Problem SDF-Data import with Mysql

User 6fe3d4c2db

12-11-2013 13:09:14


I have a problem with sdf file import in IJC. The sdf file contains a lot data fields. I import all data fields as type "text" to avoid "format" problems. Using the localdb option works fine. Using MySQL as underlying database produces the error:

com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Row size too large. The maximum row size for the used table type, not counting BLOBs, is 65535. You have to change some columns to TEXT or BLOBs

but all columns are already typed as TEXT????
I need MySQL as database to distribute the data via the enterprise version.

Any hints? Thanks,


User 6fe3d4c2db

13-11-2013 10:05:00

No hints so is another observation:
Instant JChem Version 6.1.0 works with the data. Version 6.1.3 produces the mentioned error with both variants:
(1) Running Version 6.1.0 -> update -> tables will be regenerated -> error
(2) update 6.1.0 to 6.1.3 -> fresh import from sdf (sdf works with 6.1.0 !) -> error

What is happened with the sdf data import between Version 6.1.0 and 6.1.3 ?


ChemAxon 2bdd02d1e5

14-11-2013 13:42:31

Hi Andreas,

The error: "Row size too large..." is specific to MySQL and it's
given by the DB engine restriction. We can't do anything about it. Are you using VARCHAR instead of TEXT column type in your table? BLOB and TEXT field should not count to this maximum row size 65,535 Bytes. Please see this />
This error can not happen on Oracle DB.

I can't tell more about the other problems (1) and (2).

Could you paste here what error it gives?

Or if you like send me the log file to my email - fzimandl (at) Here are the instructions where to find IJC log: