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Started by upstream project "BIOFORMATS-test-repo" build number 364 originally caused by: Started by upstream project "Trigger" build number 390 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/jenkins3737086469352464233.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57993_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] 00:34:08,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:34:08,562 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:34:08,563 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:08,564 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:08,565 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:08,565 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:08,566 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:08,566 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:08,567 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:08,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:08,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:08,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:08,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:08,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:08,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:08,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:08,779 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:08,779 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:08,779 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:08,780 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:08,780 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:34:08,781 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:34:08,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 214 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-04 00:34:08,790] [main] java.version = 11.0.16 [testng] 00:34:08,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:08,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:08,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_00-34-08.log] [testng] 00:34:08,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-04 00:34:08,840] [main] testng.directory = /data [testng] [2025-03-04 00:34:08,841] [main] testng.configDirectory = /config [testng] [2025-03-04 00:34:08,851] [main] testng.multiplier = 1.0 [testng] [2025-03-04 00:34:08,852] [main] testng.in-memory = false [testng] [2025-03-04 00:34:08,852] [main] testng.allow-missing = false [testng] [2025-03-04 00:34:08,853] [main] user.language = en [testng] [2025-03-04 00:34:08,853] [main] user.country = ${user.country} [testng] [2025-03-04 00:34:08,853] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-04 00:34:30,391] [main] ---------------------------------------- [testng] [2025-03-04 00:34:30,391] [main] Total files: 164 [testng] [2025-03-04 00:34:30,391] [main] Scan time: 21.538 s (131 ms/file) [testng] [2025-03-04 00:34:30,392] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-04 00:35:05,762] [pool-1-thread-1] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:35:05,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:35:05,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:05,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-04_00-35-05.log] [testng] 00:35:05,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18e9e59 - End of configuration. [testng] [2025-03-04 00:35:05,938] [pool-1-thread-12] Initializing /data/ome/C1.lsm: [testng] 00:35:05,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:35:05,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:05,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_00-35-05.log] [testng] 00:35:05,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b14009a - End of configuration. [testng] [2025-03-04 00:35:06,492] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:35:06,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:35:06,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:06,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-04_00-35-06.log] [testng] 00:35:06,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d5cc38f - End of configuration. [testng] [2025-03-04 00:35:06,614] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:35:06,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:35:06,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:06,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-04_00-35-06.log] [testng] 00:35:06,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1636e78a - End of configuration. [testng] [2025-03-04 00:35:06,705] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 00:35:06,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:35:06,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:06,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-04_00-35-06.log] [testng] 00:35:06,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9a88a46 - End of configuration. [testng] [2025-03-04 00:35:07,218] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 00:35:07,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:35:07,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:07,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-04_00-35-07.log] [testng] 00:35:07,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60b405f - End of configuration. [testng] [2025-03-04 00:35:08,093] [pool-1-thread-7] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:35:08,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:35:08,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:08,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-04_00-35-08.log] [testng] 00:35:08,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a4171c7 - End of configuration. [testng] [2025-03-04 00:35:09,176] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:35:09,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:35:09,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:09,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-04_00-35-09.log] [testng] 00:35:09,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f02fdee - End of configuration. [testng] [2025-03-04 00:35:09,284] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:35:09,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:35:09,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:09,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-04_00-35-09.log] [testng] 00:35:09,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee51c98 - End of configuration. [testng] [2025-03-04 00:35:09,485] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] 00:35:09,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:35:09,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:09,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_00-35-09.log] [testng] 00:35:09,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47e6e79f - End of configuration. [testng] [2025-03-04 00:35:09,596] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:35:09,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:35:09,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:09,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_00-35-09.log] [testng] 00:35:09,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d24ac66 - End of configuration. [testng] [2025-03-04 00:35:10,515] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] 00:35:10,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:35:10,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:10,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_00-35-10.log] [testng] 00:35:10,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40d0dcc7 - End of configuration. [testng] [2025-03-04 00:35:13,320] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-04 00:35:13,471] [pool-1-thread-5] Initializing /data/ome/worm.tiff: [testng] [2025-03-04 00:35:14,685] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-03-04 00:35:15,720] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-04 00:35:16,072] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-04 00:35:16,847] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-03-04 00:35:16,995] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-04 00:35:17,885] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-04 00:35:19,417] [pool-1-thread-10] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-04 00:35:20,987] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2025-03-04 00:35:21,625] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-04 00:35:21,713] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-04 00:35:22,487] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-03-04 00:35:23,920] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-03-04 00:35:24,149] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-03-04 00:35:26,206] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-04 00:35:26,564] [pool-1-thread-8] Initializing /data/ome/embryo.lsm: [testng] [2025-03-04 00:35:27,540] [pool-1-thread-6] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-04 00:35:29,805] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-04 00:35:30,905] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2025-03-04 00:35:31,036] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-03-04 00:35:31,440] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-04 00:35:32,109] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-03-04 00:35:33,540] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-03-04 00:35:34,431] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-04 00:35:35,546] [pool-1-thread-8] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-04 00:35:36,487] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-03-04 00:35:37,678] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-03-04 00:35:38,691] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-04 00:35:39,321] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2025-03-04 00:35:47,089] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-04 00:35:47,428] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-04 00:36:12,663] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-04 00:36:13,569] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-03-04 00:36:13,973] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-04 00:36:14,406] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-03-04 00:36:15,343] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-03-04 00:36:15,760] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-03-04 00:36:16,377] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-04 00:36:18,140] [pool-1-thread-11] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-03-04 00:36:18,605] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-03-04 00:36:19,648] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-04 00:36:20,043] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-03-04 00:36:21,332] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-04 00:36:21,566] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2025-03-04 00:36:22,166] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-04 00:36:23,032] [pool-1-thread-5] 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 51 seconds Finished: SUCCESS