Structures with R-groups or with specified repeating units are considered Markush structures. In order to register such compounds a separate (Markush) license is needed. The missing Markush license is listed in the log file, while during registration an "Unknown error-chemaxon.formats.MolFormatException: Could not calculate cd_markush field" is received. 


If you have a valid Markush license in place, by default, the Markush structures are not registered automatically, they are forced to be reviewed (in the Staging area) unless Advanced Registration or Registering from the Staging area is used. In order to change the default behavior, you can remove the 'RejectMarkushValidator' workflow step, and with this, the registration of Markush structures will be automatic.

More info about registering Markush structures can be found in the Compound Registration User's Guide.