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Started by upstream project "BIOFORMATS-test-repo" build number 305 originally caused by: Started by upstream project "Trigger" build number 327 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/jenkins4101086094090678589.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48280_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] 01:05:34,537 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:05:34,539 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:05:34,539 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:05:34,540 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:05:34,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:05:34,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:05:34,541 |-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] 01:05:34,541 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:05:34,541 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:05:34,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:05:34,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:05:34,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:05:34,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:05:34,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:05:34,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:05:34,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:05:34,731 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:05:34,731 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:05:34,732 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:05:34,732 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:05:34,732 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:05:34,733 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:05:34,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-01 01:05:34,741] [main] java.version = 17.0.2 [testng] 01:05:34,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:05:34,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:05:34,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-01_01-05-34.log] [testng] 01:05:34,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-01 01:05:34,788] [main] testng.directory = /data [testng] [2025-01-01 01:05:34,788] [main] testng.configDirectory = /config [testng] [2025-01-01 01:05:34,797] [main] testng.multiplier = 1.0 [testng] [2025-01-01 01:05:34,797] [main] testng.in-memory = false [testng] [2025-01-01 01:05:34,797] [main] testng.allow-missing = false [testng] [2025-01-01 01:05:34,798] [main] user.language = en [testng] [2025-01-01 01:05:34,798] [main] user.country = ${user.country} [testng] [2025-01-01 01:05:34,798] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-01 01:06:22,515] [main] ---------------------------------------- [testng] [2025-01-01 01:06:22,515] [main] Total files: 791 [testng] [2025-01-01 01:06:22,515] [main] Scan time: 47.717 s (60 ms/file) [testng] [2025-01-01 01:06:22,516] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-01 01:12:23,450] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 01:12:23,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:12:23,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:23,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-01_01-12-23.log] [testng] 01:12:23,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3143c7fa - End of configuration. [testng] [2025-01-01 01:12:29,386] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 01:12:29,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:12:29,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:29,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-01_01-12-29.log] [testng] 01:12:29,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@462ae941 - End of configuration. [testng] [2025-01-01 01:12:31,427] [pool-1-thread-11] Initializing /data/ghislain/test.flex: [testng] 01:12:31,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:12:31,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:31,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-01_01-12-31.log] [testng] 01:12:31,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6ed243 - End of configuration. [testng] [2025-01-01 01:12:32,099] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] 01:12:32,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:12:32,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:32,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-01_01-12-32.log] [testng] 01:12:32,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e93722d - End of configuration. [testng] [2025-01-01 01:12:32,751] [pool-1-thread-9] Initializing /data/tamjid/006003000.flex: [testng] 01:12:32,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:12:32,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:32,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-01_01-12-32.log] [testng] 01:12:32,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bce6f07 - End of configuration. [testng] [2025-01-01 01:12:33,324] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:12:33,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:12:33,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:33,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-01_01-12-33.log] [testng] 01:12:33,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ba7317 - End of configuration. [testng] [2025-01-01 01:12:34,066] [pool-1-thread-7] Initializing /data/qa-2983/004007000.flex: [testng] 01:12:34,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:12:34,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:34,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-01_01-12-34.log] [testng] 01:12:34,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fbbd9f - End of configuration. [testng] [2025-01-01 01:12:34,666] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:12:34,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:12:34,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:34,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-01_01-12-34.log] [testng] 01:12:34,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@176382f5 - End of configuration. [testng] [2025-01-01 01:12:40,181] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:12:40,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:12:40,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:40,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-01_01-12-40.log] [testng] 01:12:40,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eb0c2da - End of configuration. [testng] [2025-01-01 01:12:40,800] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:12:40,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:12:40,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:40,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-01_01-12-40.log] [testng] 01:12:40,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ec7cc2 - End of configuration. [testng] [2025-01-01 01:12:47,533] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex: [testng] 01:12:47,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:12:47,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:47,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-01_01-12-47.log] [testng] 01:12:47,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38105904 - End of configuration. [testng] [2025-01-01 01:12:48,326] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:12:48,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:12:48,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:12:48,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-01_01-12-48.log] [testng] 01:12:48,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@243e9552 - End of configuration. [testng] [2025-01-01 01:13:09,369] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-01-01 01:13:10,362] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex: [testng] [2025-01-01 01:13:11,184] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2025-01-01 01:13:12,154] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-01-01 01:13:18,918] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-01-01 01:13:25,594] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-01-01 01:13:28,507] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-01-01 01:13:39,946] [pool-1-thread-9] Initializing /data/tony/001001000_objects.flex: [testng] [2025-01-01 01:13:41,045] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2025-01-01 01:13:46,650] [pool-1-thread-3] Initializing /data/stephane/006013000.flex: [testng] [2025-01-01 01:13:50,452] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2025-01-01 01:13:55,920] [pool-1-thread-9] Initializing /data/qa-7469/002002.flex: [testng] [2025-01-01 01:14:00,086] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-01-01 01:14:04,115] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-01-01 01:14:11,431] [pool-1-thread-1] Initializing /data/tony/015002000.tiff: [testng] [2025-01-01 01:14:13,414] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-01-01 01:14:15,165] [pool-1-thread-3] Initializing /data/manuel/003003001.flex: [testng] [2025-01-01 01:14:19,792] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2025-01-01 01:14:28,135] [pool-1-thread-1] Initializing /data/qa-18096/002002001.flex: [testng] [2025-01-01 01:14:35,388] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2025-01-01 01:14:40,755] [pool-1-thread-5] Initializing /data/tony/test.tiff: [testng] [2025-01-01 01:14:44,763] [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] [2025-01-01 01:14:48,379] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-01-01 01:14:54,423] [pool-1-thread-8] Initializing /data/tony/003003000.tiff: [testng] [2025-01-01 01:14:58,615] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] [2025-01-01 01:15:00,580] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-01-01 01:15:13,941] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-01-01 01:15:15,734] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-01-01 01:15:19,713] [pool-1-thread-8] Initializing /data/tony/003008000.flex: [testng] [2025-01-01 01:15:24,980] [pool-1-thread-5] Initializing /data/tony/001014000 - from flex.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 15 minutes 51 seconds Finished: SUCCESS