyc”, line 288, in load_file
File “properties.pyc”, line 507, in Validate
AssertionError: PROPERTIES ERROR (db_host): Field is required with db_type=mysql.

What exactly do I have to change? And why do I have this problem? I downloaded the CP and CP analyst software just recently.

Thanks in advance for your help!

Kristin Oberländer


Hi Kristin,

The scikits/sklearn warning is just that, a warning. In fact, we have a couple people in our group looking at re-writing all this classification code, but in any case, that is not your issue. The real error is

[quote]AssertionError: PROPERTIES ERROR (db_host): Field is required with db_type=mysql.

Open your properties file in a text editor, and find the “db_host=” line. For MySQL you need to fill in the host (and other) info. This can better be filled in withinExportToDatabase. Or maybe you want to try the simpler sqlite database option, rather than MySQL?

Hope that helps,