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Started by upstream project "BIOFORMATS-test-repo" build number 222 originally caused by: Started by upstream project "Trigger" build number 249 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/jenkins3297668270807882969.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35218_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] 02:06:45,846 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:06:45,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 02:06:45,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:06:45,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:06:45,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:06:45,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:06:45,849 |-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] 02:06:45,849 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:06:45,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:06:45,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:06:45,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:06:45,851 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:06:46,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:06:46,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:06:46,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:06:46,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:06:46,037 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:06:46,037 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:06:46,038 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:06:46,038 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:06:46,038 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 02:06:46,039 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 02:06:46,039 |-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] [2024-10-16 02:06:46,048] [main] java.version = 17.0.2 [testng] 02:06:46,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:06:46,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:46,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_02-06-46.log] [testng] 02:06:46,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-16 02:06:46,102] [main] testng.directory = /data [testng] [2024-10-16 02:06:46,103] [main] testng.configDirectory = /config [testng] [2024-10-16 02:06:46,114] [main] testng.multiplier = 1.0 [testng] [2024-10-16 02:06:46,115] [main] testng.in-memory = false [testng] [2024-10-16 02:06:46,115] [main] testng.allow-missing = false [testng] [2024-10-16 02:06:46,115] [main] user.language = en [testng] [2024-10-16 02:06:46,115] [main] user.country = ${user.country} [testng] [2024-10-16 02:06:46,115] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-16 02:12:10,484] [main] ---------------------------------------- [testng] [2024-10-16 02:12:10,484] [main] Total files: 164 [testng] [2024-10-16 02:12:10,484] [main] Scan time: 324.369 s (1977 ms/file) [testng] [2024-10-16 02:12:10,484] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-16 02:20:12,409] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 02:20:12,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:20:12,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:12,410 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_02-20-12.log] [testng] 02:20:12,411 |-INFO in ch.qos.logback.core.sift.SiftProcessor@264a6f5b - End of configuration. [testng] [2024-10-16 02:20:20,583] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 02:20:20,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:20:20,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:20,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_02-20-20.log] [testng] 02:20:20,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6900ff27 - End of configuration. [testng] [2024-10-16 02:20:24,519] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 02:20:24,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:20:24,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:24,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_02-20-24.log] [testng] 02:20:24,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d2f5ab7 - End of configuration. [testng] [2024-10-16 02:20:29,839] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 02:20:29,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:20:29,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:29,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_02-20-29.log] [testng] 02:20:29,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e57b712 - End of configuration. [testng] [2024-10-16 02:20:32,077] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 02:20:32,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:20:32,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:32,078 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_02-20-32.log] [testng] 02:20:32,078 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fb05223 - End of configuration. [testng] [2024-10-16 02:20:32,972] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 02:20:32,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:20:32,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:32,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_02-20-32.log] [testng] 02:20:32,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7678d860 - End of configuration. [testng] [2024-10-16 02:20:33,698] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 02:20:33,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:20:33,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:33,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_02-20-33.log] [testng] 02:20:33,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409058cc - End of configuration. [testng] [2024-10-16 02:20:36,357] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 02:20:36,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:20:36,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:36,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_02-20-36.log] [testng] 02:20:36,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1c8076 - End of configuration. [testng] [2024-10-16 02:20:40,017] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 02:20:40,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:20:40,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:40,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_02-20-40.log] [testng] 02:20:40,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d1bfe7f - End of configuration. [testng] [2024-10-16 02:20:44,543] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 02:20:44,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:20:44,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:44,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_02-20-44.log] [testng] 02:20:44,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72538368 - End of configuration. [testng] [2024-10-16 02:20:45,438] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 02:20:45,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:20:45,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_02-20-45.log] [testng] 02:20:45,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fc4baf - End of configuration. [testng] [2024-10-16 02:20:54,226] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 02:20:54,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:20:54,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:54,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_02-20-54.log] [testng] 02:20:54,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1365dc19 - End of configuration. [testng] [2024-10-16 02:21:12,941] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-16 02:21:14,991] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-16 02:21:20,218] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-16 02:21:23,468] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-16 02:21:25,485] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-16 02:21:30,414] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-16 02:21:31,287] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-16 02:21:34,881] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-16 02:21:40,899] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-16 02:21:41,546] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-16 02:21:42,164] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-16 02:21:43,407] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-16 02:21:47,012] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-16 02:21:52,445] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-16 02:21:57,584] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-16 02:22:03,859] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-16 02:22:04,736] [pool-1-thread-12] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-16 02:22:05,734] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-16 02:22:06,784] [pool-1-thread-5] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-16 02:22:13,040] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-16 02:22:20,526] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-16 02:22:21,382] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-10-16 02:22:25,468] [pool-1-thread-10] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-16 02:22:33,295] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-16 02:22:40,093] [pool-1-thread-11] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-16 02:22:42,453] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-16 02:22:43,268] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-16 02:22:44,185] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-16 02:22:49,509] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-16 02:22:58,405] [pool-1-thread-4] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-16 02:23:11,689] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-16 02:26:50,946] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-16 02:26:58,176] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-10-16 02:27:12,600] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-16 02:27:14,195] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-16 02:27:20,479] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-16 02:27:21,814] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-16 02:27:48,765] [pool-1-thread-6] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-16 02:27:59,178] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-16 02:28:13,708] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-16 02:28:19,522] [pool-1-thread-1] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-16 02:29:47,691] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-16 02:29:54,555] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-16 02:30:12,096] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-16 02:30:13,581] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-16 02:30:15,262] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-16 02:30:23,825] [pool-1-thread-7] 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: 49 minutes 28 seconds Finished: SUCCESS