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Started by upstream project "BIOFORMATS-test-repo" build number 300 originally caused by: Started by upstream project "Trigger" build number 322 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins12025764009543010257.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47455_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] 00:59:25,664 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:59:25,666 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:59:25,666 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:59:25,668 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:59:25,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:59:25,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:59:25,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:59:25,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:59:25,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:59:25,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:59:25,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:59:25,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:59:25,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:59:25,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:59:25,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:59:25,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:59:25,964 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:59:25,964 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:59:25,965 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:59:25,965 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:59:25,965 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:59:25,966 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:59:25,966 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 297 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-27 00:59:25,976] [main] java.version = 1.8.0_342 [testng] 00:59:25,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:59:25,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:59:26,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_00-59-25.log] [testng] 00:59:26,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-27 00:59:26,031] [main] testng.directory = /data [testng] [2024-12-27 00:59:26,032] [main] testng.configDirectory = /config [testng] [2024-12-27 00:59:26,044] [main] testng.multiplier = 1.0 [testng] [2024-12-27 00:59:26,044] [main] testng.in-memory = false [testng] [2024-12-27 00:59:26,044] [main] testng.allow-missing = false [testng] [2024-12-27 00:59:26,044] [main] user.language = en [testng] [2024-12-27 00:59:26,044] [main] user.country = ${user.country} [testng] [2024-12-27 00:59:26,045] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-27 01:00:32,015] [main] ---------------------------------------- [testng] [2024-12-27 01:00:32,015] [main] Total files: 791 [testng] [2024-12-27 01:00:32,015] [main] Scan time: 65.97 s (83 ms/file) [testng] [2024-12-27 01:00:32,015] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-27 01:07:34,650] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:07:34,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:07:34,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:34,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-27_01-07-34.log] [testng] 01:07:34,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fc89ccd - End of configuration. [testng] [2024-12-27 01:07:36,104] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:07:36,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:07:36,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:36,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-27_01-07-36.log] [testng] 01:07:36,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ef665b1 - End of configuration. [testng] [2024-12-27 01:07:37,509] [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] 01:07:37,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:07:37,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:37,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-27_01-07-37.log] [testng] 01:07:37,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f416a94 - End of configuration. [testng] [2024-12-27 01:07:38,573] [pool-1-thread-10] Initializing /data/qa-2983/004007000.flex: [testng] 01:07:38,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:07:38,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:38,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-27_01-07-38.log] [testng] 01:07:38,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cfe2cdd - End of configuration. [testng] [2024-12-27 01:07:39,583] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] 01:07:39,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:07:39,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:39,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_01-07-39.log] [testng] 01:07:39,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd892e8 - End of configuration. [testng] [2024-12-27 01:07:40,675] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:07:40,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:07:40,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:40,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-27_01-07-40.log] [testng] 01:07:40,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c0b0465 - End of configuration. [testng] [2024-12-27 01:07:50,839] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] 01:07:50,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:07:50,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:50,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-27_01-07-50.log] [testng] 01:07:50,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42e829aa - End of configuration. [testng] [2024-12-27 01:07:52,303] [pool-1-thread-6] Initializing /data/manuel/003003001.flex: [testng] 01:07:52,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:07:52,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:52,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_01-07-52.log] [testng] 01:07:52,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@732b2eff - End of configuration. [testng] [2024-12-27 01:07:53,331] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:07:53,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:07:53,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:53,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_01-07-53.log] [testng] 01:07:53,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6725ca8c - End of configuration. [testng] [2024-12-27 01:08:03,026] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] 01:08:03,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:08:03,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:03,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-27_01-08-03.log] [testng] 01:08:03,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e9c2fd0 - End of configuration. [testng] [2024-12-27 01:08:05,340] [pool-1-thread-3] Initializing /data/tamjid/006005000.flex: [testng] 01:08:05,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:08:05,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:05,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-27_01-08-05.log] [testng] 01:08:05,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5066403c - End of configuration. [testng] [2024-12-27 01:08:06,597] [pool-1-thread-2] Initializing /data/tony/003003000.tiff: [testng] 01:08:06,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:08:06,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:06,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-27_01-08-06.log] [testng] 01:08:06,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50fa8e20 - End of configuration. [testng] [2024-12-27 01:08:27,003] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] [2024-12-27 01:08:28,106] [pool-1-thread-2] Initializing /data/qa-17190/002002011.flex: [testng] [2024-12-27 01:08:29,259] [pool-1-thread-7] Initializing /data/anatole/001004000.flex: [testng] [2024-12-27 01:08:30,721] [pool-1-thread-10] Initializing /data/tony/test1.flex: [testng] [2024-12-27 01:08:31,937] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-12-27 01:08:40,593] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-12-27 01:08:43,637] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-27 01:08:52,774] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [2024-12-27 01:08:57,142] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-12-27 01:08:58,392] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-12-27 01:09:01,054] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-27 01:09:02,510] [pool-1-thread-6] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-12-27 01:09:11,655] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-27 01:09:20,867] [pool-1-thread-9] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-12-27 01:09:29,569] [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] [2024-12-27 01:09:31,582] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-27 01:09:36,502] [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] [2024-12-27 01:09:37,867] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-27 01:09:39,271] [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] [2024-12-27 01:09:41,274] [pool-1-thread-9] Initializing /data/achim/003003000.flex: [testng] [2024-12-27 01:09:45,268] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-12-27 01:10:02,553] [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] [2024-12-27 01:10:05,823] [pool-1-thread-2] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-27 01:10:11,229] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-27 01:10:25,114] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-27 01:11:08,979] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-27 01:11:11,700] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-12-27 01:11:31,178] [pool-1-thread-2] Initializing /data/stephane/006013000.flex: [testng] [2024-12-27 01:11:34,090] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-27 01:11:39,618] [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: 23 minutes 23 seconds Finished: SUCCESS