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Started by upstream project "BIOFORMATS-test-repo" build number 266 originally caused by: Started by upstream project "Trigger" build number 289 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins4436236688934371975.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41970_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] 00:37:16,183 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:16,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:37:16,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:16,185 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:16,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:16,186 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:16,186 |-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] 00:37:16,186 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:16,187 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:16,187 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:16,187 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:16,188 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:16,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:16,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:16,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:16,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:16,380 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:16,380 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:16,380 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:16,380 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:16,380 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:37:16,381 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:37:16,381 |-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] [2024-11-24 00:37:16,390] [main] java.version = 17.0.2 [testng] 00:37:16,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:16,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:16,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-24_00-37-16.log] [testng] 00:37:16,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-24 00:37:16,436] [main] testng.directory = /data [testng] [2024-11-24 00:37:16,436] [main] testng.configDirectory = /config [testng] [2024-11-24 00:37:16,444] [main] testng.multiplier = 1.0 [testng] [2024-11-24 00:37:16,445] [main] testng.in-memory = false [testng] [2024-11-24 00:37:16,445] [main] testng.allow-missing = false [testng] [2024-11-24 00:37:16,445] [main] user.language = en [testng] [2024-11-24 00:37:16,445] [main] user.country = ${user.country} [testng] [2024-11-24 00:37:16,445] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-24 00:38:07,452] [main] ---------------------------------------- [testng] [2024-11-24 00:38:07,452] [main] Total files: 164 [testng] [2024-11-24 00:38:07,452] [main] Scan time: 51.006 s (311 ms/file) [testng] [2024-11-24 00:38:07,452] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-24 00:39:14,688] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:39:14,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:39:14,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:14,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-24_00-39-14.log] [testng] 00:39:14,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a59f7d3 - End of configuration. [testng] [2024-11-24 00:39:15,401] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:39:15,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:39:15,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:15,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-24_00-39-15.log] [testng] 00:39:15,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@232b079f - End of configuration. [testng] [2024-11-24 00:39:15,718] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:39:15,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:39:15,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:15,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-24_00-39-15.log] [testng] 00:39:15,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50829e6a - End of configuration. [testng] [2024-11-24 00:39:16,205] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:39:16,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:39:16,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:16,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-24_00-39-16.log] [testng] 00:39:16,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67811bc7 - End of configuration. [testng] [2024-11-24 00:39:16,380] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:39:16,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:39:16,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:16,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-24_00-39-16.log] [testng] 00:39:16,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1876d509 - End of configuration. [testng] [2024-11-24 00:39:16,459] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:39:16,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:39:16,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:16,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-24_00-39-16.log] [testng] 00:39:16,461 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e57b712 - End of configuration. [testng] [2024-11-24 00:39:16,534] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:39:16,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:39:16,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:16,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-24_00-39-16.log] [testng] 00:39:16,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@495fbf76 - End of configuration. [testng] [2024-11-24 00:39:16,834] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 00:39:16,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:39:16,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:16,835 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-24_00-39-16.log] [testng] 00:39:16,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@119c4253 - End of configuration. [testng] [2024-11-24 00:39:17,170] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:39:17,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:39:17,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:17,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-24_00-39-17.log] [testng] 00:39:17,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ebc1589 - End of configuration. [testng] [2024-11-24 00:39:17,657] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:39:17,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:39:17,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:17,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-24_00-39-17.log] [testng] 00:39:17,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2130e5c0 - End of configuration. [testng] [2024-11-24 00:39:17,766] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 00:39:17,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:39:17,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:17,767 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-24_00-39-17.log] [testng] 00:39:17,767 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409058cc - End of configuration. [testng] [2024-11-24 00:39:18,534] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:39:18,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:39:18,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:18,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-24_00-39-18.log] [testng] 00:39:18,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1c8076 - End of configuration. [testng] [2024-11-24 00:39:21,954] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-24 00:39:22,058] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-24 00:39:22,315] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-24 00:39:22,798] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-24 00:39:23,742] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-11-24 00:39:24,252] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-24 00:39:24,706] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-24 00:39:24,775] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-24 00:39:25,481] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-24 00:39:25,586] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-24 00:39:26,327] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-24 00:39:27,211] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-24 00:39:27,800] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-24 00:39:28,607] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-24 00:39:29,256] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-24 00:39:30,251] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-24 00:39:30,349] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-24 00:39:30,456] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-24 00:39:30,579] [pool-1-thread-5] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-24 00:39:31,805] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-24 00:39:32,973] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-24 00:39:33,769] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-11-24 00:39:34,596] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-24 00:39:36,039] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-24 00:39:36,972] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-24 00:39:37,215] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-24 00:39:37,394] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-24 00:39:38,601] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-24 00:39:39,443] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-24 00:39:40,833] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-24 00:39:42,511] [pool-1-thread-12] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-24 00:39:43,214] [pool-1-thread-11] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-24 00:40:04,394] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-24 00:40:04,923] [pool-1-thread-6] Initializing /data/ome/worm.tiff: [testng] [2024-11-24 00:40:05,944] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-24 00:40:07,792] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-24 00:40:08,539] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-24 00:40:09,602] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-24 00:40:10,784] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-24 00:40:13,207] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-24 00:40:15,478] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-24 00:40:24,058] [pool-1-thread-9] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-24 00:40:24,331] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-24 00:40:24,521] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-24 00:40:25,203] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-24 00:40:25,784] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-24 00:40:27,102] [pool-1-thread-2] 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: 4 minutes 41 seconds Finished: SUCCESS