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Started by upstream project "BIOFORMATS-test-repo" build number 388 originally caused by: Started by upstream project "Trigger" build number 411 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/jenkins14601976853699532105.sh + '[' flex = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61379_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/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] 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] 00:37:08,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:37:08,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:37:08,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:08,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:08,593 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:08,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:08,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:37:08,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:08,595 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:08,595 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:08,596 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:08,596 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:08,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:08,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:08,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:08,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:08,794 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:08,794 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:08,795 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:08,795 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:08,795 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:37:08,796 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:37:08,796 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-23 00:37:08,805] [main] java.version = 17.0.2 [testng] 00:37:08,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:08,809 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:08,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-23_00-37-08.log] [testng] 00:37:08,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-23 00:37:08,852] [main] testng.directory = /data [testng] [2025-03-23 00:37:08,853] [main] testng.configDirectory = /config [testng] [2025-03-23 00:37:08,862] [main] testng.multiplier = 1.0 [testng] [2025-03-23 00:37:08,863] [main] testng.in-memory = false [testng] [2025-03-23 00:37:08,863] [main] testng.allow-missing = false [testng] [2025-03-23 00:37:08,863] [main] user.language = en [testng] [2025-03-23 00:37:08,863] [main] user.country = ${user.country} [testng] [2025-03-23 00:37:08,863] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-23 00:40:47,101] [main] ---------------------------------------- [testng] [2025-03-23 00:40:47,101] [main] Total files: 791 [testng] [2025-03-23 00:40:47,101] [main] Scan time: 218.238 s (275 ms/file) [testng] [2025-03-23 00:40:47,101] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-23 00:50:26,694] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 00:50:26,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:50:26,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:26,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-23_00-50-26.log] [testng] 00:50:26,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@168cb6e5 - End of configuration. [testng] [2025-03-23 00:50:30,053] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 00:50:30,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:50:30,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:30,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-23_00-50-30.log] [testng] 00:50:30,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60bcad75 - End of configuration. [testng] [2025-03-23 00:50:44,358] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex: [testng] 00:50:44,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:50:44,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:44,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-23_00-50-44.log] [testng] 00:50:44,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c003054 - End of configuration. [testng] [2025-03-23 00:50:46,110] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:50:46,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:50:46,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:46,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-23_00-50-46.log] [testng] 00:50:46,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b6882a5 - End of configuration. [testng] [2025-03-23 00:50:58,243] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] 00:50:58,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:50:58,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:58,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-23_00-50-58.log] [testng] 00:50:58,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@492fdcde - End of configuration. [testng] [2025-03-23 00:50:59,975] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] 00:50:59,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:50:59,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:59,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-23_00-50-59.log] [testng] 00:50:59,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bd173f7 - End of configuration. [testng] [2025-03-23 00:51:03,446] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] 00:51:03,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:51:03,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:03,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-23_00-51-03.log] [testng] 00:51:03,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52670bb6 - End of configuration. [testng] [2025-03-23 00:51:05,359] [pool-1-thread-6] Initializing /data/qa-7469/002002.flex: [testng] 00:51:05,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:51:05,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:05,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-23_00-51-05.log] [testng] 00:51:05,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ca95a5 - End of configuration. [testng] [2025-03-23 00:51:07,293] [pool-1-thread-5] Initializing /data/tony/001001000_objects.flex: [testng] 00:51:07,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:51:07,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:07,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-23_00-51-07.log] [testng] 00:51:07,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14f298a6 - End of configuration. [testng] [2025-03-23 00:51:09,612] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] 00:51:09,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:51:09,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:09,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-23_00-51-09.log] [testng] 00:51:09,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29bf3889 - End of configuration. [testng] [2025-03-23 00:51:14,603] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] 00:51:14,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:51:14,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:14,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-23_00-51-14.log] [testng] 00:51:14,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cefe1dc - End of configuration. [testng] [2025-03-23 00:51:18,313] [pool-1-thread-2] Initializing /data/achim/003003000.flex: [testng] 00:51:18,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:51:18,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:18,313 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-23_00-51-18.log] [testng] 00:51:18,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f06a2b2 - End of configuration. [testng] [2025-03-23 00:51:46,653] [pool-1-thread-8] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-03-23 00:51:51,060] [pool-1-thread-7] Initializing /data/tony/015002000.tiff: [testng] [2025-03-23 00:51:55,437] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-03-23 00:51:57,972] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex: [testng] [2025-03-23 00:51:59,885] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-03-23 00:52:17,154] [pool-1-thread-5] Initializing /data/tony/003003000.tiff: [testng] [2025-03-23 00:52:25,113] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-03-23 00:52:48,628] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2025-03-23 00:53:00,092] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-03-23 00:53:08,157] [pool-1-thread-6] Initializing /data/tony/test1.flex: [testng] [2025-03-23 00:53:11,340] [pool-1-thread-9] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-03-23 00:53:14,306] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-03-23 00:53:16,527] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-03-23 00:53:31,767] [pool-1-thread-2] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-03-23 00:53:50,310] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-03-23 00:54:07,879] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-03-23 00:54:10,283] [pool-1-thread-7] Initializing /data/anatole/001004000.flex: [testng] [2025-03-23 00:54:12,529] [pool-1-thread-6] Initializing /data/stephane/002007000.flex: [testng] [2025-03-23 00:54:14,195] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2025-03-23 00:54:15,834] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [2025-03-23 00:54:28,218] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-03-23 00:54:42,546] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-03-23 00:54:55,566] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-03-23 00:54:58,262] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2025-03-23 00:55:01,316] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-03-23 00:55:31,215] [pool-1-thread-5] Initializing /data/ghislain/test.flex: [testng] [2025-03-23 00:55:43,573] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-03-23 00:56:00,421] [pool-1-thread-1] Initializing /data/tamjid/006004000.flex: [testng] [2025-03-23 00:56:02,615] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-03-23 00:56:22,414] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 40 minutes 18 seconds Finished: SUCCESS