Started by upstream project "BIOFORMATS-test-repo" build number 231 originally caused by: Started by upstream project "Trigger" build number 256 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/jenkins8527229802193284809.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36229_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] 01:40:11,079 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:40:11,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:40:11,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:40:11,082 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:40:11,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:40:11,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:40:11,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:40:11,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:40:11,084 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:40:11,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:40:11,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:40:11,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:40:11,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:40:11,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:40:11,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:40:11,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:40:11,314 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:40:11,314 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:40:11,314 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:40:11,314 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:40:11,314 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:40:11,315 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:40:11,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 231 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-22 01:40:11,326] [main] java.version = 11.0.16 [testng] 01:40:11,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:40:11,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:11,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-22_01-40-11.log] [testng] 01:40:11,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-22 01:40:11,380] [main] testng.directory = /data [testng] [2024-10-22 01:40:11,380] [main] testng.configDirectory = /config [testng] [2024-10-22 01:40:11,390] [main] testng.multiplier = 1.0 [testng] [2024-10-22 01:40:11,392] [main] testng.in-memory = false [testng] [2024-10-22 01:40:11,392] [main] testng.allow-missing = false [testng] [2024-10-22 01:40:11,392] [main] user.language = en [testng] [2024-10-22 01:40:11,392] [main] user.country = ${user.country} [testng] [2024-10-22 01:40:11,392] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-22 01:40:40,129] [main] ---------------------------------------- [testng] [2024-10-22 01:40:40,130] [main] Total files: 164 [testng] [2024-10-22 01:40:40,130] [main] Scan time: 28.737 s (175 ms/file) [testng] [2024-10-22 01:40:40,130] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-22 01:41:27,752] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] 01:41:27,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:41:27,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:27,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-22_01-41-27.log] [testng] 01:41:27,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d53e9e1 - End of configuration. [testng] [2024-10-22 01:41:27,812] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:41:27,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:41:27,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:27,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-22_01-41-27.log] [testng] 01:41:27,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1446cfdb - End of configuration. [testng] [2024-10-22 01:41:28,219] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 01:41:28,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:41:28,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:28,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-22_01-41-28.log] [testng] 01:41:28,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53f8e820 - End of configuration. [testng] [2024-10-22 01:41:28,272] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 01:41:28,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:41:28,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:28,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-22_01-41-28.log] [testng] 01:41:28,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@551ff219 - End of configuration. [testng] [2024-10-22 01:41:28,332] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:41:28,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:41:28,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:28,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-22_01-41-28.log] [testng] 01:41:28,333 |-INFO in ch.qos.logback.core.sift.SiftProcessor@456f3c9 - End of configuration. [testng] [2024-10-22 01:41:28,829] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:41:28,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:41:28,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:28,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-22_01-41-28.log] [testng] 01:41:28,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d2e63b0 - End of configuration. [testng] [2024-10-22 01:41:28,978] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:41:28,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:41:28,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:28,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-22_01-41-28.log] [testng] 01:41:28,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@467c5180 - End of configuration. [testng] [2024-10-22 01:41:29,265] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:41:29,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:41:29,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:29,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-22_01-41-29.log] [testng] 01:41:29,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39c1f8e6 - End of configuration. [testng] [2024-10-22 01:41:29,299] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:41:29,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:41:29,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:29,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-22_01-41-29.log] [testng] 01:41:29,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18c618bc - End of configuration. [testng] [2024-10-22 01:41:29,622] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] 01:41:29,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:41:29,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:29,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-22_01-41-29.log] [testng] 01:41:29,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525271be - End of configuration. [testng] [2024-10-22 01:41:29,771] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:41:29,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:41:29,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:29,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-22_01-41-29.log] [testng] 01:41:29,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f31517f - End of configuration. [testng] [2024-10-22 01:41:29,873] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:41:29,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:41:29,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:29,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-22_01-41-29.log] [testng] 01:41:29,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3db63531 - End of configuration. [testng] [2024-10-22 01:41:32,180] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-22 01:41:33,541] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-10-22 01:41:34,485] [pool-1-thread-3] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-22 01:41:53,773] [pool-1-thread-7] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-22 01:41:54,004] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-22 01:41:54,083] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-22 01:41:54,639] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-22 01:41:54,830] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-22 01:41:54,906] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-22 01:41:55,531] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-22 01:41:57,531] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-22 01:41:57,646] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-22 01:41:57,814] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-22 01:41:58,670] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-22 01:41:59,871] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-22 01:42:00,412] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-22 01:42:00,810] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-22 01:42:00,975] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-22 01:42:02,365] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-22 01:42:02,742] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-22 01:42:03,041] [pool-1-thread-11] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-22 01:42:04,758] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-22 01:42:04,917] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-22 01:42:06,378] [pool-1-thread-6] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-22 01:42:07,818] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-22 01:42:07,967] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-22 01:42:08,615] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-22 01:42:09,376] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-22 01:42:09,710] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-10-22 01:42:11,422] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-22 01:42:11,951] [pool-1-thread-12] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-22 01:42:12,799] [pool-1-thread-2] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-22 01:42:13,312] [pool-1-thread-5] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-22 01:42:14,049] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-22 01:42:14,479] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-22 01:42:17,386] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-10-22 01:42:19,640] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-22 01:42:19,731] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-22 01:42:21,538] [pool-1-thread-6] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-22 01:42:24,478] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-22 01:42:24,577] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-22 01:42:25,151] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-22 01:42:25,551] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-22 01:42:25,704] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-22 01:42:25,852] [pool-1-thread-4] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-22 01:42:26,193] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-22 01:42:27,161] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [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 30 seconds Finished: SUCCESS