Started by upstream project "BIOFORMATS-test-repo" build number 130 originally caused by: Started by upstream project "Trigger" build number 147 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins12298409453114397150.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20435_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 12:05:39,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:05:39,342 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 12:05:39,342 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:05:39,343 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:05:39,345 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:05:39,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:05:39,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:05:39,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:05:39,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:05:39,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:05:39,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:05:39,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:05:39,551 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:05:39,551 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:05:39,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:05:39,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:05:39,552 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 12:05:39,553 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 12:05:39,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-23 12:05:39,562] [main] java.version = 11.0.16 [testng] 12:05:39,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:05:39,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:05:39,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-23_12-05-39.log] [testng] 12:05:39,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-23 12:05:39,613] [main] testng.directory = /data [testng] [2024-07-23 12:05:39,614] [main] testng.configDirectory = /config [testng] [2024-07-23 12:05:39,623] [main] testng.multiplier = 1.0 [testng] [2024-07-23 12:05:39,625] [main] testng.in-memory = false [testng] [2024-07-23 12:05:39,625] [main] testng.allow-missing = false [testng] [2024-07-23 12:05:39,625] [main] user.language = en [testng] [2024-07-23 12:05:39,625] [main] user.country = ${user.country} [testng] [2024-07-23 12:05:39,625] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-23 12:09:40,599] [main] ---------------------------------------- [testng] [2024-07-23 12:09:40,600] [main] Total files: 2169 [testng] [2024-07-23 12:09:40,601] [main] Scan time: 240.974 s (111 ms/file) [testng] [2024-07-23 12:09:40,601] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-23 12:26:55,106] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 12:26:55,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:26:55,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:26:55,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-23_12-26-55.log] [testng] 12:26:55,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@df70f0 - End of configuration. [testng] [2024-07-23 12:26:55,569] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 12:26:55,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:26:55,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:26:55,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-23_12-26-55.log] [testng] 12:26:55,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@297b9abe - End of configuration. [testng] [2024-07-23 12:26:55,873] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 12:26:55,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:26:55,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:26:55,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-23_12-26-55.log] [testng] 12:26:55,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b03250 - End of configuration. [testng] [2024-07-23 12:27:05,633] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 12:27:05,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:27:05,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:05,634 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-23_12-27-05.log] [testng] 12:27:05,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460d039f - End of configuration. [testng] [2024-07-23 12:27:05,736] [pool-1-thread-9] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 12:27:05,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:27:05,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:05,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-23_12-27-05.log] [testng] 12:27:05,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dd73262 - End of configuration. [testng] [2024-07-23 12:27:05,893] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 12:27:05,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:27:05,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:05,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-23_12-27-05.log] [testng] 12:27:05,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34f43095 - End of configuration. [testng] [2024-07-23 12:27:14,732] [pool-1-thread-7] Initializing /data/gideon/experiment_descriptor.xml: [testng] 12:27:14,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:27:14,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:14,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-23_12-27-14.log] [testng] 12:27:14,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450312c5 - End of configuration. [testng] [2024-07-23 12:27:21,273] [pool-1-thread-6] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 12:27:21,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:27:21,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:21,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-23_12-27-21.log] [testng] 12:27:21,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb3ba8 - End of configuration. [testng] [2024-07-23 12:27:23,392] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 12:27:23,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:27:23,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:23,392 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-23_12-27-23.log] [testng] 12:27:23,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbbdc7f - End of configuration. [testng] [2024-07-23 12:27:26,263] [pool-1-thread-4] Initializing /data/nadine/experiment_descriptor.xml: [testng] 12:27:26,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:27:26,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:26,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-23_12-27-26.log] [testng] 12:27:26,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36a5f084 - End of configuration. [testng] [2024-07-23 12:27:26,293] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 12:27:26,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:27:26,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:26,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-23_12-27-26.log] [testng] 12:27:26,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c5111a9 - End of configuration. [testng] [2024-07-23 12:27:27,324] [pool-1-thread-2] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 12:27:27,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:27:27,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:27:27,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-23_12-27-27.log] [testng] 12:27:27,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62a5b0a - End of configuration. [testng] [2024-07-23 12:27:28,267] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:28,468] [pool-1-thread-4] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:29,856] [pool-1-thread-10] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-07-23 12:27:29,903] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-07-23 12:27:31,391] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:32,361] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-07-23 12:27:40,391] [pool-1-thread-2] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:40,878] [pool-1-thread-2] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-07-23 12:27:47,961] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:48,016] [pool-1-thread-4] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:53,346] [pool-1-thread-12] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:27:55,981] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] [2024-07-23 12:28:09,623] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:28:47,636] [pool-1-thread-7] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:30:23,453] [pool-1-thread-3] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:30:24,623] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:30:35,674] [pool-1-thread-11] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:31:05,430] [pool-1-thread-5] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:31:13,555] [pool-1-thread-6] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:31:15,064] [pool-1-thread-8] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:31:18,766] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-23 12:31:38,197] [pool-1-thread-2] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 17, Skips: 0 [testng] =============================================== [testng] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 27 minutes 2 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE