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Started by upstream project "BIOFORMATS-test-repo" build number 312 originally caused by: Started by upstream project "Trigger" build number 334 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/jenkins10692820125655677331.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49408_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] 00:36:01,461 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:01,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:36:01,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:01,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:01,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:01,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:01,464 |-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] 00:36:01,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:01,465 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:01,465 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:01,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:01,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:01,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:01,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:01,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:01,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:01,648 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:01,648 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:01,648 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:01,648 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:01,648 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:36:01,649 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:36:01,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 184 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-08 00:36:01,657] [main] java.version = 17.0.2 [testng] 00:36:01,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:01,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:01,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-08_00-36-01.log] [testng] 00:36:01,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-08 00:36:01,703] [main] testng.directory = /data [testng] [2025-01-08 00:36:01,703] [main] testng.configDirectory = /config [testng] [2025-01-08 00:36:01,711] [main] testng.multiplier = 1.0 [testng] [2025-01-08 00:36:01,711] [main] testng.in-memory = false [testng] [2025-01-08 00:36:01,712] [main] testng.allow-missing = false [testng] [2025-01-08 00:36:01,712] [main] user.language = en [testng] [2025-01-08 00:36:01,712] [main] user.country = ${user.country} [testng] [2025-01-08 00:36:01,712] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-08 00:36:33,257] [main] ---------------------------------------- [testng] [2025-01-08 00:36:33,257] [main] Total files: 164 [testng] [2025-01-08 00:36:33,257] [main] Scan time: 31.545 s (192 ms/file) [testng] [2025-01-08 00:36:33,257] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-08 00:37:12,951] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:37:12,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:37:12,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:12,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-08_00-37-12.log] [testng] 00:37:12,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70d4d074 - End of configuration. [testng] [2025-01-08 00:37:13,118] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:37:13,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:37:13,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-08_00-37-13.log] [testng] 00:37:13,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@270e6730 - End of configuration. [testng] [2025-01-08 00:37:13,263] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] 00:37:13,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:37:13,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-08_00-37-13.log] [testng] 00:37:13,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@407a49f9 - End of configuration. [testng] [2025-01-08 00:37:13,453] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:37:13,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:37:13,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-08_00-37-13.log] [testng] 00:37:13,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4a1534 - End of configuration. [testng] [2025-01-08 00:37:13,490] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:37:13,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:37:13,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-08_00-37-13.log] [testng] 00:37:13,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a262677 - End of configuration. [testng] [2025-01-08 00:37:13,520] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:37:13,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:37:13,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-08_00-37-13.log] [testng] 00:37:13,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8837219 - End of configuration. [testng] [2025-01-08 00:37:13,547] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:37:13,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:37:13,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-08_00-37-13.log] [testng] 00:37:13,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@232b079f - End of configuration. [testng] [2025-01-08 00:37:13,937] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:37:13,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:37:13,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:13,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-08_00-37-13.log] [testng] 00:37:13,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6543fac1 - End of configuration. [testng] [2025-01-08 00:37:14,114] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:37:14,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:37:14,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:14,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-08_00-37-14.log] [testng] 00:37:14,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3974bf28 - End of configuration. [testng] [2025-01-08 00:37:14,523] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] 00:37:14,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:37:14,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:14,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-08_00-37-14.log] [testng] 00:37:14,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@685b77b6 - End of configuration. [testng] [2025-01-08 00:37:16,774] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:37:16,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:37:16,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:16,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-08_00-37-16.log] [testng] 00:37:16,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18eff806 - End of configuration. [testng] [2025-01-08 00:37:17,195] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:37:17,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:37:17,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:17,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-08_00-37-17.log] [testng] 00:37:17,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aca4c51 - End of configuration. [testng] [2025-01-08 00:37:20,102] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-01-08 00:37:20,225] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-01-08 00:37:21,053] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-01-08 00:37:22,434] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-01-08 00:37:22,940] [pool-1-thread-1] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-01-08 00:37:23,328] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-01-08 00:37:24,796] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-01-08 00:37:24,889] [pool-1-thread-12] Initializing /data/ome/embryo.lsm: [testng] [2025-01-08 00:37:25,882] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-01-08 00:37:26,173] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-01-08 00:37:26,680] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-01-08 00:37:27,684] [pool-1-thread-8] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-01-08 00:37:28,096] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-01-08 00:37:28,918] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-01-08 00:37:30,189] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2025-01-08 00:37:30,240] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2025-01-08 00:37:30,300] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-01-08 00:37:30,356] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-01-08 00:37:31,068] [pool-1-thread-5] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-01-08 00:37:31,587] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-01-08 00:37:31,663] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-01-08 00:37:32,541] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-01-08 00:37:32,821] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-01-08 00:37:33,128] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-01-08 00:37:33,633] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2025-01-08 00:37:33,774] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2025-01-08 00:37:34,128] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-01-08 00:37:34,806] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-01-08 00:37:35,462] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-01-08 00:37:35,639] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-01-08 00:37:35,756] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-01-08 00:37:36,199] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-01-08 00:37:46,988] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] [2025-01-08 00:37:48,295] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-01-08 00:37:48,664] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-01-08 00:37:49,230] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-01-08 00:37:49,660] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-01-08 00:37:49,752] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-01-08 00:37:50,126] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-01-08 00:37:51,861] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-01-08 00:37:52,565] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-01-08 00:37:52,803] [pool-1-thread-5] Initializing /data/ome/654Atemp.stk: [testng] [2025-01-08 00:37:54,777] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-01-08 00:37:54,908] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-01-08 00:37:55,365] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-01-08 00:37:55,846] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2025-01-08 00:37:57,036] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [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 8 seconds Finished: SUCCESS