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Started by upstream project "BIOFORMATS-test-repo" build number 219 originally caused by: Started by upstream project "Trigger" build number 246 originally caused by: Started by timer 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/jenkins6355438709390327060.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34726_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:36:28,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:28,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:36:28,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:28,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:28,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:28,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:28,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:28,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:28,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:28,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:28,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:28,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:28,398 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:28,398 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:28,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:28,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:28,399 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:36:28,400 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:36:28,400 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-13 01:36:28,408] [main] java.version = 17.0.2 [testng] 01:36:28,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:28,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:28,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_01-36-28.log] [testng] 01:36:28,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-13 01:36:28,453] [main] testng.directory = /data [testng] [2024-10-13 01:36:28,453] [main] testng.configDirectory = /config [testng] [2024-10-13 01:36:28,461] [main] testng.multiplier = 1.0 [testng] [2024-10-13 01:36:28,462] [main] testng.in-memory = false [testng] [2024-10-13 01:36:28,462] [main] testng.allow-missing = false [testng] [2024-10-13 01:36:28,462] [main] user.language = en [testng] [2024-10-13 01:36:28,463] [main] user.country = ${user.country} [testng] [2024-10-13 01:36:28,463] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-13 01:37:33,535] [main] ---------------------------------------- [testng] [2024-10-13 01:37:33,535] [main] Total files: 164 [testng] [2024-10-13 01:37:33,535] [main] Scan time: 65.072 s (396 ms/file) [testng] [2024-10-13 01:37:33,535] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-13 01:38:59,178] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 01:38:59,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:38:59,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:59,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-13_01-38-59.log] [testng] 01:38:59,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@128e22ca - End of configuration. [testng] [2024-10-13 01:39:00,093] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 01:39:00,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:39:00,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:00,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-13_01-39-00.log] [testng] 01:39:00,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5952fd83 - End of configuration. [testng] [2024-10-13 01:39:00,519] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:39:00,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:39:00,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:00,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-13_01-39-00.log] [testng] 01:39:00,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c88ec - End of configuration. [testng] [2024-10-13 01:39:01,162] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:39:01,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:39:01,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:01,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-13_01-39-01.log] [testng] 01:39:01,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f33c897 - End of configuration. [testng] [2024-10-13 01:39:01,367] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 01:39:01,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:39:01,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:01,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-13_01-39-01.log] [testng] 01:39:01,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2eaf4 - End of configuration. [testng] [2024-10-13 01:39:01,455] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 01:39:01,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:39:01,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:01,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-13_01-39-01.log] [testng] 01:39:01,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4922ba - End of configuration. [testng] [2024-10-13 01:39:01,539] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:39:01,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:39:01,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:01,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-13_01-39-01.log] [testng] 01:39:01,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration. [testng] [2024-10-13 01:39:01,853] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 01:39:01,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:39:01,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:01,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-13_01-39-01.log] [testng] 01:39:01,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1a1e58 - End of configuration. [testng] [2024-10-13 01:39:02,230] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:39:02,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:39:02,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:02,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-13_01-39-02.log] [testng] 01:39:02,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5e1c72 - End of configuration. [testng] [2024-10-13 01:39:02,838] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:39:02,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:39:02,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:02,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-13_01-39-02.log] [testng] 01:39:02,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8a5b823 - End of configuration. [testng] [2024-10-13 01:39:02,951] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 01:39:02,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:39:02,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:02,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-13_01-39-02.log] [testng] 01:39:02,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25904576 - End of configuration. [testng] [2024-10-13 01:39:03,809] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 01:39:03,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:39:03,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:03,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-13_01-39-03.log] [testng] 01:39:03,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6732c8bc - End of configuration. [testng] [2024-10-13 01:39:07,531] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-13 01:39:07,628] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-13 01:39:07,860] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-13 01:39:08,364] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-13 01:39:08,869] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-13 01:39:09,421] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-13 01:39:10,068] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-13 01:39:10,142] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-13 01:39:11,000] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-13 01:39:11,132] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-13 01:39:11,897] [pool-1-thread-1] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-13 01:39:12,337] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-13 01:39:12,907] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-13 01:39:13,618] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-13 01:39:14,293] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-13 01:39:15,807] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-13 01:39:15,929] [pool-1-thread-8] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-13 01:39:16,428] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-13 01:39:16,555] [pool-1-thread-9] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-13 01:39:17,028] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-13 01:39:17,571] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-13 01:39:17,700] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-10-13 01:39:18,276] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-13 01:39:20,146] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-13 01:39:21,001] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-13 01:39:21,356] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-13 01:39:21,520] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-13 01:39:21,780] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-13 01:39:21,916] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-13 01:39:23,482] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-13 01:39:24,589] [pool-1-thread-12] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-13 01:39:25,040] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-13 01:39:41,646] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-13 01:39:42,292] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-13 01:39:42,562] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-10-13 01:39:45,928] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-13 01:39:46,114] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-13 01:39:47,562] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-13 01:39:50,423] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-13 01:39:51,893] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-13 01:39:52,430] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-13 01:40:04,447] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-13 01:40:05,463] [pool-1-thread-1] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-13 01:40:07,437] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-13 01:40:07,579] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-13 01:40:07,829] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-13 01:40:08,735] [pool-1-thread-1] 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: 5 minutes 17 seconds Finished: SUCCESS