Started by upstream project "BIOFORMATS-test-repo" build number 80 originally caused by: Started by upstream project "Trigger" build number 88 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins5934257760768431683.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12139_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 test-automated: [testng] File leak detector installed [testng] 01:26:24,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:26:24,573 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:26:24,573 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:24,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:24,574 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:26:24,574 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:26:24,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:26:24,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:24,575 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:24,575 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:26:24,575 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:26:24,575 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:26:24,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:26:24,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:26:24,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:26:24,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:26:24,898 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:26:24,898 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:26:24,898 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:26:24,899 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:26:24,899 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:26:24,900 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:26:24,900 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 325 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-31 01:26:24,910] [main] java.version = 1.8.0_342 [testng] 01:26:24,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:26:24,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:24,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-31_01-26-24.log] [testng] 01:26:24,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-31 01:26:24,976] [main] testng.directory = /data [testng] [2024-05-31 01:26:24,976] [main] testng.configDirectory = /config [testng] [2024-05-31 01:26:24,989] [main] testng.multiplier = 1.0 [testng] [2024-05-31 01:26:24,990] [main] testng.in-memory = false [testng] [2024-05-31 01:26:24,990] [main] testng.allow-missing = false [testng] [2024-05-31 01:26:24,990] [main] user.language = en [testng] [2024-05-31 01:26:24,990] [main] user.country = ${user.country} [testng] [2024-05-31 01:26:24,990] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-31 01:26:51,626] [main] ---------------------------------------- [testng] [2024-05-31 01:26:51,626] [main] Total files: 164 [testng] [2024-05-31 01:26:51,626] [main] Scan time: 26.636 s (162 ms/file) [testng] [2024-05-31 01:26:51,626] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-31 01:27:02,229] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:27:02,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:27:02,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-31_01-27-02.log] [testng] 01:27:02,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cfe0041 - End of configuration. [testng] [2024-05-31 01:27:02,289] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 01:27:02,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:27:02,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,291 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-31_01-27-02.log] [testng] 01:27:02,292 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6164c616 - End of configuration. [testng] [2024-05-31 01:27:02,320] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 01:27:02,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:27:02,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-31_01-27-02.log] [testng] 01:27:02,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22286887 - End of configuration. [testng] [2024-05-31 01:27:02,367] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] 01:27:02,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:27:02,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-31_01-27-02.log] [testng] 01:27:02,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d8fb12b - End of configuration. [testng] [2024-05-31 01:27:02,420] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 01:27:02,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:27:02,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-31_01-27-02.log] [testng] 01:27:02,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6604530a - End of configuration. [testng] [2024-05-31 01:27:02,446] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:27:02,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:27:02,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-31_01-27-02.log] [testng] 01:27:02,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58c4acab - End of configuration. [testng] [2024-05-31 01:27:02,475] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:27:02,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:27:02,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,476 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-31_01-27-02.log] [testng] 01:27:02,477 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e534646 - End of configuration. [testng] [2024-05-31 01:27:02,533] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 01:27:02,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:27:02,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-31_01-27-02.log] [testng] 01:27:02,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@138efcc6 - End of configuration. [testng] [2024-05-31 01:27:02,544] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:27:02,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:27:02,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-31_01-27-02.log] [testng] 01:27:02,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f500bf4 - End of configuration. [testng] [2024-05-31 01:27:02,562] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 01:27:02,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:27:02,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-31_01-27-02.log] [testng] 01:27:02,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cba730c - End of configuration. [testng] [2024-05-31 01:27:02,591] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] 01:27:02,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:27:02,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,593 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-31_01-27-02.log] [testng] 01:27:02,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@501e4f23 - End of configuration. [testng] [2024-05-31 01:27:02,625] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:27:02,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:27:02,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:02,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-31_01-27-02.log] [testng] 01:27:02,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f0ac3 - End of configuration. [testng] [2024-05-31 01:27:04,968] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-31 01:27:04,983] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-31 01:27:05,139] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-31 01:27:05,158] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-05-31 01:27:05,180] [pool-1-thread-7] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-31 01:27:05,383] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-05-31 01:27:05,869] [pool-1-thread-10] Initializing /data/ome/embryo.lsm: [testng] [2024-05-31 01:27:05,935] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-31 01:27:05,998] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-05-31 01:27:06,069] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-05-31 01:27:06,351] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-05-31 01:27:06,361] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-31 01:27:06,510] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-05-31 01:27:06,815] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-05-31 01:27:06,829] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-05-31 01:27:06,903] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-05-31 01:27:07,213] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-31 01:27:07,223] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-31 01:27:07,234] [pool-1-thread-10] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-31 01:27:07,379] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-31 01:27:07,615] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-05-31 01:27:07,968] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-05-31 01:27:07,978] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-05-31 01:27:08,042] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-31 01:27:08,162] [pool-1-thread-7] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-05-31 01:27:08,271] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-31 01:27:09,067] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-31 01:27:09,120] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-05-31 01:27:09,219] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-31 01:27:09,484] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-05-31 01:27:09,651] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-05-31 01:27:09,661] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-05-31 01:27:09,708] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-05-31 01:27:09,933] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-31 01:27:11,698] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-31 01:27:11,817] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-05-31 01:27:12,058] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-05-31 01:27:12,330] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-05-31 01:27:12,337] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-31 01:27:12,362] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-31 01:27:12,443] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-05-31 01:27:12,610] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-31 01:27:12,882] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-31 01:27:13,030] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-05-31 01:27:13,263] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-31 01:27:13,313] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-31 01:27:13,601] [pool-1-thread-10] Initializing /data/ome/t1_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: 2 minutes 36 seconds Finished: SUCCESS