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Started by upstream project "BIOFORMATS-test-repo" build number 26 originally caused by: Started by upstream project "Trigger" build number 29 originally caused by: Started by timer 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/jenkins1439022607470508066.sh + '[' flex = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3309_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] 01:31:11,535 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:31:11,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:31:11,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:31:11,537 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:31:11,538 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:31:11,538 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:31:11,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:31:11,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:31:11,539 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:31:11,539 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:31:11,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:31:11,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:31:11,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:31:11,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:31:11,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:31:11,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:31:11,777 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:31:11,777 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:31:11,777 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:31:11,778 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:31:11,778 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:31:11,779 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:31:11,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 240 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-07 01:31:11,788] [main] java.version = 17.0.2 [testng] 01:31:11,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:31:11,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:11,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-07_01-31-11.log] [testng] 01:31:11,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-07 01:31:11,844] [main] testng.directory = /data [testng] [2024-04-07 01:31:11,844] [main] testng.configDirectory = /config [testng] [2024-04-07 01:31:11,917] [main] testng.multiplier = 1.0 [testng] [2024-04-07 01:31:11,918] [main] testng.in-memory = false [testng] [2024-04-07 01:31:11,918] [main] testng.allow-missing = false [testng] [2024-04-07 01:31:11,918] [main] user.language = en [testng] [2024-04-07 01:31:11,918] [main] user.country = ${user.country} [testng] [2024-04-07 01:31:11,918] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-07 01:31:25,299] [main] ---------------------------------------- [testng] [2024-04-07 01:31:25,299] [main] Total files: 791 [testng] [2024-04-07 01:31:25,299] [main] Scan time: 13.38 s (16 ms/file) [testng] [2024-04-07 01:31:25,299] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-07 01:38:22,033] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:38:22,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:38:22,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:22,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-07_01-38-22.log] [testng] 01:38:22,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3765e75 - End of configuration. [testng] [2024-04-07 01:38:22,077] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] 01:38:22,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:38:22,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:22,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-07_01-38-22.log] [testng] 01:38:22,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67fbeca0 - End of configuration. [testng] [2024-04-07 01:38:22,139] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] 01:38:22,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:38:22,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:22,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-07_01-38-22.log] [testng] 01:38:22,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e7a5c8a - End of configuration. [testng] [2024-04-07 01:38:22,964] [pool-1-thread-10] Initializing /data/qa-7469/002002.flex: [testng] 01:38:22,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:38:22,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:22,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-07_01-38-22.log] [testng] 01:38:22,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@85ea298 - End of configuration. [testng] [2024-04-07 01:38:23,003] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:38:23,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:38:23,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-07_01-38-23.log] [testng] 01:38:23,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5000dd6c - End of configuration. [testng] [2024-04-07 01:38:23,453] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 01:38:23,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:38:23,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-07_01-38-23.log] [testng] 01:38:23,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61caa8d7 - End of configuration. [testng] [2024-04-07 01:38:23,854] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:38:23,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:38:23,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-07_01-38-23.log] [testng] 01:38:23,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b531779 - End of configuration. [testng] [2024-04-07 01:38:23,890] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] 01:38:23,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:38:23,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-07_01-38-23.log] [testng] 01:38:23,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8584b3 - End of configuration. [testng] [2024-04-07 01:38:23,938] [pool-1-thread-5] Initializing /data/tony/003008000.flex: [testng] 01:38:23,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:38:23,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-07_01-38-23.log] [testng] 01:38:23,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration. [testng] [2024-04-07 01:38:23,981] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] 01:38:23,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:38:23,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-07_01-38-23.log] [testng] 01:38:23,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b74f060 - End of configuration. [testng] [2024-04-07 01:38:24,007] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 01:38:24,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:38:24,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:24,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-07_01-38-24.log] [testng] 01:38:24,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1753cd3f - End of configuration. [testng] [2024-04-07 01:38:24,101] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:38:24,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:38:24,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:24,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-07_01-38-24.log] [testng] 01:38:24,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@612dbea7 - End of configuration. [testng] [2024-04-07 01:38:36,681] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] [2024-04-07 01:38:36,742] [pool-1-thread-6] Initializing /data/qa-17190/002002011.flex: [testng] [2024-04-07 01:38:36,785] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-04-07 01:38:36,829] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-04-07 01:38:36,904] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-04-07 01:38:37,380] [pool-1-thread-3] Initializing /data/tony/test.tiff: [testng] [2024-04-07 01:38:38,003] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-04-07 01:38:38,561] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-04-07 01:38:38,683] [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] [2024-04-07 01:38:38,740] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-04-07 01:38:39,223] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] [2024-04-07 01:38:39,335] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-04-07 01:38:39,393] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-04-07 01:38:40,081] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-04-07 01:38:40,685] [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] [2024-04-07 01:38:40,947] [pool-1-thread-3] Initializing /data/ghislain/test.flex: [testng] [2024-04-07 01:38:41,867] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex: [testng] [2024-04-07 01:38:42,109] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-04-07 01:38:42,993] [pool-1-thread-3] Initializing /data/tony/test1.flex: [testng] [2024-04-07 01:38:43,063] [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] [2024-04-07 01:38:43,450] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-04-07 01:38:44,085] [pool-1-thread-1] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-04-07 01:38:45,975] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-04-07 01:38:47,227] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-04-07 01:38:47,412] [pool-1-thread-3] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-04-07 01:38:47,904] [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] [2024-04-07 01:38:48,826] [pool-1-thread-4] Initializing /data/manuel/003003001.flex: [testng] [2024-04-07 01:38:49,542] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [2024-04-07 01:38:50,141] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] [2024-04-07 01:38:50,701] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 8 seconds Finished: SUCCESS