Started by upstream project "BIOFORMATS-test-repo" build number 306 originally caused by: Started by upstream project "Trigger" build number 328 originally caused by: Started by timer 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/jenkins4497112381764210416.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48514_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 03:33:45,214 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:33:45,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 03:33:45,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:33:45,217 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:33:45,217 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:33:45,218 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:33:45,218 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:33:45,218 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:33:45,219 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:33:45,219 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:33:45,220 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:33:45,220 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:33:45,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:33:45,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:33:45,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:33:45,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:33:45,459 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:33:45,459 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:33:45,459 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:33:45,460 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:33:45,460 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 03:33:45,461 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 03:33:45,461 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 242 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-02 03:33:45,470] [main] java.version = 21 [testng] 03:33:45,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:33:45,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:33:45,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-02_03-33-45.log] [testng] 03:33:45,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2025-01-02 03:33:45,524] [main] testng.directory = /data [testng] [2025-01-02 03:33:45,524] [main] testng.configDirectory = /config [testng] [2025-01-02 03:33:45,533] [main] testng.multiplier = 1.0 [testng] [2025-01-02 03:33:45,534] [main] testng.in-memory = false [testng] [2025-01-02 03:33:45,534] [main] testng.allow-missing = false [testng] [2025-01-02 03:33:45,534] [main] user.language = en [testng] [2025-01-02 03:33:45,534] [main] user.country = ${user.country} [testng] [2025-01-02 03:33:45,535] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-02 03:38:17,119] [main] ---------------------------------------- [testng] [2025-01-02 03:38:17,119] [main] Total files: 2169 [testng] [2025-01-02 03:38:17,120] [main] Scan time: 271.584 s (125 ms/file) [testng] [2025-01-02 03:38:17,120] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-02 03:57:34,266] [pool-1-thread-1] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:57:34,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:57:34,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:57:34,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-02_03-57-34.log] [testng] 03:57:34,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ec9eb9f - End of configuration. [testng] [2025-01-02 03:59:42,597] [pool-1-thread-12] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:59:42,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:59:42,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:42,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-02_03-59-42.log] [testng] 03:59:42,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f60ef6e - End of configuration. [testng] [2025-01-02 04:01:06,418] [pool-1-thread-11] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:01:06,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:01:06,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:06,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-02_04-01-06.log] [testng] 04:01:06,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24fe875f - End of configuration. [testng] [2025-01-02 04:01:25,382] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:01:25,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:01:25,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:25,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-02_04-01-25.log] [testng] 04:01:25,383 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cb4b556 - End of configuration. [testng] [2025-01-02 04:01:26,222] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:01:26,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:01:26,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:26,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-02_04-01-26.log] [testng] 04:01:26,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e480bb4 - End of configuration. [testng] [2025-01-02 04:02:09,435] [pool-1-thread-8] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:02:09,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:02:09,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:09,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-02_04-02-09.log] [testng] 04:02:09,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@136436c8 - End of configuration. [testng] [2025-01-02 04:02:36,461] [pool-1-thread-7] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:02:36,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:02:36,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:36,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-02_04-02-36.log] [testng] 04:02:36,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b46a36f - End of configuration. [testng] [2025-01-02 04:02:37,329] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 04:02:37,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:02:37,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:37,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-02_04-02-37.log] [testng] 04:02:37,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@626501d4 - End of configuration. [testng] [2025-01-02 04:02:43,112] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 04:02:43,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:02:43,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:43,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-02_04-02-43.log] [testng] 04:02:43,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c8b9033 - End of configuration. [testng] [2025-01-02 04:04:42,802] [pool-1-thread-4] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:04:42,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:04:42,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:42,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-02_04-04-42.log] [testng] 04:04:42,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b99d60f - End of configuration. [testng] [2025-01-02 04:04:52,517] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:04:52,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:04:52,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:52,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-02_04-04-52.log] [testng] 04:04:52,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ed2469 - End of configuration. [testng] [2025-01-02 04:07:54,992] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 04:07:54,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:07:54,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:07:54,993 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-02_04-07-54.log] [testng] 04:07:54,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656eb8af - End of configuration. [testng] [2025-01-02 04:10:27,502] [pool-1-thread-10] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2025-01-02 04:12:00,601] [pool-1-thread-7] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2025-01-02 04:19:07,392] [pool-1-thread-6] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2025-01-02 04:21:41,607] [pool-1-thread-7] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2025-01-02 04:22:21,550] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 05:33:45,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:33:45,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:33:45,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-02_05-33-45.log] [testng] 05:33:45,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bff6ae4 - End of configuration. [testng] 05:33:59,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:33:59,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:33:59,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-02_05-33-59.log] [testng] 05:33:59,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59e77f4a - End of configuration. [testng] 05:36:19,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:36:19,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:36:19,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-02_05-36-19.log] [testng] 05:36:19,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ed0b302 - End of configuration. [testng] 05:36:48,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:36:48,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:36:48,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-02_05-36-48.log] [testng] 05:36:48,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@557acc64 - End of configuration. [testng] 05:43:59,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:43:59,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:43:59,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-02_05-43-59.log] [testng] 05:43:59,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fbf59af - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 130 minutes 19 seconds Finished: SUCCESS