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Started by upstream project "BIOFORMATS-test-repo" build number 295 originally caused by: Started by upstream project "Trigger" build number 314 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/jenkins3745722276656110166.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46602_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 00:38:58,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:38:58,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:38:58,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:38:58,562 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:38:58,563 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:38:58,563 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:38:58,564 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:38:58,564 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:38:58,564 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:38:58,565 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:38:58,565 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:38:58,566 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:38:58,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:38:58,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:38:58,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:38:58,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:38:58,756 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:38:58,756 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:38:58,756 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:38:58,756 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:38:58,757 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:38:58,757 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:38:58,757 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-19 00:38:58,766] [main] java.version = 21 [testng] 00:38:58,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:38:58,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:58,810 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-19_00-38-58.log] [testng] 00:38:58,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-19 00:38:58,813] [main] testng.directory = /data [testng] [2024-12-19 00:38:58,813] [main] testng.configDirectory = /config [testng] [2024-12-19 00:38:58,822] [main] testng.multiplier = 1.0 [testng] [2024-12-19 00:38:58,822] [main] testng.in-memory = false [testng] [2024-12-19 00:38:58,823] [main] testng.allow-missing = false [testng] [2024-12-19 00:38:58,823] [main] user.language = en [testng] [2024-12-19 00:38:58,823] [main] user.country = ${user.country} [testng] [2024-12-19 00:38:58,823] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-19 00:39:52,566] [main] ---------------------------------------- [testng] [2024-12-19 00:39:52,566] [main] Total files: 164 [testng] [2024-12-19 00:39:52,566] [main] Scan time: 53.743 s (327 ms/file) [testng] [2024-12-19 00:39:52,567] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-19 00:41:20,114] [pool-1-thread-1] Initializing /data/sdub/sdub.pattern: [testng] 00:41:20,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:41:20,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:20,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-19_00-41-20.log] [testng] 00:41:20,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@745c3500 - End of configuration. [testng] [2024-12-19 00:41:27,434] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:41:27,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:41:27,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:27,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-19_00-41-27.log] [testng] 00:41:27,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@282a07d2 - End of configuration. [testng] [2024-12-19 00:41:28,673] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 00:41:28,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:41:28,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:28,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-19_00-41-28.log] [testng] 00:41:28,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fbae551 - End of configuration. [testng] [2024-12-19 00:41:28,782] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:41:28,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:41:28,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:28,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-19_00-41-28.log] [testng] 00:41:28,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67f430e3 - End of configuration. [testng] [2024-12-19 00:41:28,912] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:41:28,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:41:28,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:28,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-19_00-41-28.log] [testng] 00:41:28,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3620deb0 - End of configuration. [testng] [2024-12-19 00:41:29,087] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] 00:41:29,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:41:29,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:29,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-19_00-41-29.log] [testng] 00:41:29,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59277bf5 - End of configuration. [testng] [2024-12-19 00:41:30,374] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] 00:41:30,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:41:30,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:30,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-19_00-41-30.log] [testng] 00:41:30,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58a25dde - End of configuration. [testng] [2024-12-19 00:41:30,506] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:41:30,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:41:30,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:30,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-19_00-41-30.log] [testng] 00:41:30,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b6aaa29 - End of configuration. [testng] [2024-12-19 00:41:31,076] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:41:31,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:41:31,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:31,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-19_00-41-31.log] [testng] 00:41:31,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7052b39b - End of configuration. [testng] [2024-12-19 00:41:32,129] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:41:32,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:41:32,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:32,130 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-19_00-41-32.log] [testng] 00:41:32,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@636d9bc4 - End of configuration. [testng] [2024-12-19 00:41:33,611] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:41:33,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:41:33,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:33,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-19_00-41-33.log] [testng] 00:41:33,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e7648d2 - End of configuration. [testng] [2024-12-19 00:41:33,730] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:41:33,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:41:33,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:33,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-19_00-41-33.log] [testng] 00:41:33,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@654b8b60 - End of configuration. [testng] [2024-12-19 00:41:37,411] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-19 00:41:37,737] [pool-1-thread-11] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-19 00:41:38,102] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-19 00:41:38,514] [pool-1-thread-9] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-19 00:41:39,183] [pool-1-thread-3] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-19 00:41:39,447] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-19 00:41:40,559] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-19 00:41:40,903] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-19 00:41:41,268] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] [2024-12-19 00:41:42,187] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-19 00:41:42,557] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-12-19 00:41:44,529] [pool-1-thread-5] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-19 00:41:45,965] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-19 00:41:47,130] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-19 00:41:47,616] [pool-1-thread-10] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-12-19 00:41:48,552] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-19 00:41:50,609] [pool-1-thread-9] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-12-19 00:41:51,835] [pool-1-thread-11] Initializing /data/ome/embryo.lsm: [testng] [2024-12-19 00:41:52,393] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-19 00:41:53,243] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-19 00:41:53,534] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-19 00:41:53,724] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-19 00:41:54,458] [pool-1-thread-5] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-19 00:41:55,176] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-19 00:41:55,572] [pool-1-thread-2] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-19 00:41:57,525] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-19 00:41:58,002] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-19 00:41:58,085] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-19 00:41:58,236] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-19 00:41:58,772] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-19 00:41:59,900] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-19 00:42:00,738] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-19 00:42:00,918] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-19 00:42:02,355] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-19 00:42:03,213] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-19 00:42:04,771] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-19 00:42:05,387] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-19 00:42:05,642] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-12-19 00:42:08,091] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-19 00:42:09,686] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-19 00:42:10,181] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-19 00:42:11,279] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-19 00:42:12,358] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-19 00:42:12,863] [pool-1-thread-4] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-19 00:42:30,931] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-19 00:42:32,270] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-19 00:42:32,989] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [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 38 seconds Finished: SUCCESS