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Started by upstream project "BIOFORMATS-test-repo" build number 365 originally caused by: Started by upstream project "Trigger" build number 391 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins8603526046904388453.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58158_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] 00:32:45,493 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:32:45,494 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:32:45,494 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:45,495 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:45,497 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:45,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:32:45,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:32:45,498 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:32:45,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:32:45,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:32:45,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:32:45,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:32:45,690 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:32:45,690 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:32:45,690 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:32:45,691 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:32:45,691 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:32:45,692 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:32:45,692 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-05 00:32:45,701] [main] java.version = 17.0.2 [testng] 00:32:45,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:32:45,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:45,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_00-32-45.log] [testng] 00:32:45,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-05 00:32:45,748] [main] testng.directory = /data [testng] [2025-03-05 00:32:45,748] [main] testng.configDirectory = /config [testng] [2025-03-05 00:32:45,757] [main] testng.multiplier = 1.0 [testng] [2025-03-05 00:32:45,757] [main] testng.in-memory = false [testng] [2025-03-05 00:32:45,758] [main] testng.allow-missing = false [testng] [2025-03-05 00:32:45,758] [main] user.language = en [testng] [2025-03-05 00:32:45,758] [main] user.country = ${user.country} [testng] [2025-03-05 00:32:45,758] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-05 00:33:28,578] [main] ---------------------------------------- [testng] [2025-03-05 00:33:28,578] [main] Total files: 164 [testng] [2025-03-05 00:33:28,579] [main] Scan time: 42.82 s (261 ms/file) [testng] [2025-03-05 00:33:28,579] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-05 00:34:13,261] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:34:13,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:13,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:13,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_00-34-13.log] [testng] 00:34:13,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460b4533 - End of configuration. [testng] [2025-03-05 00:34:14,054] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:34:14,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:14,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:14,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_00-34-14.log] [testng] 00:34:14,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a5b45 - End of configuration. [testng] [2025-03-05 00:34:14,101] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:34:14,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:14,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:14,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_00-34-14.log] [testng] 00:34:14,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c1bf6dd - End of configuration. [testng] [2025-03-05 00:34:14,199] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] 00:34:14,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:14,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:14,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_00-34-14.log] [testng] 00:34:14,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f4cc7aa - End of configuration. [testng] [2025-03-05 00:34:17,625] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] 00:34:17,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:17,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:17,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_00-34-17.log] [testng] 00:34:17,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1c8076 - End of configuration. [testng] [2025-03-05 00:34:17,694] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] 00:34:17,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:17,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:17,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_00-34-17.log] [testng] 00:34:17,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e10020f - End of configuration. [testng] [2025-03-05 00:34:17,841] [pool-1-thread-7] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:34:17,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:17,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:17,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_00-34-17.log] [testng] 00:34:17,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39b57268 - End of configuration. [testng] [2025-03-05 00:34:18,924] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] 00:34:18,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:18,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:18,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_00-34-18.log] [testng] 00:34:18,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60240f0b - End of configuration. [testng] [2025-03-05 00:34:19,392] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:34:19,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:19,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:19,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_00-34-19.log] [testng] 00:34:19,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6703580a - End of configuration. [testng] [2025-03-05 00:34:19,473] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:34:19,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:19,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:19,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_00-34-19.log] [testng] 00:34:19,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55b7c62c - End of configuration. [testng] [2025-03-05 00:34:20,263] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:34:20,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:20,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:20,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_00-34-20.log] [testng] 00:34:20,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166a90ed - End of configuration. [testng] [2025-03-05 00:34:21,315] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] 00:34:21,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:21,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:21,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_00-34-21.log] [testng] 00:34:21,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration. [testng] [2025-03-05 00:34:24,325] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2025-03-05 00:34:24,879] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-03-05 00:34:24,969] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-03-05 00:34:25,042] [pool-1-thread-11] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-05 00:34:26,420] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-05 00:34:27,603] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-05 00:34:27,773] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-05 00:34:28,827] [pool-1-thread-12] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-03-05 00:34:29,731] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-05 00:34:30,127] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-03-05 00:34:31,301] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-03-05 00:34:31,579] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-03-05 00:34:32,069] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-05 00:34:32,173] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-05 00:34:32,734] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-05 00:34:33,855] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-03-05 00:34:33,996] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-05 00:34:34,481] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-05 00:34:34,593] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-05 00:34:35,428] [pool-1-thread-4] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-05 00:34:35,899] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] [2025-03-05 00:34:36,864] [pool-1-thread-5] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-03-05 00:34:37,192] [pool-1-thread-11] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-05 00:34:38,068] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-03-05 00:34:38,665] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-05 00:34:57,691] [pool-1-thread-7] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-03-05 00:34:58,033] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-03-05 00:34:58,320] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-05 00:34:58,480] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-03-05 00:34:58,967] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-05 00:34:59,576] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-03-05 00:35:00,602] [pool-1-thread-3] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-03-05 00:35:01,013] [pool-1-thread-9] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-05 00:35:01,547] [pool-1-thread-7] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-05 00:35:01,877] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2025-03-05 00:35:02,435] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-05 00:35:03,587] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-05 00:35:04,240] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2025-03-05 00:35:04,572] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2025-03-05 00:35:05,650] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-05 00:35:06,180] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-03-05 00:35:06,999] [pool-1-thread-7] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-05 00:35:08,169] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-05 00:35:08,397] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-03-05 00:35:08,597] [pool-1-thread-9] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-03-05 00:35:09,199] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-03-05 00:35:10,538] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 54 seconds Finished: SUCCESS