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Started by upstream project "BIOFORMATS-test-repo" build number 281 originally caused by: Started by upstream project "Trigger" build number 301 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins4508879832054231122.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44303_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 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] 00:36:00,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:00,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:36:00,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:00,531 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:00,531 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:00,532 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:00,532 |-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] 00:36:00,532 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:00,532 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:00,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:00,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:00,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:00,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:00,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:00,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:00,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:00,789 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:00,789 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:00,789 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:00,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:00,790 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:36:00,790 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:36:00,791 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 00:36:00,800] [main] java.version = 1.8.0_342 [testng] 00:36:00,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:00,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:00,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_00-36-00.log] [testng] 00:36:00,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 00:36:00,868] [main] testng.directory = /data [testng] [2024-12-06 00:36:00,868] [main] testng.configDirectory = /config [testng] [2024-12-06 00:36:00,887] [main] testng.multiplier = 1.0 [testng] [2024-12-06 00:36:00,887] [main] testng.in-memory = false [testng] [2024-12-06 00:36:00,887] [main] testng.allow-missing = false [testng] [2024-12-06 00:36:00,887] [main] user.language = en [testng] [2024-12-06 00:36:00,887] [main] user.country = ${user.country} [testng] [2024-12-06 00:36:00,888] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 00:36:31,050] [main] ---------------------------------------- [testng] [2024-12-06 00:36:31,050] [main] Total files: 164 [testng] [2024-12-06 00:36:31,051] [main] Scan time: 30.162 s (183 ms/file) [testng] [2024-12-06 00:36:31,051] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 00:37:45,010] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:37:45,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:37:45,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:45,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_00-37-45.log] [testng] 00:37:45,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@602a8caf - End of configuration. [testng] [2024-12-06 00:37:46,350] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:37:46,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:37:46,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:46,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_00-37-46.log] [testng] 00:37:46,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e6d141a - End of configuration. [testng] [2024-12-06 00:37:46,539] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:37:46,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:37:46,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:46,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_00-37-46.log] [testng] 00:37:46,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52c085b1 - End of configuration. [testng] [2024-12-06 00:37:47,394] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:37:47,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:37:47,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:47,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_00-37-47.log] [testng] 00:37:47,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@97dae36 - End of configuration. [testng] [2024-12-06 00:37:48,174] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 00:37:48,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:37:48,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:48,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_00-37-48.log] [testng] 00:37:48,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d46184e - End of configuration. [testng] [2024-12-06 00:37:50,697] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:37:50,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:37:50,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:50,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_00-37-50.log] [testng] 00:37:50,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5790e2a5 - End of configuration. [testng] [2024-12-06 00:37:50,791] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 00:37:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:37:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:50,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_00-37-50.log] [testng] 00:37:50,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bf506d1 - End of configuration. [testng] [2024-12-06 00:37:51,412] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 00:37:51,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:37:51,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:51,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_00-37-51.log] [testng] 00:37:51,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@122c6b61 - End of configuration. [testng] [2024-12-06 00:37:51,540] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:37:51,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:37:51,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:51,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_00-37-51.log] [testng] 00:37:51,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a45989e - End of configuration. [testng] [2024-12-06 00:37:51,945] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 00:37:51,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:37:51,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:51,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_00-37-51.log] [testng] 00:37:51,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22e730c9 - End of configuration. [testng] [2024-12-06 00:37:51,994] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 00:37:51,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:37:51,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:51,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_00-37-51.log] [testng] 00:37:51,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a987c78 - End of configuration. [testng] [2024-12-06 00:37:52,886] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:37:52,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:37:52,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:52,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_00-37-52.log] [testng] 00:37:52,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1952b94f - End of configuration. [testng] [2024-12-06 00:37:56,635] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-12-06 00:37:57,065] [pool-1-thread-6] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-06 00:37:57,295] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-06 00:37:57,432] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-06 00:37:58,770] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-06 00:37:59,670] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-06 00:38:01,421] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-06 00:38:07,200] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-06 00:38:07,773] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-06 00:38:08,700] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-06 00:38:08,830] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-06 00:38:10,374] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-06 00:38:10,552] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-06 00:38:11,047] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-06 00:38:12,600] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-06 00:38:12,907] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-06 00:38:13,519] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-06 00:38:13,841] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-06 00:38:15,114] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-06 00:38:16,937] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-06 00:38:17,212] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-06 00:38:17,711] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-06 00:38:18,035] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-06 00:38:18,255] [pool-1-thread-8] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-06 00:38:19,407] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-06 00:38:20,218] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-06 00:38:20,680] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-06 00:38:22,361] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-06 00:38:23,717] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-06 00:38:24,223] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-06 00:38:25,672] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-06 00:38:25,811] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-06 00:38:26,870] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-06 00:38:26,969] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-06 00:38:27,332] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-06 00:38:30,303] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-06 00:38:30,416] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-06 00:38:32,702] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-06 00:38:59,397] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-06 00:39:00,051] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-06 00:39:00,808] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-06 00:39:01,458] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-06 00:39:04,596] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-06 00:39:05,086] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-06 00:39:05,216] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-06 00:39:09,394] [pool-1-thread-8] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-06 00:39:10,919] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [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 53 seconds Finished: SUCCESS