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Started by upstream project "BIOFORMATS-test-repo" build number 361 originally caused by: Started by upstream project "Trigger" build number 387 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins153580995661442358.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57498_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] 00:32:47,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:32:47,116 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:32:47,116 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:47,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:47,117 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:32:47,118 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:32:47,118 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:32:47,118 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:47,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:47,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:32:47,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:32:47,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:32:47,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:32:47,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:32:47,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:32:47,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:32:47,319 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:32:47,320 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:32:47,320 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:32:47,320 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:32:47,320 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:32:47,321 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:32:47,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-01 00:32:47,330] [main] java.version = 11.0.16 [testng] 00:32:47,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:32:47,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:47,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-01_00-32-47.log] [testng] 00:32:47,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-01 00:32:47,380] [main] testng.directory = /data [testng] [2025-03-01 00:32:47,380] [main] testng.configDirectory = /config [testng] [2025-03-01 00:32:47,391] [main] testng.multiplier = 1.0 [testng] [2025-03-01 00:32:47,392] [main] testng.in-memory = false [testng] [2025-03-01 00:32:47,392] [main] testng.allow-missing = false [testng] [2025-03-01 00:32:47,392] [main] user.language = en [testng] [2025-03-01 00:32:47,392] [main] user.country = ${user.country} [testng] [2025-03-01 00:32:47,392] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-01 00:33:26,603] [main] ---------------------------------------- [testng] [2025-03-01 00:33:26,603] [main] Total files: 164 [testng] [2025-03-01 00:33:26,603] [main] Scan time: 39.211 s (239 ms/file) [testng] [2025-03-01 00:33:26,604] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-01 00:34:22,901] [pool-1-thread-1] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:34:22,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:22,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:22,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-01_00-34-22.log] [testng] 00:34:22,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@286ecdc2 - End of configuration. [testng] [2025-03-01 00:34:22,998] [pool-1-thread-12] Initializing /data/ome/C1.lsm: [testng] 00:34:22,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:22,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:22,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-01_00-34-22.log] [testng] 00:34:22,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f76d5d5 - End of configuration. [testng] [2025-03-01 00:34:23,263] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:34:23,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:23,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:23,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-01_00-34-23.log] [testng] 00:34:23,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2836d128 - End of configuration. [testng] [2025-03-01 00:34:23,323] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:34:23,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:23,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:23,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-01_00-34-23.log] [testng] 00:34:23,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7165a76e - End of configuration. [testng] [2025-03-01 00:34:23,374] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 00:34:23,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:23,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:23,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-01_00-34-23.log] [testng] 00:34:23,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@577fc55a - End of configuration. [testng] [2025-03-01 00:34:23,645] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 00:34:23,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:23,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:23,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-01_00-34-23.log] [testng] 00:34:23,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12ca35b8 - End of configuration. [testng] [2025-03-01 00:34:24,047] [pool-1-thread-7] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:34:24,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:24,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:24,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-01_00-34-24.log] [testng] 00:34:24,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@333f9bd5 - End of configuration. [testng] [2025-03-01 00:34:24,886] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:34:24,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:24,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:24,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-01_00-34-24.log] [testng] 00:34:24,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2544eb6b - End of configuration. [testng] [2025-03-01 00:34:24,953] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:34:24,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:24,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:24,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-01_00-34-24.log] [testng] 00:34:24,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3614ea80 - End of configuration. [testng] [2025-03-01 00:34:25,079] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] 00:34:25,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:25,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:25,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-01_00-34-25.log] [testng] 00:34:25,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d85bf8a - End of configuration. [testng] [2025-03-01 00:34:25,136] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:34:25,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:25,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:25,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-01_00-34-25.log] [testng] 00:34:25,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33bf24be - End of configuration. [testng] [2025-03-01 00:34:26,010] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] 00:34:26,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:26,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:26,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-01_00-34-26.log] [testng] 00:34:26,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dd36a1f - End of configuration. [testng] [2025-03-01 00:34:28,797] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-01 00:34:28,894] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-01 00:34:29,090] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2025-03-01 00:34:29,957] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-03-01 00:34:30,870] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-01 00:34:31,456] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-03-01 00:34:31,888] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-01 00:34:32,318] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-01 00:34:33,467] [pool-1-thread-2] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-01 00:34:34,558] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-01 00:34:35,093] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] [2025-03-01 00:34:35,454] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-03-01 00:34:36,348] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-03-01 00:34:36,413] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-01 00:34:36,503] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-03-01 00:34:38,366] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-01 00:34:38,834] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2025-03-01 00:34:39,371] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-01 00:34:39,486] [pool-1-thread-9] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-01 00:34:40,461] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2025-03-01 00:34:41,113] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-03-01 00:34:41,492] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-01 00:34:41,874] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-03-01 00:34:42,413] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-03-01 00:34:42,833] [pool-1-thread-10] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-01 00:34:43,452] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-01 00:34:44,552] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-03-01 00:34:45,099] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-03-01 00:34:45,203] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-01 00:34:46,088] [pool-1-thread-3] Initializing /data/sdub/sdub.pattern: [testng] [2025-03-01 00:34:51,426] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-01 00:34:51,545] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-01 00:35:12,783] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-01 00:35:14,169] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-03-01 00:35:14,943] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-01 00:35:15,387] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-03-01 00:35:16,119] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-03-01 00:35:16,365] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-03-01 00:35:17,047] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-01 00:35:18,394] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-03-01 00:35:19,830] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-03-01 00:35:20,820] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-01 00:35:21,651] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-03-01 00:35:22,189] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-01 00:35:22,501] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2025-03-01 00:35:23,331] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-01 00:35:23,914] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [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 38 seconds Finished: SUCCESS