Solution : https://service.sap.com/sap/support/notes/891905 (SAP Service marketplace login required)
Key words :
netweaver 2004s / business suite 2005 java upgrade sapjup upgrade tool, /usr/sap/<sid>/<central_instance>/j2ee/configtool, 'jc_<hostname>_<sid>_00 ', log file <jupgrade_directory>/log/deploy_slot_1__xx, tab -> bootstrap java settings ->, bootstrap settings tab, sap j2ee engine, sap j2ee engincheck, j2ee startup timeout, bootstrap process takes
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