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Started by upstream project "BIOFORMATS-test-repo" build number 308 originally caused by: Started by upstream project "Trigger" build number 330 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins17098328036701949145.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48748_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] 00:36:33,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:33,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:36:33,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:33,786 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:33,787 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:33,787 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:33,788 |-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] 00:36:33,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:33,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:33,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:33,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:33,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:33,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:33,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:33,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:33,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:33,988 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:33,989 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:33,989 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:33,989 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:33,989 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:36:33,990 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:36:33,990 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-04 00:36:33,999] [main] java.version = 11.0.16 [testng] 00:36:34,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:34,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:34,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-04_00-36-34.log] [testng] 00:36:34,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2025-01-04 00:36:34,047] [main] testng.directory = /data [testng] [2025-01-04 00:36:34,047] [main] testng.configDirectory = /config [testng] [2025-01-04 00:36:34,057] [main] testng.multiplier = 1.0 [testng] [2025-01-04 00:36:34,058] [main] testng.in-memory = false [testng] [2025-01-04 00:36:34,058] [main] testng.allow-missing = false [testng] [2025-01-04 00:36:34,058] [main] user.language = en [testng] [2025-01-04 00:36:34,058] [main] user.country = ${user.country} [testng] [2025-01-04 00:36:34,058] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-04 00:37:15,664] [main] ---------------------------------------- [testng] [2025-01-04 00:37:15,664] [main] Total files: 164 [testng] [2025-01-04 00:37:15,664] [main] Scan time: 41.606 s (253 ms/file) [testng] [2025-01-04 00:37:15,664] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-04 00:38:02,725] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 00:38:02,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:38:02,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:02,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-04_00-38-02.log] [testng] 00:38:02,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44fbdc58 - End of configuration. [testng] [2025-01-04 00:38:02,755] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:38:02,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:38:02,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:02,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-04_00-38-02.log] [testng] 00:38:02,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d58dd44 - End of configuration. [testng] [2025-01-04 00:38:02,948] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:38:02,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:38:02,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:02,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-04_00-38-02.log] [testng] 00:38:02,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ccf3057 - End of configuration. [testng] [2025-01-04 00:38:03,136] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:38:03,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:38:03,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:03,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-04_00-38-03.log] [testng] 00:38:03,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51fb89f1 - End of configuration. [testng] [2025-01-04 00:38:03,362] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:38:03,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:38:03,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:03,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-04_00-38-03.log] [testng] 00:38:03,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ab4916f - End of configuration. [testng] [2025-01-04 00:38:03,643] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 00:38:03,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:38:03,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:03,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-04_00-38-03.log] [testng] 00:38:03,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee51c98 - End of configuration. [testng] [2025-01-04 00:38:04,359] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] 00:38:04,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:38:04,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:04,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-04_00-38-04.log] [testng] 00:38:04,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20f8b3e1 - End of configuration. [testng] [2025-01-04 00:38:05,499] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:38:05,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:38:05,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:05,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-04_00-38-05.log] [testng] 00:38:05,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@650f12e7 - End of configuration. [testng] [2025-01-04 00:38:05,915] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:38:05,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:38:05,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:05,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-04_00-38-05.log] [testng] 00:38:05,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4979bb79 - End of configuration. [testng] [2025-01-04 00:38:06,420] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:38:06,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:38:06,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:06,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-04_00-38-06.log] [testng] 00:38:06,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e2c43bb - End of configuration. [testng] [2025-01-04 00:38:06,640] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:38:06,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:38:06,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:06,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-04_00-38-06.log] [testng] 00:38:06,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@757f54d3 - End of configuration. [testng] [2025-01-04 00:38:06,738] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:38:06,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:38:06,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:06,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-04_00-38-06.log] [testng] 00:38:06,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ab61d0 - End of configuration. [testng] [2025-01-04 00:38:09,178] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-01-04 00:38:12,902] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-01-04 00:38:12,988] [pool-1-thread-9] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-01-04 00:38:13,703] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-01-04 00:38:14,134] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-01-04 00:38:17,086] [pool-1-thread-2] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-01-04 00:38:20,855] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-01-04 00:38:20,990] [pool-1-thread-11] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-01-04 00:38:21,136] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-01-04 00:38:21,429] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-01-04 00:38:21,861] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-01-04 00:38:21,984] [pool-1-thread-8] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-01-04 00:38:22,103] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2025-01-04 00:38:23,383] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-01-04 00:38:24,634] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-01-04 00:38:25,522] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-01-04 00:38:26,593] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-01-04 00:38:27,406] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2025-01-04 00:38:28,366] [pool-1-thread-7] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-01-04 00:38:29,174] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-01-04 00:38:29,268] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-01-04 00:38:29,918] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-01-04 00:38:49,215] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-01-04 00:38:51,543] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-01-04 00:38:52,458] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-01-04 00:38:53,228] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-01-04 00:38:54,929] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-01-04 00:38:55,782] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-01-04 00:38:56,310] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-01-04 00:38:56,615] [pool-1-thread-11] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-01-04 00:38:57,440] [pool-1-thread-4] Initializing /data/ome/embryo.lsm: [testng] [2025-01-04 00:38:57,751] [pool-1-thread-8] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-01-04 00:38:58,520] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2025-01-04 00:39:03,605] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-01-04 00:39:03,989] [pool-1-thread-12] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-01-04 00:39:05,365] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-01-04 00:39:05,468] [pool-1-thread-2] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-01-04 00:39:07,347] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-01-04 00:39:07,571] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-01-04 00:39:07,860] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-01-04 00:39:08,477] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2025-01-04 00:39:10,079] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-01-04 00:39:10,846] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-01-04 00:39:11,017] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2025-01-04 00:39:12,381] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-01-04 00:39:13,547] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-01-04 00:39:13,876] [pool-1-thread-11] 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: 4 minutes 4 seconds Finished: SUCCESS