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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins5250386362402915502.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35461_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 11:38:32,267 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:38:32,268 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 11:38:32,268 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:38:32,269 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:38:32,269 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:38:32,270 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:38:32,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:38:32,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:38:32,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:38:32,271 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:38:32,271 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:38:32,272 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:38:32,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:38:32,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:38:32,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:38:32,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:38:32,457 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:38:32,457 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:38:32,457 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:38:32,458 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:38:32,458 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 11:38:32,459 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 11:38:32,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 11:38:32,468] [main] java.version = 21 [testng] 11:38:32,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:38:32,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:38:32,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_11-38-32.log] [testng] 11:38:32,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 11:38:32,514] [main] testng.directory = /data [testng] [2024-10-17 11:38:32,514] [main] testng.configDirectory = /config [testng] [2024-10-17 11:38:32,523] [main] testng.multiplier = 1.0 [testng] [2024-10-17 11:38:32,523] [main] testng.in-memory = false [testng] [2024-10-17 11:38:32,523] [main] testng.allow-missing = false [testng] [2024-10-17 11:38:32,523] [main] user.language = en [testng] [2024-10-17 11:38:32,523] [main] user.country = ${user.country} [testng] [2024-10-17 11:38:32,523] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 11:41:23,740] [main] ---------------------------------------- [testng] [2024-10-17 11:41:23,740] [main] Total files: 164 [testng] [2024-10-17 11:41:23,740] [main] Scan time: 171.216 s (1044 ms/file) [testng] [2024-10-17 11:41:23,740] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 11:47:26,113] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 11:47:26,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:47:26,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:26,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_11-47-26.log] [testng] 11:47:26,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29cf3481 - End of configuration. [testng] [2024-10-17 11:47:28,639] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] 11:47:28,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:47:28,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:28,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_11-47-28.log] [testng] 11:47:28,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61f10958 - End of configuration. [testng] [2024-10-17 11:47:28,937] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] 11:47:28,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:47:28,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:28,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_11-47-28.log] [testng] 11:47:28,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1a2b47 - End of configuration. [testng] [2024-10-17 11:47:31,164] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 11:47:31,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:47:31,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:31,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_11-47-31.log] [testng] 11:47:31,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62fe6083 - End of configuration. [testng] [2024-10-17 11:47:31,803] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 11:47:31,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:47:31,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:31,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_11-47-31.log] [testng] 11:47:31,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c345ea4 - End of configuration. [testng] [2024-10-17 11:47:32,404] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 11:47:32,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:47:32,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:32,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_11-47-32.log] [testng] 11:47:32,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b355ef7 - End of configuration. [testng] [2024-10-17 11:47:33,028] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 11:47:33,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:47:33,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:33,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_11-47-33.log] [testng] 11:47:33,030 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cf7f07f - End of configuration. [testng] [2024-10-17 11:47:40,256] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] 11:47:40,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:47:40,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:40,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_11-47-40.log] [testng] 11:47:40,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4521890b - End of configuration. [testng] [2024-10-17 11:47:41,745] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 11:47:41,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:47:41,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:41,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_11-47-41.log] [testng] 11:47:41,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16be7471 - End of configuration. [testng] [2024-10-17 11:47:42,173] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] 11:47:42,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:47:42,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:42,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_11-47-42.log] [testng] 11:47:42,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52f57abc - End of configuration. [testng] [2024-10-17 11:47:45,179] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] 11:47:45,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:47:45,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:45,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_11-47-45.log] [testng] 11:47:45,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b9aa2b - End of configuration. [testng] [2024-10-17 11:47:53,670] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 11:47:53,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:47:53,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:47:53,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_11-47-53.log] [testng] 11:47:53,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61a35e4d - End of configuration. [testng] [2024-10-17 11:48:02,588] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-17 11:48:03,329] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-10-17 11:48:08,529] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-17 11:48:09,004] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-17 11:48:19,604] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-17 11:48:23,874] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-17 11:49:04,522] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-17 11:49:05,497] [pool-1-thread-6] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-17 11:49:10,197] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-17 11:49:10,655] [pool-1-thread-11] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-17 11:49:12,047] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-17 11:49:16,287] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-17 11:49:19,317] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-17 11:49:20,281] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-17 11:49:25,815] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-17 11:51:33,559] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-17 11:51:34,315] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-10-17 11:51:39,505] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-17 11:51:42,429] [pool-1-thread-2] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-17 11:51:47,592] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-17 11:51:54,343] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-17 11:51:58,076] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-17 11:52:01,907] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-17 11:52:04,980] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-17 11:52:05,228] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-17 11:52:07,959] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-17 11:52:10,454] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-17 11:52:17,440] [pool-1-thread-4] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-17 11:52:19,674] [pool-1-thread-5] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-17 11:52:24,204] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-17 11:52:26,914] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-17 11:52:28,313] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-17 11:52:30,275] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-17 11:52:32,519] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-17 11:52:33,388] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-17 11:52:33,913] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-10-17 11:52:35,457] [pool-1-thread-12] Initializing /data/ome/worm.tiff: [testng] [2024-10-17 11:52:44,569] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-17 11:52:45,005] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-17 11:52:45,713] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-17 11:52:47,302] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-17 11:52:51,899] [pool-1-thread-1] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-17 11:52:57,873] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-17 11:52:59,073] [pool-1-thread-11] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-17 11:53:01,887] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-17 11:53:05,893] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-17 11:53:10,620] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 25 minutes 13 seconds Finished: SUCCESS