Started by upstream project "BIOFORMATS-test-repo" build number 122 originally caused by: Started by upstream project "Trigger" build number 139 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins12870327014826038511.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19027_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] 01:23:37,622 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:37,624 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:23:37,624 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:37,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:37,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:37,628 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:37,628 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:23:37,628 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:37,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:37,630 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:37,630 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:37,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:37,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:37,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:37,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:37,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:37,978 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:37,978 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:37,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:37,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:37,979 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:23:37,981 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:23:37,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 352 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-16 01:23:37,997] [main] java.version = 11.0.16 [testng] 01:23:38,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:38,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:38,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-16_01-23-38.log] [testng] 01:23:38,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-16 01:23:38,089] [main] testng.directory = /data [testng] [2024-07-16 01:23:38,089] [main] testng.configDirectory = /config [testng] [2024-07-16 01:23:38,108] [main] testng.multiplier = 1.0 [testng] [2024-07-16 01:23:38,111] [main] testng.in-memory = false [testng] [2024-07-16 01:23:38,111] [main] testng.allow-missing = false [testng] [2024-07-16 01:23:38,111] [main] user.language = en [testng] [2024-07-16 01:23:38,111] [main] user.country = ${user.country} [testng] [2024-07-16 01:23:38,111] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-16 01:23:56,426] [main] ---------------------------------------- [testng] [2024-07-16 01:23:56,426] [main] Total files: 164 [testng] [2024-07-16 01:23:56,426] [main] Scan time: 18.314 s (111 ms/file) [testng] [2024-07-16 01:23:56,426] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-16 01:24:04,433] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] 01:24:04,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:04,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-16_01-24-04.log] [testng] 01:24:04,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25729998 - End of configuration. [testng] [2024-07-16 01:24:04,474] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] 01:24:04,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:04,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-16_01-24-04.log] [testng] 01:24:04,476 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b64d1d1 - End of configuration. [testng] [2024-07-16 01:24:04,490] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:04,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:04,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-16_01-24-04.log] [testng] 01:24:04,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e48b3d1 - End of configuration. [testng] [2024-07-16 01:24:04,505] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:24:04,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:04,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-16_01-24-04.log] [testng] 01:24:04,509 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2236ab5e - End of configuration. [testng] [2024-07-16 01:24:04,528] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:24:04,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:04,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-16_01-24-04.log] [testng] 01:24:04,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a3e809b - End of configuration. [testng] [2024-07-16 01:24:04,568] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:04,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:04,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-16_01-24-04.log] [testng] 01:24:04,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7783ee5e - End of configuration. [testng] [2024-07-16 01:24:04,595] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:24:04,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:04,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-16_01-24-04.log] [testng] 01:24:04,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ad05215 - End of configuration. [testng] [2024-07-16 01:24:04,766] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] 01:24:04,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:04,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-16_01-24-04.log] [testng] 01:24:04,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e36ceaa - End of configuration. [testng] [2024-07-16 01:24:04,778] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:04,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:04,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-16_01-24-04.log] [testng] 01:24:04,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43fb23d7 - End of configuration. [testng] [2024-07-16 01:24:04,829] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:04,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:04,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-16_01-24-04.log] [testng] 01:24:04,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fdfe159 - End of configuration. [testng] [2024-07-16 01:24:04,842] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:24:04,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:04,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-16_01-24-04.log] [testng] 01:24:04,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@734c02e1 - End of configuration. [testng] [2024-07-16 01:24:04,903] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] 01:24:04,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:04,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:04,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-16_01-24-04.log] [testng] 01:24:04,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d9f4ae3 - End of configuration. [testng] [2024-07-16 01:24:07,416] [pool-1-thread-4] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-16 01:24:07,527] [pool-1-thread-10] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-16 01:24:07,621] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-07-16 01:24:07,627] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-07-16 01:24:07,658] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-16 01:24:07,668] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-16 01:24:07,679] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-07-16 01:24:07,774] [pool-1-thread-9] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-16 01:24:08,184] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-07-16 01:24:08,227] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-07-16 01:24:08,251] [pool-1-thread-5] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-16 01:24:08,386] [pool-1-thread-2] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-16 01:24:08,425] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-16 01:24:08,473] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-16 01:24:08,558] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-07-16 01:24:08,711] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-16 01:24:08,861] [pool-1-thread-5] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-16 01:24:09,945] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-16 01:24:10,077] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-16 01:24:10,125] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-07-16 01:24:10,362] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-07-16 01:24:10,635] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-07-16 01:24:10,684] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-16 01:24:10,787] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-16 01:24:10,797] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-16 01:24:10,960] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-16 01:24:10,985] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-16 01:24:11,418] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-16 01:24:11,446] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-07-16 01:24:11,554] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-07-16 01:24:11,937] [pool-1-thread-12] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-16 01:24:11,961] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-16 01:24:12,007] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-16 01:24:12,856] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-16 01:24:12,894] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-07-16 01:24:13,039] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-07-16 01:24:13,064] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-16 01:24:13,110] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-07-16 01:24:13,361] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-16 01:24:13,488] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-16 01:24:13,622] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-07-16 01:24:14,192] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-07-16 01:24:14,389] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-07-16 01:24:14,428] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-16 01:24:14,493] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-07-16 01:24:14,746] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] [2024-07-16 01:24:15,058] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 10 seconds Finished: SUCCESS