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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins11153003192375938921.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35488_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 13:33:00,777 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:33:00,778 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 13:33:00,778 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:33:00,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:33:00,779 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:33:00,780 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:33:00,780 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:33:00,780 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:33:00,780 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:33:00,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:33:00,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:33:00,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:33:00,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:33:00,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:33:00,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:33:00,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:33:00,959 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:33:00,959 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:33:00,959 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:33:00,959 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:33:00,959 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 13:33:00,960 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 13:33:00,960 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 180 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 13:33:00,969] [main] java.version = 21 [testng] 13:33:00,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:33:00,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:33:01,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_13-33-00.log] [testng] 13:33:01,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 13:33:01,014] [main] testng.directory = /data [testng] [2024-10-17 13:33:01,014] [main] testng.configDirectory = /config [testng] [2024-10-17 13:33:01,022] [main] testng.multiplier = 1.0 [testng] [2024-10-17 13:33:01,023] [main] testng.in-memory = false [testng] [2024-10-17 13:33:01,023] [main] testng.allow-missing = false [testng] [2024-10-17 13:33:01,023] [main] user.language = en [testng] [2024-10-17 13:33:01,023] [main] user.country = ${user.country} [testng] [2024-10-17 13:33:01,023] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 13:40:54,778] [main] ---------------------------------------- [testng] [2024-10-17 13:40:54,778] [main] Total files: 791 [testng] [2024-10-17 13:40:54,778] [main] Scan time: 473.755 s (598 ms/file) [testng] [2024-10-17 13:40:54,779] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 13:59:25,534] [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] 13:59:25,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:59:25,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:59:25,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_13-59-25.log] [testng] 13:59:25,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5564340a - End of configuration. [testng] [2024-10-17 13:59:31,986] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] 13:59:31,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:59:31,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:59:31,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_13-59-31.log] [testng] 13:59:31,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ee74a4 - End of configuration. [testng] [2024-10-17 13:59:37,847] [pool-1-thread-11] Initializing /data/stephane/002007000.flex: [testng] 13:59:37,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:59:37,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:59:37,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_13-59-37.log] [testng] 13:59:37,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72ca7894 - End of configuration. [testng] [2024-10-17 13:59:42,248] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex: [testng] 13:59:42,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:59:42,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:59:42,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_13-59-42.log] [testng] 13:59:42,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78792ff0 - End of configuration. [testng] [2024-10-17 13:59:48,009] [pool-1-thread-9] Initializing /data/tony/015002000.tiff: [testng] 13:59:48,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:59:48,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:59:48,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_13-59-48.log] [testng] 13:59:48,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6229c7bd - End of configuration. [testng] [2024-10-17 14:00:02,225] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 14:00:02,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:00:02,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:00:02,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_14-00-02.log] [testng] 14:00:02,226 |-INFO in ch.qos.logback.core.sift.SiftProcessor@240c3835 - End of configuration. [testng] [2024-10-17 14:00:39,638] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 14:00:39,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:00:39,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:00:39,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_14-00-39.log] [testng] 14:00:39,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4537863e - End of configuration. [testng] [2024-10-17 14:00:44,437] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 14:00:44,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:00:44,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:00:44,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_14-00-44.log] [testng] 14:00:44,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32e5bb33 - End of configuration. [testng] [2024-10-17 14:01:22,208] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] 14:01:22,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:01:22,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:01:22,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_14-01-22.log] [testng] 14:01:22,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1995b358 - End of configuration. [testng] [2024-10-17 14:01:26,344] [pool-1-thread-4] Initializing /data/tony/003008000.flex: [testng] 14:01:26,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:01:26,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:01:26,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_14-01-26.log] [testng] 14:01:26,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@559edb09 - End of configuration. [testng] [2024-10-17 14:01:31,944] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 14:01:31,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:01:31,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:01:31,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_14-01-31.log] [testng] 14:01:31,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b60146d - End of configuration. [testng] [2024-10-17 14:01:37,260] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] 14:01:37,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:01:37,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:01:37,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_14-01-37.log] [testng] 14:01:37,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cd5fa79 - End of configuration. [testng] [2024-10-17 14:02:41,953] [pool-1-thread-9] Initializing /data/tony/test.tiff: [testng] [2024-10-17 14:02:53,423] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-17 14:02:57,311] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-17 14:03:02,788] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-17 14:03:35,097] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-17 14:03:49,255] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-17 14:04:13,740] [pool-1-thread-7] Initializing /data/achim/003003000.flex: [testng] [2024-10-17 14:04:19,798] [pool-1-thread-3] Initializing /data/stephane/006013000.flex: [testng] [2024-10-17 14:04:33,814] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-10-17 14:05:42,650] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-10-17 14:05:52,215] [pool-1-thread-12] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-17 14:06:06,368] [pool-1-thread-10] Initializing /data/tamjid/006004000.flex: [testng] [2024-10-17 14:06:13,185] [pool-1-thread-5] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-10-17 14:06:50,098] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-17 14:07:50,773] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-17 14:07:57,609] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-17 14:08:39,826] [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] [2024-10-17 14:08:44,782] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-17 14:08:50,892] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-10-17 14:09:55,458] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-17 14:11:19,241] [pool-1-thread-3] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-17 14:11:25,795] [pool-1-thread-12] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-17 14:11:38,485] [pool-1-thread-2] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-17 14:12:08,288] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-17 14:12:44,779] [pool-1-thread-12] Initializing /data/tony/003003000.tiff: [testng] [2024-10-17 14:12:56,556] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-17 14:13:03,101] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-17 14:13:12,895] [pool-1-thread-4] Initializing /data/ghislain/test.flex: [testng] [2024-10-17 14:13:33,561] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-17 14:13:55,635] [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] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 78 minutes 23 seconds Finished: SUCCESS