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Are you using SEP to start code coverage? If yes, do you set the SEP on the runner program or the test case? If you set an SEP on the test case, the SEP location >might have an impact on whether code coverage is invoked for a test. If the SEP is set on the test program, code coverage should be invoked for every test case >run. However, if the SEP is set on a procedure inside the test case, then code coverage is only invoked when the procedure is called in a particular test run.
Also make sure that when you set the SEP on the runner application, you go into the 'Open Launch Configuration' dialog (right click on SEP in the IBM i Service >Entry Points view) and add it to the programs to be analyzed list.
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