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Started by upstream project "BIOFORMATS-test-repo" build number 216 originally caused by: Started by upstream project "Trigger" build number 243 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins6751192650894961505.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34329_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 05:49:34,997 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:49:34,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 05:49:34,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:49:34,999 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:49:34,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:49:35,000 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:49:35,000 |-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] 05:49:35,000 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:49:35,001 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:49:35,001 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:49:35,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:49:35,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:49:35,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:49:35,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:49:35,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:49:35,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:49:35,206 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:49:35,207 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:49:35,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:49:35,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:49:35,207 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 05:49:35,208 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 05:49:35,208 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-10 05:49:35,219] [main] java.version = 21 [testng] 05:49:35,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:49:35,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:35,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-10_05-49-35.log] [testng] 05:49:35,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-10 05:49:35,267] [main] testng.directory = /data [testng] [2024-10-10 05:49:35,267] [main] testng.configDirectory = /config [testng] [2024-10-10 05:49:35,276] [main] testng.multiplier = 1.0 [testng] [2024-10-10 05:49:35,276] [main] testng.in-memory = false [testng] [2024-10-10 05:49:35,276] [main] testng.allow-missing = false [testng] [2024-10-10 05:49:35,276] [main] user.language = en [testng] [2024-10-10 05:49:35,276] [main] user.country = ${user.country} [testng] [2024-10-10 05:49:35,276] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-10 05:56:15,869] [main] ---------------------------------------- [testng] [2024-10-10 05:56:15,870] [main] Total files: 2169 [testng] [2024-10-10 05:56:15,870] [main] Scan time: 400.592 s (184 ms/file) [testng] [2024-10-10 05:56:15,871] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-10 06:20:45,611] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 06:20:45,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:20:45,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:20:45,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-10_06-20-45.log] [testng] 06:20:45,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@589216c7 - End of configuration. [testng] [2024-10-10 06:21:50,700] [pool-1-thread-12] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 06:21:50,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:21:50,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:21:50,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-10_06-21-50.log] [testng] 06:21:50,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e952875 - End of configuration. [testng] [2024-10-10 06:21:54,727] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 06:21:54,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:21:54,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:21:54,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-10_06-21-54.log] [testng] 06:21:54,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d727ce8 - End of configuration. [testng] [2024-10-10 06:24:05,187] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml: [testng] 06:24:05,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:24:05,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:24:05,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-10_06-24-05.log] [testng] 06:24:05,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33d3b67f - End of configuration. [testng] [2024-10-10 06:24:51,536] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 06:24:51,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:24:51,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:24:51,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-10_06-24-51.log] [testng] 06:24:51,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a38c728 - End of configuration. [testng] [2024-10-10 06:24:52,858] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 06:24:52,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:24:52,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:24:52,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-10_06-24-52.log] [testng] 06:24:52,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@110f8673 - End of configuration. [testng] [2024-10-10 06:24:54,515] [pool-1-thread-7] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 06:24:54,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:24:54,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:24:54,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-10_06-24-54.log] [testng] 06:24:54,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee831c3 - End of configuration. [testng] [2024-10-10 06:28:41,448] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 06:28:41,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:28:41,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:28:41,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-10_06-28-41.log] [testng] 06:28:41,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@737d2467 - End of configuration. [testng] [2024-10-10 06:28:54,015] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 06:28:54,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:28:54,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:28:54,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-10_06-28-54.log] [testng] 06:28:54,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ed08a2 - End of configuration. [testng] [2024-10-10 06:32:45,162] [pool-1-thread-4] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 06:32:45,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:32:45,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:45,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-10_06-32-45.log] [testng] 06:32:45,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64830adf - End of configuration. [testng] [2024-10-10 06:32:55,048] [pool-1-thread-3] Initializing /data/nadine/experiment_descriptor.xml: [testng] 06:32:55,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:32:55,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:55,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-10_06-32-55.log] [testng] 06:32:55,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57dae4d6 - End of configuration. [testng] [2024-10-10 06:32:56,839] [pool-1-thread-2] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 06:32:56,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:32:56,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:56,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-10_06-32-56.log] [testng] 06:32:56,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1efc830f - End of configuration. [testng] [2024-10-10 06:33:50,568] [pool-1-thread-9] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-10-10 06:38:05,878] [pool-1-thread-8] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] [2024-10-10 06:39:16,920] [pool-1-thread-3] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-10-10 06:43:21,657] [pool-1-thread-12] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-10-10 06:45:01,707] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 08:15:54,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:15:54,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:15:54,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-10_08-15-54.log] [testng] 08:15:54,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c209940 - End of configuration. [testng] 08:26:19,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:26:19,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:26:19,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-10_08-26-19.log] [testng] 08:26:19,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a05bc7d - End of configuration. [testng] 08:28:29,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:28:29,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:28:29,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-10_08-28-29.log] [testng] 08:28:29,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64d0ef9 - End of configuration. [testng] 08:30:53,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:30:53,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:30:53,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-10_08-30-53.log] [testng] 08:30:53,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1936025f - End of configuration. [testng] 08:31:39,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:31:39,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:31:39,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-10_08-31-39.log] [testng] 08:31:39,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37453ad2 - End of configuration. [testng] 08:39:58,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:39:58,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:39:58,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-10_08-39-58.log] [testng] 08:39:58,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@280b0df9 - 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: 170 minutes 26 seconds Finished: SUCCESS