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Started by upstream project "BIOFORMATS-test-repo" build number 289 originally caused by: Started by upstream project "Trigger" build number 308 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins13212523750003274564.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45615_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 test-automated: [testng] File leak detector installed [testng] 00:44:02,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:44:02,186 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:44:02,186 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:44:02,187 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:44:02,188 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:44:02,188 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:44:02,188 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:44:02,188 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:44:02,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:44:02,189 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:44:02,189 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:44:02,189 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:44:02,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:44:02,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:44:02,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:44:02,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:44:02,441 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:44:02,441 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:44:02,441 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:44:02,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:44:02,442 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:44:02,443 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:44:02,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 254 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-13 00:44:02,452] [main] java.version = 1.8.0_342 [testng] 00:44:02,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:44:02,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:02,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-13_00-44-02.log] [testng] 00:44:02,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-13 00:44:02,504] [main] testng.directory = /data [testng] [2024-12-13 00:44:02,504] [main] testng.configDirectory = /config [testng] [2024-12-13 00:44:02,516] [main] testng.multiplier = 1.0 [testng] [2024-12-13 00:44:02,516] [main] testng.in-memory = false [testng] [2024-12-13 00:44:02,516] [main] testng.allow-missing = false [testng] [2024-12-13 00:44:02,516] [main] user.language = en [testng] [2024-12-13 00:44:02,516] [main] user.country = ${user.country} [testng] [2024-12-13 00:44:02,516] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-13 00:45:29,517] [main] ---------------------------------------- [testng] [2024-12-13 00:45:29,518] [main] Total files: 164 [testng] [2024-12-13 00:45:29,634] [main] Scan time: 87.001 s (530 ms/file) [testng] [2024-12-13 00:45:29,634] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-13 00:47:21,520] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:47:21,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:47:21,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:21,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-13_00-47-21.log] [testng] 00:47:21,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@390989bd - End of configuration. [testng] [2024-12-13 00:47:22,806] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:47:22,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:47:22,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:22,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-13_00-47-22.log] [testng] 00:47:22,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34f5516 - End of configuration. [testng] [2024-12-13 00:47:22,981] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:47:22,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:47:22,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:22,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-13_00-47-22.log] [testng] 00:47:22,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e35a034 - End of configuration. [testng] [2024-12-13 00:47:23,811] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:47:23,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:47:23,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:23,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-13_00-47-23.log] [testng] 00:47:23,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22490d60 - End of configuration. [testng] [2024-12-13 00:47:24,671] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 00:47:24,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:47:24,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:24,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-13_00-47-24.log] [testng] 00:47:24,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f35b78e - End of configuration. [testng] [2024-12-13 00:47:26,454] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:47:26,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:47:26,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:26,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-13_00-47-26.log] [testng] 00:47:26,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e91729c - End of configuration. [testng] [2024-12-13 00:47:26,597] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 00:47:26,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:47:26,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:26,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-13_00-47-26.log] [testng] 00:47:26,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@334f8613 - End of configuration. [testng] [2024-12-13 00:47:27,331] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 00:47:27,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:47:27,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:27,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-13_00-47-27.log] [testng] 00:47:27,333 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38568ab8 - End of configuration. [testng] [2024-12-13 00:47:27,478] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:47:27,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:47:27,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:27,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-13_00-47-27.log] [testng] 00:47:27,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b18c545 - End of configuration. [testng] [2024-12-13 00:47:28,480] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 00:47:28,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:47:28,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:28,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-13_00-47-28.log] [testng] 00:47:28,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34e21dd - End of configuration. [testng] [2024-12-13 00:47:28,621] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 00:47:28,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:47:28,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:28,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-13_00-47-28.log] [testng] 00:47:28,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a625802 - End of configuration. [testng] [2024-12-13 00:47:30,720] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:47:30,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:47:30,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:30,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-13_00-47-30.log] [testng] 00:47:30,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47fd049f - End of configuration. [testng] [2024-12-13 00:47:36,154] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-12-13 00:47:37,364] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-13 00:47:37,672] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-13 00:47:38,604] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-13 00:47:41,063] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-13 00:47:41,718] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-13 00:47:53,558] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-13 00:47:54,464] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-13 00:47:55,237] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-13 00:47:56,389] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-13 00:47:57,167] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-13 00:47:58,179] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-13 00:47:59,518] [pool-1-thread-8] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-13 00:48:00,419] [pool-1-thread-2] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-13 00:48:02,686] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-13 00:48:04,225] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-13 00:48:05,358] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-13 00:48:05,518] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-13 00:48:07,271] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-13 00:48:09,246] [pool-1-thread-7] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-13 00:48:09,633] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-13 00:48:10,064] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-13 00:48:10,530] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-13 00:48:10,791] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-13 00:48:11,426] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-13 00:48:13,055] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-13 00:48:14,300] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-13 00:48:16,452] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-13 00:48:16,794] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-13 00:48:18,133] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-13 00:48:18,305] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-13 00:48:19,089] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-13 00:48:20,886] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-13 00:48:21,061] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-13 00:48:21,438] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-13 00:48:22,611] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-13 00:48:23,289] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-13 00:48:25,721] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-13 00:48:54,653] [pool-1-thread-1] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-13 00:48:56,568] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-13 00:48:57,552] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-13 00:48:57,704] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-13 00:48:59,559] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-13 00:49:03,635] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-13 00:49:03,940] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-13 00:49:05,630] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-13 00:49:07,793] [pool-1-thread-8] 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: 7 minutes 13 seconds Finished: SUCCESS