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Started by upstream project "BIOFORMATS-test-repo" build number 84 originally caused by: Started by upstream project "Trigger" build number 95 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins17427666789375490292.sh + '[' avi = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12851_merge_ci -v /uod/idr/repos/curated/avi:/data -v /uod/idr-scratch/merge-ci/curated/avi:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 09:33:01,143 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:33:01,148 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 09:33:01,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:33:01,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:33:01,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:33:01,154 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:33:01,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 3 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:33:01,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:33:01,156 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:33:01,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:33:01,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:33:01,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:33:01,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:33:01,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:33:01,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:33:01,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:33:01,469 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:33:01,469 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:33:01,469 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:33:01,469 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:33:01,469 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 09:33:01,470 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 09:33:01,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 314 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-06 09:33:01,481] [main] java.version = 21 [testng] 09:33:01,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:33:01,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:33:01,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-06_09-33-01.log] [testng] 09:33:01,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-06-06 09:33:01,535] [main] testng.directory = /data [testng] [2024-06-06 09:33:01,536] [main] testng.configDirectory = /config [testng] [2024-06-06 09:33:01,558] [main] testng.multiplier = 1.0 [testng] [2024-06-06 09:33:01,559] [main] testng.in-memory = false [testng] [2024-06-06 09:33:01,559] [main] testng.allow-missing = false [testng] [2024-06-06 09:33:01,559] [main] user.language = en [testng] [2024-06-06 09:33:01,559] [main] user.country = ${user.country} [testng] [2024-06-06 09:33:01,559] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-06 09:33:02,930] [main] ---------------------------------------- [testng] [2024-06-06 09:33:02,931] [main] Total files: 40 [testng] [2024-06-06 09:33:02,931] [main] Scan time: 1.37 s (34 ms/file) [testng] [2024-06-06 09:33:02,931] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-06 09:37:06,596] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] 09:37:06,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:37:06,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:06,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-06_09-37-06.log] [testng] 09:37:06,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c3c936f - End of configuration. [testng] [2024-06-06 09:37:06,661] [pool-1-thread-12] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] 09:37:06,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:37:06,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:06,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-06_09-37-06.log] [testng] 09:37:06,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cb224b4 - End of configuration. [testng] [2024-06-06 09:37:06,678] [pool-1-thread-11] Initializing /data/roger/spheroid1.lsm movie.avi: [testng] 09:37:06,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:37:06,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:06,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-06_09-37-06.log] [testng] 09:37:06,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23b225b5 - End of configuration. [testng] [2024-06-06 09:37:06,761] [pool-1-thread-10] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] 09:37:06,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:37:06,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:06,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-06_09-37-06.log] [testng] 09:37:06,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7924cc7d - End of configuration. [testng] [2024-06-06 09:37:06,776] [pool-1-thread-9] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] 09:37:06,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:37:06,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:06,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-06_09-37-06.log] [testng] 09:37:06,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59cfd96e - End of configuration. [testng] [2024-06-06 09:37:07,004] [pool-1-thread-8] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] 09:37:07,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:37:07,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,005 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-06_09-37-07.log] [testng] 09:37:07,006 |-INFO in ch.qos.logback.core.sift.SiftProcessor@716b1e22 - End of configuration. [testng] [2024-06-06 09:37:07,053] [pool-1-thread-7] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] 09:37:07,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:37:07,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-06_09-37-07.log] [testng] 09:37:07,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25882978 - End of configuration. [testng] [2024-06-06 09:37:07,060] [pool-1-thread-6] Initializing /data/simon/24_bit_problem.avi: [testng] 09:37:07,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:37:07,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-06_09-37-07.log] [testng] 09:37:07,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ccaa0df - End of configuration. [testng] [2024-06-06 09:37:07,108] [pool-1-thread-5] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] 09:37:07,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:37:07,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-06_09-37-07.log] [testng] 09:37:07,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e3364b8 - End of configuration. [testng] [2024-06-06 09:37:07,122] [pool-1-thread-4] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] 09:37:07,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:37:07,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-06_09-37-07.log] [testng] 09:37:07,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54f61534 - End of configuration. [testng] [2024-06-06 09:37:07,154] [pool-1-thread-3] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] 09:37:07,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:37:07,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-06_09-37-07.log] [testng] 09:37:07,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7810aaea - End of configuration. [testng] [2024-06-06 09:37:07,191] [pool-1-thread-2] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] 09:37:07,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:37:07,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:07,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-06_09-37-07.log] [testng] 09:37:07,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@565ad560 - End of configuration. [testng] [2024-06-06 09:37:09,329] [pool-1-thread-7] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] [2024-06-06 09:37:09,343] [pool-1-thread-3] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-06-06 09:37:09,755] [pool-1-thread-12] Initializing /data/qa-7450/MVI_3610.AVI: [testng] [2024-06-06 09:37:10,995] [pool-1-thread-10] Initializing /data/kurt/40x_6um.avi: [testng] [2024-06-06 09:37:11,253] [pool-1-thread-8] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-06-06 09:37:32,403] [pool-1-thread-5] Initializing /data/ascb/TIRF.avi: [testng] [2024-06-06 09:37:32,973] [pool-1-thread-2] Initializing /data/kurt/63x_6um.avi: [testng] [2024-06-06 09:37:33,283] [pool-1-thread-9] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] [2024-06-06 09:37:33,699] [pool-1-thread-1] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] [2024-06-06 09:37:33,799] [pool-1-thread-6] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] [2024-06-06 09:37:33,893] [pool-1-thread-11] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-06-06 09:37:33,980] [pool-1-thread-4] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] [2024-06-06 09:37:34,319] [pool-1-thread-7] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [2024-06-06 09:37:38,762] [pool-1-thread-3] Initializing /data/william/worm.avi: [testng] [2024-06-06 09:37:38,769] [pool-1-thread-6] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-06-06 09:37:39,354] [pool-1-thread-11] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] [2024-06-06 09:37:39,448] [pool-1-thread-12] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-06-06 09:37:39,924] [pool-1-thread-5] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-06-06 09:37:39,946] [pool-1-thread-10] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-06-06 09:37:40,780] [pool-1-thread-3] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] [2024-06-06 09:37:40,815] [pool-1-thread-2] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] [2024-06-06 09:37:41,998] [pool-1-thread-1] Initializing /data/chris/APZ04_009.avi: [testng] [2024-06-06 09:37:45,094] [pool-1-thread-4] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-06-06 09:37:45,104] [pool-1-thread-9] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-06-06 09:37:45,214] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-06-06 09:37:45,413] [pool-1-thread-3] Initializing /data/kurt/40x_6um_2.avi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2014, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 56 seconds Finished: SUCCESS