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Started by upstream project "BIOFORMATS-test-repo" build number 254 originally caused by: Started by upstream project "Trigger" build number 278 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/jenkins1190696233505669089.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40029_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] 00:50:39,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:50:39,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:50:39,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:39,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:39,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:50:39,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:50:39,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:50:39,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:39,320 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:39,320 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:50:39,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:50:39,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:50:39,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:50:39,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:50:39,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:50:39,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:50:39,515 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:50:39,515 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:50:39,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:50:39,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:50:39,515 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:50:39,516 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:50:39,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-13 00:50:39,525] [main] java.version = 17.0.2 [testng] 00:50:39,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:50:39,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:39,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-13_00-50-39.log] [testng] 00:50:39,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-13 00:50:39,572] [main] testng.directory = /data [testng] [2024-11-13 00:50:39,573] [main] testng.configDirectory = /config [testng] [2024-11-13 00:50:39,581] [main] testng.multiplier = 1.0 [testng] [2024-11-13 00:50:39,582] [main] testng.in-memory = false [testng] [2024-11-13 00:50:39,582] [main] testng.allow-missing = false [testng] [2024-11-13 00:50:39,582] [main] user.language = en [testng] [2024-11-13 00:50:39,582] [main] user.country = ${user.country} [testng] [2024-11-13 00:50:39,583] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-13 00:52:01,902] [main] ---------------------------------------- [testng] [2024-11-13 00:52:01,902] [main] Total files: 791 [testng] [2024-11-13 00:52:01,902] [main] Scan time: 82.319 s (104 ms/file) [testng] [2024-11-13 00:52:01,902] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-13 00:57:16,112] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] 00:57:16,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:57:16,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:16,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-13_00-57-16.log] [testng] 00:57:16,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1630eac1 - End of configuration. [testng] [2024-11-13 00:57:16,618] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 00:57:16,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:57:16,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:16,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-13_00-57-16.log] [testng] 00:57:16,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f12ee7 - End of configuration. [testng] [2024-11-13 00:57:17,128] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] 00:57:17,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:57:17,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:17,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-13_00-57-17.log] [testng] 00:57:17,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e536289 - End of configuration. [testng] [2024-11-13 00:57:17,685] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:57:17,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:57:17,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:17,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-13_00-57-17.log] [testng] 00:57:17,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2451a5c5 - End of configuration. [testng] [2024-11-13 00:57:18,817] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 00:57:18,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:57:18,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:18,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-13_00-57-18.log] [testng] 00:57:18,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f397a48 - End of configuration. [testng] [2024-11-13 00:57:19,403] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex: [testng] 00:57:19,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:57:19,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:19,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-13_00-57-19.log] [testng] 00:57:19,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6efb14cb - End of configuration. [testng] [2024-11-13 00:57:19,925] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 00:57:19,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:57:19,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:19,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-13_00-57-19.log] [testng] 00:57:19,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@521e5250 - End of configuration. [testng] [2024-11-13 00:57:24,070] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:57:24,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:57:24,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:24,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-13_00-57-24.log] [testng] 00:57:24,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4981f76 - End of configuration. [testng] [2024-11-13 00:57:28,776] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] 00:57:28,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:57:28,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:28,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-13_00-57-28.log] [testng] 00:57:28,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748dac42 - End of configuration. [testng] [2024-11-13 00:57:29,386] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] 00:57:29,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:57:29,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:29,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-13_00-57-29.log] [testng] 00:57:29,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633055dc - End of configuration. [testng] [2024-11-13 00:57:30,763] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 00:57:30,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:57:30,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:30,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-13_00-57-30.log] [testng] 00:57:30,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55896030 - End of configuration. [testng] [2024-11-13 00:57:36,338] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] 00:57:36,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:57:36,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:36,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-13_00-57-36.log] [testng] 00:57:36,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d312120 - End of configuration. [testng] [2024-11-13 00:57:47,432] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-11-13 00:57:53,438] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-11-13 00:57:54,269] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-11-13 00:57:55,040] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-11-13 00:57:55,798] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-11-13 00:58:00,664] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-11-13 00:58:01,402] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2024-11-13 00:58:02,113] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-11-13 00:58:07,186] [pool-1-thread-5] Initializing /data/tony/test.tiff: [testng] [2024-11-13 00:58:08,745] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-11-13 00:58:14,784] [pool-1-thread-8] Initializing /data/tony/001001000_objects.flex: [testng] [2024-11-13 00:58:15,657] [pool-1-thread-1] Initializing /data/achim/003003000.flex: [testng] [2024-11-13 00:58:16,631] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] [2024-11-13 00:58:21,723] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-11-13 00:58:25,812] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-11-13 00:58:26,730] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-11-13 00:58:27,942] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-11-13 00:58:29,019] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-11-13 00:58:36,295] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-11-13 00:58:43,971] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-11-13 00:58:45,011] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-11-13 00:58:47,096] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-11-13 00:58:56,721] [pool-1-thread-5] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-11-13 00:58:58,975] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-11-13 00:59:02,974] [pool-1-thread-8] Initializing /data/tony/015002000.tiff: [testng] [2024-11-13 00:59:07,679] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-11-13 00:59:13,513] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex: [testng] [2024-11-13 00:59:15,589] [pool-1-thread-8] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-11-13 00:59:25,485] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-11-13 00:59:38,198] [pool-1-thread-8] Initializing /data/tony/test1.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 minutes 32 seconds Finished: SUCCESS