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Started by upstream project "BIOFORMATS-test-repo" build number 367 originally caused by: Started by upstream project "Trigger" build number 393 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins13991566193391614989.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58515_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 test-automated: [testng] File leak detector installed [testng] 01:20:57,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:20:57,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 01:20:57,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:57,632 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:57,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:20:57,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:20:57,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:20:57,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:57,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:57,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:20:57,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:20:57,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:20:57,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:57,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:57,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:57,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:57,882 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:57,882 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:57,882 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:57,882 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:57,882 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 01:20:57,883 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 01:20:57,883 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 250 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-07 01:20:57,893] [main] java.version = 1.8.0_342 [testng] 01:20:57,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:57,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:57,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-07_01-20-57.log] [testng] 01:20:57,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-07 01:20:57,944] [main] testng.directory = /data [testng] [2025-03-07 01:20:57,944] [main] testng.configDirectory = /config [testng] [2025-03-07 01:20:57,955] [main] testng.multiplier = 1.0 [testng] [2025-03-07 01:20:57,956] [main] testng.in-memory = false [testng] [2025-03-07 01:20:57,956] [main] testng.allow-missing = false [testng] [2025-03-07 01:20:57,956] [main] user.language = en [testng] [2025-03-07 01:20:57,956] [main] user.country = ${user.country} [testng] [2025-03-07 01:20:57,956] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-07 01:23:59,101] [main] ---------------------------------------- [testng] [2025-03-07 01:23:59,101] [main] Total files: 791 [testng] [2025-03-07 01:23:59,101] [main] Scan time: 181.145 s (229 ms/file) [testng] [2025-03-07 01:23:59,101] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-07 01:33:46,830] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 01:33:46,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:33:46,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:46,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-07_01-33-46.log] [testng] 01:33:46,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b01d87c - End of configuration. [testng] [2025-03-07 01:33:58,543] [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] 01:33:58,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:33:58,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:58,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-07_01-33-58.log] [testng] 01:33:58,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fdcfa5f - End of configuration. [testng] [2025-03-07 01:34:00,246] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] 01:34:00,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:34:00,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:00,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-07_01-34-00.log] [testng] 01:34:00,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eebeb59 - End of configuration. [testng] [2025-03-07 01:34:01,844] [pool-1-thread-10] Initializing /data/achim/003003000.flex: [testng] 01:34:01,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:34:01,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:01,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-07_01-34-01.log] [testng] 01:34:01,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60d9f6d0 - End of configuration. [testng] [2025-03-07 01:34:03,590] [pool-1-thread-9] Initializing /data/tony/test.tiff: [testng] 01:34:03,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:34:03,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:03,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-07_01-34-03.log] [testng] 01:34:03,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18fd55db - End of configuration. [testng] [2025-03-07 01:34:07,054] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:34:07,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:34:07,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:07,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-07_01-34-07.log] [testng] 01:34:07,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2422e094 - End of configuration. [testng] [2025-03-07 01:34:19,819] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:34:19,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:34:19,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:19,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-07_01-34-19.log] [testng] 01:34:19,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437a0520 - End of configuration. [testng] [2025-03-07 01:34:23,094] [pool-1-thread-6] Initializing /data/anatole/001004000.flex: [testng] 01:34:23,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:34:23,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:23,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-07_01-34-23.log] [testng] 01:34:23,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3895890b - End of configuration. [testng] [2025-03-07 01:34:25,229] [pool-1-thread-5] Initializing /data/stephane/002007000.flex: [testng] 01:34:25,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:34:25,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:25,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-07_01-34-25.log] [testng] 01:34:25,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@575729e - End of configuration. [testng] [2025-03-07 01:34:27,108] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 01:34:27,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:34:27,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:27,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-07_01-34-27.log] [testng] 01:34:27,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bd47444 - End of configuration. [testng] [2025-03-07 01:34:28,839] [pool-1-thread-3] Initializing /data/stephane/006013000.flex: [testng] 01:34:28,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:34:28,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:28,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-07_01-34-28.log] [testng] 01:34:28,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1710bb35 - End of configuration. [testng] [2025-03-07 01:34:30,537] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:34:30,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:34:30,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:30,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-07_01-34-30.log] [testng] 01:34:30,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@641933db - End of configuration. [testng] [2025-03-07 01:34:52,664] [pool-1-thread-7] Initializing /data/manuel/003003001.flex: [testng] [2025-03-07 01:34:54,440] [pool-1-thread-9] Initializing /data/tony/003003000.tiff: [testng] [2025-03-07 01:34:58,162] [pool-1-thread-11] Initializing /data/tamjid/006005000.flex: [testng] [2025-03-07 01:34:59,934] [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] [2025-03-07 01:35:12,258] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-03-07 01:35:29,966] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-03-07 01:35:32,394] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] [2025-03-07 01:35:40,202] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] [2025-03-07 01:35:47,621] [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] [2025-03-07 01:35:51,967] [pool-1-thread-6] Initializing /data/tony/003008000.flex: [testng] [2025-03-07 01:35:54,770] [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] [2025-03-07 01:36:02,358] [pool-1-thread-12] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-03-07 01:36:07,135] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2025-03-07 01:36:11,907] [pool-1-thread-3] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-03-07 01:36:14,346] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-03-07 01:36:37,504] [pool-1-thread-4] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-03-07 01:36:39,865] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-03-07 01:37:12,319] [pool-1-thread-5] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-03-07 01:37:32,347] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-03-07 01:37:38,427] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2025-03-07 01:37:41,707] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2025-03-07 01:38:04,831] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-03-07 01:38:16,695] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-03-07 01:38:35,878] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-03-07 01:39:08,257] [pool-1-thread-11] Initializing /data/qa-2983/004007000.flex: [testng] [2025-03-07 01:39:11,252] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2025-03-07 01:39:26,674] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] [2025-03-07 01:39:41,226] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex: [testng] [2025-03-07 01:39:43,525] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] [2025-03-07 01:39:59,121] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 34 minutes 52 seconds Finished: SUCCESS