Started by upstream project "BIOFORMATS-test-repo" build number 305 originally caused by: Started by upstream project "Trigger" build number 327 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins11880223509430641539.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48253_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] 00:47:11,387 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:47:11,388 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:47:11,388 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:47:11,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:47:11,389 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:47:11,390 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:47:11,390 |-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] 00:47:11,390 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:47:11,390 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:47:11,391 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:47:11,391 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:47:11,391 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:47:11,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:47:11,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:47:11,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:47:11,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:47:11,582 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:47:11,582 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:47:11,582 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:47:11,583 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:47:11,583 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:47:11,584 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:47:11,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-01 00:47:11,593] [main] java.version = 17.0.2 [testng] 00:47:11,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:47:11,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:11,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-01_00-47-11.log] [testng] 00:47:11,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-01 00:47:11,640] [main] testng.directory = /data [testng] [2025-01-01 00:47:11,640] [main] testng.configDirectory = /config [testng] [2025-01-01 00:47:11,648] [main] testng.multiplier = 1.0 [testng] [2025-01-01 00:47:11,649] [main] testng.in-memory = false [testng] [2025-01-01 00:47:11,650] [main] testng.allow-missing = false [testng] [2025-01-01 00:47:11,650] [main] user.language = en [testng] [2025-01-01 00:47:11,650] [main] user.country = ${user.country} [testng] [2025-01-01 00:47:11,650] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-01 00:47:42,774] [main] ---------------------------------------- [testng] [2025-01-01 00:47:42,774] [main] Total files: 164 [testng] [2025-01-01 00:47:42,774] [main] Scan time: 31.123 s (189 ms/file) [testng] [2025-01-01 00:47:42,774] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-01 00:48:19,743] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:48:19,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:48:19,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:19,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-01_00-48-19.log] [testng] 00:48:19,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@347a9e95 - End of configuration. [testng] [2025-01-01 00:48:20,007] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:48:20,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:48:20,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-01_00-48-20.log] [testng] 00:48:20,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765a4c1 - End of configuration. [testng] [2025-01-01 00:48:20,161] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] 00:48:20,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:48:20,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-01_00-48-20.log] [testng] 00:48:20,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@270e6730 - End of configuration. [testng] [2025-01-01 00:48:20,315] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:48:20,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:48:20,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-01_00-48-20.log] [testng] 00:48:20,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@407a49f9 - End of configuration. [testng] [2025-01-01 00:48:20,377] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:48:20,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:48:20,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-01_00-48-20.log] [testng] 00:48:20,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4a1534 - End of configuration. [testng] [2025-01-01 00:48:20,414] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:48:20,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:48:20,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-01_00-48-20.log] [testng] 00:48:20,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a262677 - End of configuration. [testng] [2025-01-01 00:48:20,442] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:48:20,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:48:20,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-01_00-48-20.log] [testng] 00:48:20,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5051355c - End of configuration. [testng] [2025-01-01 00:48:20,822] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:48:20,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:48:20,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-01_00-48-20.log] [testng] 00:48:20,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@639df500 - End of configuration. [testng] [2025-01-01 00:48:20,964] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:48:20,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:48:20,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:20,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-01_00-48-20.log] [testng] 00:48:20,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57423d07 - End of configuration. [testng] [2025-01-01 00:48:21,269] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] 00:48:21,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:48:21,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:21,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-01_00-48-21.log] [testng] 00:48:21,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3974bf28 - End of configuration. [testng] [2025-01-01 00:48:23,233] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:48:23,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:48:23,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:23,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-01_00-48-23.log] [testng] 00:48:23,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@685b77b6 - End of configuration. [testng] [2025-01-01 00:48:23,451] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:48:23,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:48:23,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:23,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-01_00-48-23.log] [testng] 00:48:23,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18eff806 - End of configuration. [testng] [2025-01-01 00:48:26,329] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-01-01 00:48:26,443] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-01-01 00:48:26,799] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-01-01 00:48:28,204] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-01-01 00:48:28,979] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2025-01-01 00:48:29,386] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-01-01 00:48:29,506] [pool-1-thread-1] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-01-01 00:48:29,773] [pool-1-thread-12] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-01-01 00:48:30,732] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-01-01 00:48:30,781] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-01-01 00:48:31,233] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-01-01 00:48:32,181] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-01-01 00:48:33,003] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-01-01 00:48:33,853] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-01-01 00:48:34,457] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2025-01-01 00:48:34,569] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2025-01-01 00:48:34,674] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-01-01 00:48:34,750] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-01-01 00:48:35,093] [pool-1-thread-2] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-01-01 00:48:35,562] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-01-01 00:48:35,758] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-01-01 00:48:36,829] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-01-01 00:48:37,253] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-01-01 00:48:37,459] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-01-01 00:48:37,650] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2025-01-01 00:48:37,772] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2025-01-01 00:48:38,363] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-01-01 00:48:38,800] [pool-1-thread-12] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-01-01 00:48:39,536] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-01-01 00:48:39,767] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-01-01 00:48:40,080] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-01-01 00:48:40,315] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-01-01 00:48:49,148] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] [2025-01-01 00:48:50,129] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-01-01 00:48:50,419] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-01-01 00:48:51,049] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-01-01 00:48:51,516] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-01-01 00:48:51,597] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-01-01 00:48:52,042] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-01-01 00:48:52,611] [pool-1-thread-6] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-01-01 00:48:53,000] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-01-01 00:48:53,477] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2025-01-01 00:48:54,411] [pool-1-thread-1] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-01-01 00:48:54,728] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-01-01 00:48:55,015] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-01-01 00:48:55,219] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2025-01-01 00:48:55,626] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [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 10 seconds Finished: SUCCESS