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Started by upstream project "BIOFORMATS-test-repo" build number 202 originally caused by: Started by upstream project "Trigger" build number 228 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/jenkins2688872446991140835.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_31999_merge_ci -v /uod/idr/repos/curated/perkinelmer-operetta:/data -v /uod/idr-scratch/merge-ci/curated/perkinelmer-operetta:/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] 05:39:07,487 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:39:07,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 05:39:07,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:39:07,490 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:39:07,490 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:39:07,490 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:39:07,490 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:39:07,490 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:39:07,491 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:39:07,491 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:39:07,491 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:39:07,491 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:39:07,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:39:07,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:39:07,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:39:07,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:39:07,776 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:39:07,777 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:39:07,777 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:39:07,777 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:39:07,778 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 05:39:07,779 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 05:39:07,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 288 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-27 05:39:07,792] [main] java.version = 1.8.0_342 [testng] 05:39:07,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:39:07,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:39:07,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-27_05-39-07.log] [testng] 05:39:07,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-09-27 05:39:07,852] [main] testng.directory = /data [testng] [2024-09-27 05:39:07,852] [main] testng.configDirectory = /config [testng] [2024-09-27 05:39:07,865] [main] testng.multiplier = 1.0 [testng] [2024-09-27 05:39:07,865] [main] testng.in-memory = false [testng] [2024-09-27 05:39:07,865] [main] testng.allow-missing = false [testng] [2024-09-27 05:39:07,865] [main] user.language = en [testng] [2024-09-27 05:39:07,865] [main] user.country = ${user.country} [testng] [2024-09-27 05:39:07,865] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-09-27 05:45:42,742] [main] ---------------------------------------- [testng] [2024-09-27 05:45:42,742] [main] Total files: 14663 [testng] [2024-09-27 05:45:42,743] [main] Scan time: 394.877 s (26 ms/file) [testng] [2024-09-27 05:45:42,743] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 16 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-27 05:48:58,511] [pool-1-thread-1] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 05:48:58,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:48:58,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:58,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-27_05-48-58.log] [testng] 05:48:58,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a3fe0de - End of configuration. [testng] [2024-09-27 05:48:58,591] [pool-1-thread-12] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 05:48:58,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:48:58,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:58,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-27_05-48-58.log] [testng] 05:48:58,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a567a6 - End of configuration. [testng] [2024-09-27 05:48:58,602] [pool-1-thread-11] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 05:48:58,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:48:58,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:58,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-27_05-48-58.log] [testng] 05:48:58,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f442e7 - End of configuration. [testng] [2024-09-27 05:48:58,970] [pool-1-thread-10] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 05:48:58,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:48:58,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:58,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-27_05-48-58.log] [testng] 05:48:58,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56e81967 - End of configuration. [testng] [2024-09-27 05:48:59,370] [pool-1-thread-9] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 05:48:59,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:48:59,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:59,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-27_05-48-59.log] [testng] 05:48:59,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f7f8593 - End of configuration. [testng] [2024-09-27 05:48:59,919] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 05:48:59,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:48:59,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:59,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-27_05-48-59.log] [testng] 05:48:59,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ce73149 - End of configuration. [testng] [2024-09-27 05:49:00,968] [pool-1-thread-7] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 05:49:00,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:49:00,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:00,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-27_05-49-00.log] [testng] 05:49:00,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57426f53 - End of configuration. [testng] [2024-09-27 05:49:02,672] [pool-1-thread-6] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 05:49:02,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:49:02,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:02,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-27_05-49-02.log] [testng] 05:49:02,673 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65399f6b - End of configuration. [testng] [2024-09-27 05:49:02,774] [pool-1-thread-5] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 05:49:02,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:49:02,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:02,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-27_05-49-02.log] [testng] 05:49:02,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79548bee - End of configuration. [testng] [2024-09-27 05:49:03,291] [pool-1-thread-4] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 05:49:03,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:49:03,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:03,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-27_05-49-03.log] [testng] 05:49:03,292 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bd9fc94 - End of configuration. [testng] [2024-09-27 05:49:03,361] [pool-1-thread-3] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 05:49:03,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:49:03,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:03,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-27_05-49-03.log] [testng] 05:49:03,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e056100 - End of configuration. [testng] [2024-09-27 05:49:03,506] [pool-1-thread-2] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 05:49:03,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:49:03,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:03,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-27_05-49-03.log] [testng] 05:49:03,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dea92f7 - End of configuration. [testng] [2024-09-27 05:49:05,575] [pool-1-thread-12] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-09-27 05:49:07,168] [pool-1-thread-4] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] [2024-09-27 05:49:17,270] [pool-1-thread-1] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] [2024-09-27 05:49:34,365] [pool-1-thread-11] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 07:37:32,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:37:32,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:37:32,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-27_07-37-32.log] [testng] 07:37:32,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48d5db53 - End of configuration. [testng] 07:47:02,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:47:02,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:47:02,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-27_07-47-02.log] [testng] 07:47:02,629 |-INFO in ch.qos.logback.core.sift.SiftProcessor@627a0318 - End of configuration. [testng] 07:47:02,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:47:02,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:47:02,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-27_07-47-02.log] [testng] 07:47:02,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75ed8fd1 - End of configuration. [testng] 07:47:28,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:47:28,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:47:28,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-27_07-47-28.log] [testng] 07:47:28,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d7f57f4 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 848, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 128 minutes 24 seconds Finished: SUCCESS