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Started by upstream project "BIOFORMATS-test-repo" build number 274 originally caused by: Started by upstream project "Trigger" build number 295 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/jenkins3466854537943802259.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43153_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:33:35,524 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:33:35,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:33:35,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:35,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:35,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:33:35,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:33:35,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:33:35,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:35,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:35,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:33:35,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:33:35,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:33:35,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:33:35,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:33:35,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:33:35,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:33:35,745 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:33:35,745 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:33:35,746 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:33:35,746 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:33:35,746 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:33:35,747 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:33:35,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 219 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-30 00:33:35,756] [main] java.version = 11.0.16 [testng] 00:33:35,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:33:35,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:35,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-30_00-33-35.log] [testng] 00:33:35,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-30 00:33:35,827] [main] testng.directory = /data [testng] [2024-11-30 00:33:35,827] [main] testng.configDirectory = /config [testng] [2024-11-30 00:33:35,838] [main] testng.multiplier = 1.0 [testng] [2024-11-30 00:33:35,839] [main] testng.in-memory = false [testng] [2024-11-30 00:33:35,839] [main] testng.allow-missing = false [testng] [2024-11-30 00:33:35,839] [main] user.language = en [testng] [2024-11-30 00:33:35,839] [main] user.country = ${user.country} [testng] [2024-11-30 00:33:35,839] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-30 00:34:03,217] [main] ---------------------------------------- [testng] [2024-11-30 00:34:03,218] [main] Total files: 164 [testng] [2024-11-30 00:34:03,218] [main] Scan time: 27.377 s (166 ms/file) [testng] [2024-11-30 00:34:03,218] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-30 00:34:38,277] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] 00:34:38,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:38,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:38,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-30_00-34-38.log] [testng] 00:34:38,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20a1dc20 - End of configuration. [testng] [2024-11-30 00:34:38,330] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:34:38,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:38,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:38,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-30_00-34-38.log] [testng] 00:34:38,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a37f068 - End of configuration. [testng] [2024-11-30 00:34:38,687] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:34:38,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:38,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:38,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-30_00-34-38.log] [testng] 00:34:38,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13654114 - End of configuration. [testng] [2024-11-30 00:34:38,727] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:34:38,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:38,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:38,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-30_00-34-38.log] [testng] 00:34:38,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29b20693 - End of configuration. [testng] [2024-11-30 00:34:38,767] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:34:38,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:38,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:38,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-30_00-34-38.log] [testng] 00:34:38,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7518d72 - End of configuration. [testng] [2024-11-30 00:34:39,271] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:34:39,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:39,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:39,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-30_00-34-39.log] [testng] 00:34:39,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75613e3c - End of configuration. [testng] [2024-11-30 00:34:39,654] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:34:39,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:39,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:39,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-30_00-34-39.log] [testng] 00:34:39,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd76a7c - End of configuration. [testng] [2024-11-30 00:34:40,169] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:34:40,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:40,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:40,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-30_00-34-40.log] [testng] 00:34:40,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ea61a97 - End of configuration. [testng] [2024-11-30 00:34:40,230] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:34:40,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:40,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:40,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-30_00-34-40.log] [testng] 00:34:40,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@502ff3fc - End of configuration. [testng] [2024-11-30 00:34:40,807] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] 00:34:40,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:40,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:40,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-30_00-34-40.log] [testng] 00:34:40,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c83b817 - End of configuration. [testng] [2024-11-30 00:34:41,074] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:34:41,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:41,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:41,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-30_00-34-41.log] [testng] 00:34:41,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3394f1f9 - End of configuration. [testng] [2024-11-30 00:34:41,255] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:34:41,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:41,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:41,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-30_00-34-41.log] [testng] 00:34:41,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab3299f - End of configuration. [testng] [2024-11-30 00:34:44,293] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-30 00:34:45,701] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-11-30 00:34:46,477] [pool-1-thread-11] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-30 00:35:01,885] [pool-1-thread-8] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-30 00:35:02,023] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-30 00:35:02,233] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-30 00:35:02,279] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-11-30 00:35:02,323] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-30 00:35:02,361] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-30 00:35:03,159] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-30 00:35:04,216] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-30 00:35:04,292] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-30 00:35:04,355] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-30 00:35:04,757] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-30 00:35:05,019] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-30 00:35:05,706] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-30 00:35:05,812] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-30 00:35:06,473] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-11-30 00:35:06,993] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-30 00:35:07,469] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-30 00:35:07,779] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-30 00:35:07,846] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-30 00:35:08,995] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-30 00:35:10,781] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-30 00:35:11,273] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-30 00:35:11,917] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-30 00:35:12,517] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-30 00:35:13,772] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-30 00:35:14,420] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-11-30 00:35:14,963] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-30 00:35:15,554] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-30 00:35:15,659] [pool-1-thread-3] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-11-30 00:35:16,170] [pool-1-thread-5] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-30 00:35:16,710] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-30 00:35:16,910] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-30 00:35:17,565] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-11-30 00:35:17,814] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-30 00:35:18,095] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-30 00:35:18,672] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-30 00:35:22,745] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-30 00:35:22,812] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-30 00:35:23,215] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-30 00:35:23,730] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-30 00:35:24,077] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-30 00:35:24,637] [pool-1-thread-4] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-30 00:35:25,085] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-30 00:35:26,892] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.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 9 seconds Finished: SUCCESS