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Started by upstream project "BIOFORMATS-test-repo" build number 267 originally caused by: Started by upstream project "Trigger" build number 290 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins2500265157968789007.sh + '[' samples = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_42134_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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] 00:40:08,731 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:40:08,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:40:08,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:40:08,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:40:08,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:40:08,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:40:08,734 |-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] 00:40:08,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:40:08,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:40:08,734 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:40:08,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:40:08,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:40:08,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:40:08,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:40:08,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:40:08,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:40:08,983 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:40:08,983 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:40:08,984 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:40:08,984 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:40:08,984 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:40:08,985 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:40:08,985 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-25 00:40:08,994] [main] java.version = 1.8.0_342 [testng] 00:40:08,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:40:08,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:09,041 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-25_00-40-09.log] [testng] 00:40:09,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-25 00:40:09,044] [main] testng.directory = /data [testng] [2024-11-25 00:40:09,045] [main] testng.configDirectory = /config [testng] [2024-11-25 00:40:09,057] [main] testng.multiplier = 1.0 [testng] [2024-11-25 00:40:09,057] [main] testng.in-memory = false [testng] [2024-11-25 00:40:09,057] [main] testng.allow-missing = false [testng] [2024-11-25 00:40:09,057] [main] user.language = fr [testng] [2024-11-25 00:40:09,057] [main] user.country = FR [testng] [2024-11-25 00:40:09,057] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-25 00:41:00,014] [main] ---------------------------------------- [testng] [2024-11-25 00:41:00,014] [main] Total files: 164 [testng] [2024-11-25 00:41:00,014] [main] Scan time: 50.957 s (310 ms/file) [testng] [2024-11-25 00:41:00,014] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-25 00:42:11,803] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:42:11,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:11,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:11,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-25_00-42-11.log] [testng] 00:42:11,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49071957 - End of configuration. [testng] [2024-11-25 00:42:12,105] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:42:12,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:42:12,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:12,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-25_00-42-12.log] [testng] 00:42:12,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5405236 - End of configuration. [testng] [2024-11-25 00:42:12,540] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:42:12,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:42:12,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:12,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-25_00-42-12.log] [testng] 00:42:12,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10a3be7f - End of configuration. [testng] [2024-11-25 00:42:12,941] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:42:12,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:42:12,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:12,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-25_00-42-12.log] [testng] 00:42:12,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49e4c5ff - End of configuration. [testng] [2024-11-25 00:42:13,523] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:42:13,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:42:13,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:13,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-25_00-42-13.log] [testng] 00:42:13,525 |-INFO in ch.qos.logback.core.sift.SiftProcessor@243d8f2a - End of configuration. [testng] [2024-11-25 00:42:13,974] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:42:13,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:42:13,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:13,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-25_00-42-13.log] [testng] 00:42:13,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@410bb8e3 - End of configuration. [testng] [2024-11-25 00:42:14,399] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 00:42:14,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:42:14,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:14,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-25_00-42-14.log] [testng] 00:42:14,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b93df8f - End of configuration. [testng] [2024-11-25 00:42:14,479] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 00:42:14,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:42:14,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:14,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-25_00-42-14.log] [testng] 00:42:14,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ed3807 - End of configuration. [testng] [2024-11-25 00:42:36,842] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 00:42:36,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:42:36,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:36,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-25_00-42-36.log] [testng] 00:42:36,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b1df125 - End of configuration. [testng] [2024-11-25 00:42:37,831] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 00:42:37,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:42:37,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:37,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-25_00-42-37.log] [testng] 00:42:37,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70b7ee5c - End of configuration. [testng] [2024-11-25 00:42:38,002] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:42:38,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:42:38,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:38,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-25_00-42-38.log] [testng] 00:42:38,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62fc8b60 - End of configuration. [testng] [2024-11-25 00:42:38,106] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:42:38,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:42:38,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:38,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-25_00-42-38.log] [testng] 00:42:38,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63df2aef - End of configuration. [testng] [2024-11-25 00:42:42,624] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-25 00:42:42,992] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-25 00:42:43,096] [pool-1-thread-3] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-25 00:42:43,653] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-25 00:42:43,957] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-25 00:42:44,396] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-25 00:42:45,416] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-25 00:42:46,265] [pool-1-thread-7] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-25 00:42:47,419] [pool-1-thread-1] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-25 00:42:48,037] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-25 00:42:48,531] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-11-25 00:42:49,978] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-25 00:42:51,562] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-25 00:42:52,262] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-25 00:42:52,949] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] [2024-11-25 00:42:53,565] [pool-1-thread-3] Initializing /data/ome/embryo.lsm: [testng] [2024-11-25 00:42:55,753] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-11-25 00:42:57,579] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-25 00:42:58,921] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-25 00:42:59,443] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-25 00:43:00,252] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-25 00:43:00,683] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-11-25 00:43:01,530] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-25 00:43:01,944] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-25 00:43:02,587] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-25 00:43:03,985] [pool-1-thread-1] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-25 00:43:05,132] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-25 00:43:05,742] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-25 00:43:06,028] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-25 00:43:06,412] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-25 00:43:07,125] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-25 00:43:07,652] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-25 00:43:07,769] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-25 00:43:09,291] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-25 00:43:10,081] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-25 00:43:10,288] [pool-1-thread-10] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-25 00:43:11,759] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-25 00:43:12,666] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-25 00:43:13,376] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-25 00:43:14,506] [pool-1-thread-1] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-25 00:43:20,565] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-25 00:43:21,729] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-25 00:43:21,899] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-25 00:43:23,261] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-25 00:43:23,374] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-25 00:43:25,737] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-25 00:43:26,302] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 34 seconds Finished: SUCCESS