You have the following;
ERROR: I/O or zip error while attempting to read entry oracle/apps/iby/xml/xml/data/citibank/creditcard/ONLINE_VISA_RESPONSE.xml in zip file /u01/appl/appsr12/fs1/EBSapps/comn/java/classes
About to Generate oklall.jar : Wed May 24 2017 16:30:19
ERROR: I/O or zip error while attempting to read entry oracle/apps/okl/origination/contracts/lov/server/ORKhrTNCRVIStrmTypesLovVO.xml in zip file /u01/appl/appsr12/fs1/EBSapps/comn/java/classes
So, you encounterd zip errors while generating those jar files.
Do you have the following xml files ? (with proper permissions)
ls -al $COMMON_TOP/java/classes/oracle/apps/iby/xml/xml/data/citibank/creditcard/ONLINE_VISA_RESPONSE.xml
ls -al $COMMON_TOP/java/classes/oracle/apps/okl/origination/contracts/lov/server/ORKhrTNCRVIStrmTypesLovVO.xml
Check this issue as well -> (it is similar and solved)
http://erman-arslan-s-oracle-forum.2340467.n4.nabble.com/perall-jar-error-td200.html