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Started by upstream project "BIOFORMATS-test-repo" build number 287 originally caused by: Started by upstream project "Trigger" build number 306 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins11398952614914182350.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45287_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] 00:37:02,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:02,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:37:02,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:02,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:02,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:02,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:02,252 |-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] 00:37:02,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:02,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:02,253 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:02,254 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:02,254 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:02,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:02,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:02,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:02,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:02,439 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:02,439 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:02,439 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:02,440 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:02,440 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:37:02,440 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:37:02,440 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-11 00:37:02,449] [main] java.version = 17.0.2 [testng] 00:37:02,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:02,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:02,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_00-37-02.log] [testng] 00:37:02,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-11 00:37:02,495] [main] testng.directory = /data [testng] [2024-12-11 00:37:02,495] [main] testng.configDirectory = /config [testng] [2024-12-11 00:37:02,503] [main] testng.multiplier = 1.0 [testng] [2024-12-11 00:37:02,504] [main] testng.in-memory = false [testng] [2024-12-11 00:37:02,504] [main] testng.allow-missing = false [testng] [2024-12-11 00:37:02,504] [main] user.language = en [testng] [2024-12-11 00:37:02,504] [main] user.country = ${user.country} [testng] [2024-12-11 00:37:02,504] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-11 00:38:09,020] [main] ---------------------------------------- [testng] [2024-12-11 00:38:09,020] [main] Total files: 164 [testng] [2024-12-11 00:38:09,020] [main] Scan time: 66.516 s (405 ms/file) [testng] [2024-12-11 00:38:09,020] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-11 00:39:44,722] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:39:44,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:39:44,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:44,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-11_00-39-44.log] [testng] 00:39:44,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50be385 - End of configuration. [testng] [2024-12-11 00:39:45,896] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:39:45,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:39:45,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:45,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-11_00-39-45.log] [testng] 00:39:45,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48325e7a - End of configuration. [testng] [2024-12-11 00:39:47,111] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:39:47,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:39:47,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:47,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-11_00-39-47.log] [testng] 00:39:47,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f6a1903 - End of configuration. [testng] [2024-12-11 00:39:48,364] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:39:48,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:39:48,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:48,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-11_00-39-48.log] [testng] 00:39:48,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6900ff27 - End of configuration. [testng] [2024-12-11 00:39:48,741] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:39:48,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:39:48,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:48,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-11_00-39-48.log] [testng] 00:39:48,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36080fc3 - End of configuration. [testng] [2024-12-11 00:39:48,870] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:39:48,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:39:48,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:48,870 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-11_00-39-48.log] [testng] 00:39:48,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@495fbf76 - End of configuration. [testng] [2024-12-11 00:39:49,022] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:39:49,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:39:49,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:49,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-11_00-39-49.log] [testng] 00:39:49,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bea91e0 - End of configuration. [testng] [2024-12-11 00:39:49,661] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 00:39:49,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:39:49,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:49,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-11_00-39-49.log] [testng] 00:39:49,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7678d860 - End of configuration. [testng] [2024-12-11 00:39:50,417] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:39:50,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:39:50,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:50,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-11_00-39-50.log] [testng] 00:39:50,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@360b5e23 - End of configuration. [testng] [2024-12-11 00:39:51,516] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:39:51,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:39:51,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:51,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-11_00-39-51.log] [testng] 00:39:51,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@119c4253 - End of configuration. [testng] [2024-12-11 00:39:51,739] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 00:39:51,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:39:51,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:51,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-11_00-39-51.log] [testng] 00:39:51,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ebc1589 - End of configuration. [testng] [2024-12-11 00:39:53,310] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:39:53,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:39:53,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:53,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-11_00-39-53.log] [testng] 00:39:53,311 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2130e5c0 - End of configuration. [testng] [2024-12-11 00:39:58,684] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-11 00:39:59,151] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-11 00:40:00,616] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-11 00:40:01,823] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-11 00:40:03,393] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-12-11 00:40:04,876] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-11 00:40:05,139] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-11 00:40:05,348] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-11 00:40:07,180] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-11 00:40:08,471] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-11 00:40:09,514] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-11 00:40:10,513] [pool-1-thread-11] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-11 00:40:12,096] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-11 00:40:14,731] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-11 00:40:16,093] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-11 00:40:17,687] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-11 00:40:17,831] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-11 00:40:18,025] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-11 00:40:18,907] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-11 00:40:19,656] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-11 00:40:21,185] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-11 00:40:21,437] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-12-11 00:40:22,307] [pool-1-thread-2] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-11 00:40:24,794] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-11 00:40:26,381] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-11 00:40:27,001] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-11 00:40:27,212] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-11 00:40:29,001] [pool-1-thread-6] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-11 00:40:29,267] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-11 00:40:30,955] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-11 00:40:32,657] [pool-1-thread-8] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-11 00:41:04,806] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-11 00:41:05,760] [pool-1-thread-1] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-11 00:41:06,534] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-11 00:41:06,948] [pool-1-thread-12] Initializing /data/ome/worm.tiff: [testng] [2024-12-11 00:41:11,280] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-11 00:41:11,538] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-11 00:41:13,639] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-11 00:41:15,181] [pool-1-thread-4] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-11 00:41:16,841] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-11 00:41:18,253] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-11 00:41:29,084] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-11 00:41:31,067] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-11 00:41:31,194] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-11 00:41:33,073] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-11 00:41:33,736] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-11 00:41:34,557] [pool-1-thread-12] 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: 6 minutes 46 seconds Finished: SUCCESS