Tests that check the return code are not Windows compatible (threading tests), along with some tests that use regular expressions:

Test edu.illinois.ncsa.daffodil.CLI.executing.TestCLIexecuting.test_1001_CLI_Executing_Listing_execRegex01
Test edu.illinois.ncsa.daffodil.CLI.executing.TestCLIexecuting.test_999_CLI_Executing_Listing_listRegex01
Test edu.illinois.ncsa.daffodil.CLI.executing.TestCLIexecuting.test_1000_CLI_Executing_Listing_listRegex02
Test edu.illinois.ncsa.daffodil.CLI.executing.TestCLIexecuting.test_994_CLI_Executing_Listing_execAll
Test edu.illinois.ncsa.daffodil.CLI.executing.TestCLIexecuting.test_993_CLI_Executing_Listing_listAll
Test edu.illinois.ncsa.daffodil.performance.TestCLIPerformance.test_3394_CLI_Performance_3_Threads_20_Times
Test edu.illinois.ncsa.daffodil.performance.TestCLIPerformance.test_3395_CLI_Performance_5_Threads_50_Times
Test edu.illinois.ncsa.daffodil.performance.TestCLIPerformance.test_3393_CLI_Performance_2_Threads_2_Times
Test edu.illinois.ncsa.daffodil.saving.TestCLISaveParser.test_3039_CLI_Saving_SaveParser_emptyNamespace
Test edu.illinois.ncsa.daffodil.saving.TestCLISaveParser.test_3023_CLI_Saving_SaveParser_verboseMode