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Started by upstream project "BIOFORMATS-test-repo" build number 111 originally caused by: Started by upstream project "Trigger" build number 124 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/jenkins6140833647400782972.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17250_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:32:40,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:32:40,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:32:40,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:40,277 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:40,277 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:32:40,277 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:32:40,278 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:32:40,278 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:40,278 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:40,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:32:40,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:32:40,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:32:40,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:32:40,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:32:40,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:32:40,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:32:40,487 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:32:40,487 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:32:40,487 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:32:40,488 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:32:40,488 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:32:40,488 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:32:40,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-04 01:32:40,499] [main] java.version = 21 [testng] 01:32:40,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:32:40,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:40,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-04_01-32-40.log] [testng] 01:32:40,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-04 01:32:40,548] [main] testng.directory = /data [testng] [2024-07-04 01:32:40,548] [main] testng.configDirectory = /config [testng] [2024-07-04 01:32:40,557] [main] testng.multiplier = 1.0 [testng] [2024-07-04 01:32:40,558] [main] testng.in-memory = false [testng] [2024-07-04 01:32:40,558] [main] testng.allow-missing = false [testng] [2024-07-04 01:32:40,558] [main] user.language = en [testng] [2024-07-04 01:32:40,558] [main] user.country = ${user.country} [testng] [2024-07-04 01:32:40,558] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-04 01:32:53,238] [main] ---------------------------------------- [testng] [2024-07-04 01:32:53,238] [main] Total files: 791 [testng] [2024-07-04 01:32:53,238] [main] Scan time: 12.68 s (16 ms/file) [testng] [2024-07-04 01:32:53,239] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-04 01:38:57,690] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:38:57,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:38:57,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-04_01-38-57.log] [testng] 01:38:57,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9fb7703 - End of configuration. [testng] [2024-07-04 01:38:57,738] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] 01:38:57,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:38:57,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-04_01-38-57.log] [testng] 01:38:57,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310e1db0 - End of configuration. [testng] [2024-07-04 01:38:57,771] [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] 01:38:57,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:38:57,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-04_01-38-57.log] [testng] 01:38:57,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50edd8b4 - End of configuration. [testng] [2024-07-04 01:38:57,818] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 01:38:57,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:38:57,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-04_01-38-57.log] [testng] 01:38:57,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20abc31a - End of configuration. [testng] [2024-07-04 01:38:57,881] [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] 01:38:57,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:38:57,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-04_01-38-57.log] [testng] 01:38:57,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5517552 - End of configuration. [testng] [2024-07-04 01:38:57,922] [pool-1-thread-8] Initializing /data/tony/test1.flex: [testng] 01:38:57,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:38:57,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-04_01-38-57.log] [testng] 01:38:57,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20c1a759 - End of configuration. [testng] [2024-07-04 01:38:57,945] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:38:57,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:38:57,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:57,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-04_01-38-57.log] [testng] 01:38:57,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d02813b - End of configuration. [testng] [2024-07-04 01:38:58,042] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex: [testng] 01:38:58,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:38:58,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:58,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-04_01-38-58.log] [testng] 01:38:58,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2562c7be - End of configuration. [testng] [2024-07-04 01:38:58,066] [pool-1-thread-5] Initializing /data/stephane/006013000.flex: [testng] 01:38:58,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:38:58,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:58,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-04_01-38-58.log] [testng] 01:38:58,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7084f9b8 - End of configuration. [testng] [2024-07-04 01:38:58,114] [pool-1-thread-4] Initializing /data/achim/003003000.flex: [testng] 01:38:58,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:38:58,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:58,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-04_01-38-58.log] [testng] 01:38:58,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2112ad2a - End of configuration. [testng] [2024-07-04 01:38:58,232] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 01:38:58,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:38:58,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:58,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-04_01-38-58.log] [testng] 01:38:58,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3093af12 - End of configuration. [testng] [2024-07-04 01:38:58,289] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] 01:38:58,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:38:58,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:58,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-04_01-38-58.log] [testng] 01:38:58,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36b1fce1 - End of configuration. [testng] [2024-07-04 01:39:00,313] [pool-1-thread-8] Initializing /data/tony/003003000.tiff: [testng] [2024-07-04 01:39:00,400] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-07-04 01:39:00,442] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [2024-07-04 01:39:00,468] [pool-1-thread-6] Initializing /data/tamjid/006004000.flex: [testng] [2024-07-04 01:39:00,494] [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] [2024-07-04 01:39:00,521] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-07-04 01:39:00,940] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] [2024-07-04 01:39:01,124] [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] [2024-07-04 01:39:01,159] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-07-04 01:39:01,188] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-07-04 01:39:01,886] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-07-04 01:39:02,367] [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] [2024-07-04 01:39:02,627] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] [2024-07-04 01:39:02,846] [pool-1-thread-8] Initializing /data/qa-17190/002002011.flex: [testng] [2024-07-04 01:39:03,015] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex: [testng] [2024-07-04 01:39:03,067] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-07-04 01:39:03,235] [pool-1-thread-1] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-07-04 01:39:03,361] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-07-04 01:39:03,397] [pool-1-thread-8] Initializing /data/anatole/001004000.flex: [testng] [2024-07-04 01:39:03,648] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-07-04 01:39:04,129] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-07-04 01:39:04,770] [pool-1-thread-5] Initializing /data/tony/015002000.tiff: [testng] [2024-07-04 01:39:04,827] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-07-04 01:39:05,699] [pool-1-thread-2] Initializing /data/tony/003008000.flex: [testng] [2024-07-04 01:39:05,856] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-07-04 01:39:06,389] [pool-1-thread-4] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-07-04 01:39:07,267] [pool-1-thread-10] Initializing /data/qa-18096/002002001.flex: [testng] [2024-07-04 01:39:07,904] [pool-1-thread-10] Initializing /data/stephane/002007000.flex: [testng] [2024-07-04 01:39:08,310] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-07-04 01:39:09,357] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 36 seconds Finished: SUCCESS