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Started by upstream project "BIOFORMATS-test-repo" build number 311 originally caused by: Started by upstream project "Trigger" build number 333 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/jenkins13285625854897420178.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49243_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] 00:34:35,496 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:34:35,498 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:34:35,498 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:35,499 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:35,500 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:35,501 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:35,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:35,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:35,502 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:35,503 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:35,504 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:35,504 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:35,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:35,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:35,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:35,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:35,707 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:35,707 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:35,707 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:35,708 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:35,708 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:34:35,709 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:34:35,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-07 00:34:35,718] [main] java.version = 11.0.16 [testng] 00:34:35,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:35,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:35,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-07_00-34-35.log] [testng] 00:34:35,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2025-01-07 00:34:35,767] [main] testng.directory = /data [testng] [2025-01-07 00:34:35,768] [main] testng.configDirectory = /config [testng] [2025-01-07 00:34:35,777] [main] testng.multiplier = 1.0 [testng] [2025-01-07 00:34:35,778] [main] testng.in-memory = false [testng] [2025-01-07 00:34:35,779] [main] testng.allow-missing = false [testng] [2025-01-07 00:34:35,779] [main] user.language = en [testng] [2025-01-07 00:34:35,779] [main] user.country = ${user.country} [testng] [2025-01-07 00:34:35,779] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-07 00:35:14,019] [main] ---------------------------------------- [testng] [2025-01-07 00:35:14,019] [main] Total files: 164 [testng] [2025-01-07 00:35:14,019] [main] Scan time: 38.24 s (233 ms/file) [testng] [2025-01-07 00:35:14,019] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-07 00:36:10,708] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 00:36:10,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:36:10,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:10,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-07_00-36-10.log] [testng] 00:36:10,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b3e637 - End of configuration. [testng] [2025-01-07 00:36:10,932] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:36:10,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:36:10,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:10,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-07_00-36-10.log] [testng] 00:36:10,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@284002f2 - End of configuration. [testng] [2025-01-07 00:36:11,245] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:36:11,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:36:11,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,246 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-07_00-36-11.log] [testng] 00:36:11,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49e0772a - End of configuration. [testng] [2025-01-07 00:36:11,461] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:36:11,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:36:11,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,462 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-07_00-36-11.log] [testng] 00:36:11,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@369d4db0 - End of configuration. [testng] [2025-01-07 00:36:11,708] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:36:11,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:36:11,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-07_00-36-11.log] [testng] 00:36:11,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ccd95a - End of configuration. [testng] [2025-01-07 00:36:11,807] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 00:36:11,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:36:11,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-07_00-36-11.log] [testng] 00:36:11,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42b8b11a - End of configuration. [testng] [2025-01-07 00:36:12,036] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] 00:36:12,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:36:12,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-07_00-36-12.log] [testng] 00:36:12,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5302b0de - End of configuration. [testng] [2025-01-07 00:36:12,340] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:36:12,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:36:12,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-07_00-36-12.log] [testng] 00:36:12,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44de0e25 - End of configuration. [testng] [2025-01-07 00:36:12,517] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:36:12,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:36:12,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-07_00-36-12.log] [testng] 00:36:12,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7447a8d4 - End of configuration. [testng] [2025-01-07 00:36:12,603] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:36:12,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:36:12,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-07_00-36-12.log] [testng] 00:36:12,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3986a4cb - End of configuration. [testng] [2025-01-07 00:36:12,641] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:36:12,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:36:12,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-07_00-36-12.log] [testng] 00:36:12,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a146fb - End of configuration. [testng] [2025-01-07 00:36:12,680] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:36:12,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:36:12,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-07_00-36-12.log] [testng] 00:36:12,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a9cffce - End of configuration. [testng] [2025-01-07 00:36:15,564] [pool-1-thread-4] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-01-07 00:36:16,266] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-01-07 00:36:16,326] [pool-1-thread-9] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-01-07 00:36:16,401] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-01-07 00:36:16,953] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-01-07 00:36:18,049] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-01-07 00:36:18,544] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-01-07 00:36:18,621] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-01-07 00:36:18,898] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-01-07 00:36:19,263] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-01-07 00:36:19,591] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-01-07 00:36:19,846] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-01-07 00:36:20,086] [pool-1-thread-9] Initializing /data/ome/C1.lsm: [testng] [2025-01-07 00:36:21,100] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-01-07 00:36:21,692] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-01-07 00:36:22,779] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-01-07 00:36:23,308] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-01-07 00:36:24,648] [pool-1-thread-1] Initializing /data/ome/worm.tiff: [testng] [2025-01-07 00:36:25,361] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-01-07 00:36:25,941] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-01-07 00:36:25,987] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-01-07 00:36:26,053] [pool-1-thread-5] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-01-07 00:36:34,330] [pool-1-thread-9] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-01-07 00:36:34,602] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-01-07 00:36:35,492] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-01-07 00:36:35,940] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-01-07 00:36:36,297] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-01-07 00:36:37,283] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-01-07 00:36:37,929] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-01-07 00:36:37,994] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-01-07 00:36:38,428] [pool-1-thread-11] Initializing /data/ome/embryo.lsm: [testng] [2025-01-07 00:36:38,636] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-01-07 00:36:39,070] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2025-01-07 00:36:41,839] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-01-07 00:36:43,114] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-01-07 00:36:44,367] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-01-07 00:36:44,577] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-01-07 00:36:45,454] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-01-07 00:36:45,599] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-01-07 00:36:45,737] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-01-07 00:36:48,065] [pool-1-thread-8] Initializing /data/ome/cb_1.r3d: [testng] [2025-01-07 00:36:48,809] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-01-07 00:36:49,460] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-01-07 00:36:49,551] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] [2025-01-07 00:36:51,051] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-01-07 00:36:51,621] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-01-07 00:36:51,915] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [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 40 seconds Finished: SUCCESS