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Started by upstream project "BIOFORMATS-test-repo" build number 65 originally caused by: Started by upstream project "Trigger" build number 72 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins8056089108700250547.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9679_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:24:21,200 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:21,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:24:21,202 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:21,203 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:21,203 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:21,204 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:21,204 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:21,204 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:21,204 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:21,205 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:21,205 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:21,206 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:21,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:21,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:21,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:21,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:21,411 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:21,411 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:21,411 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:21,412 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:21,412 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:24:21,413 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:24:21,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-16 01:24:21,422] [main] java.version = 21 [testng] 01:24:21,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:21,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:21,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-16_01-24-21.log] [testng] 01:24:21,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-05-16 01:24:21,474] [main] testng.directory = /data [testng] [2024-05-16 01:24:21,474] [main] testng.configDirectory = /config [testng] [2024-05-16 01:24:21,484] [main] testng.multiplier = 1.0 [testng] [2024-05-16 01:24:21,485] [main] testng.in-memory = false [testng] [2024-05-16 01:24:21,485] [main] testng.allow-missing = false [testng] [2024-05-16 01:24:21,485] [main] user.language = en [testng] [2024-05-16 01:24:21,485] [main] user.country = ${user.country} [testng] [2024-05-16 01:24:21,485] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-16 01:24:42,547] [main] ---------------------------------------- [testng] [2024-05-16 01:24:42,547] [main] Total files: 164 [testng] [2024-05-16 01:24:42,547] [main] Scan time: 21.062 s (128 ms/file) [testng] [2024-05-16 01:24:42,547] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-16 01:24:52,731] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:24:52,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:52,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:52,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-16_01-24-52.log] [testng] 01:24:52,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17031506 - End of configuration. [testng] [2024-05-16 01:24:52,750] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 01:24:52,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:52,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:52,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-16_01-24-52.log] [testng] 01:24:52,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db551c4 - End of configuration. [testng] [2024-05-16 01:24:52,948] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:24:52,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:52,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:52,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-16_01-24-52.log] [testng] 01:24:52,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e78380 - End of configuration. [testng] [2024-05-16 01:24:52,962] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:24:52,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:52,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:52,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-16_01-24-52.log] [testng] 01:24:52,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@667846ad - End of configuration. [testng] [2024-05-16 01:24:53,149] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:24:53,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:53,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-16_01-24-53.log] [testng] 01:24:53,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4911acaa - End of configuration. [testng] [2024-05-16 01:24:53,173] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:53,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:53,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-16_01-24-53.log] [testng] 01:24:53,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb13370 - End of configuration. [testng] [2024-05-16 01:24:53,190] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 01:24:53,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:53,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-16_01-24-53.log] [testng] 01:24:53,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13856a3b - End of configuration. [testng] [2024-05-16 01:24:53,229] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 01:24:53,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:53,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-16_01-24-53.log] [testng] 01:24:53,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f505f7c - End of configuration. [testng] [2024-05-16 01:24:53,238] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:24:53,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:53,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-16_01-24-53.log] [testng] 01:24:53,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@723985f2 - End of configuration. [testng] [2024-05-16 01:24:53,247] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:24:53,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:53,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-16_01-24-53.log] [testng] 01:24:53,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36dccf5d - End of configuration. [testng] [2024-05-16 01:24:53,348] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 01:24:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:53,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-16_01-24-53.log] [testng] 01:24:53,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@679df212 - End of configuration. [testng] [2024-05-16 01:24:53,369] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:53,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:53,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:53,370 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-16_01-24-53.log] [testng] 01:24:53,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44aa33ce - End of configuration. [testng] [2024-05-16 01:24:55,329] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-05-16 01:24:55,337] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-16 01:24:55,435] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-05-16 01:24:55,551] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-16 01:24:55,856] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-16 01:24:55,865] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-16 01:24:56,269] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-16 01:24:57,004] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-16 01:24:57,076] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-16 01:24:57,157] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-05-16 01:24:57,427] [pool-1-thread-12] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-16 01:24:57,658] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-16 01:24:57,682] [pool-1-thread-12] Initializing /data/ome/C1.lsm: [testng] [2024-05-16 01:24:57,821] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-05-16 01:24:57,849] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-16 01:24:57,916] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-16 01:24:57,935] [pool-1-thread-3] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-16 01:24:58,060] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-05-16 01:24:58,149] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-05-16 01:24:58,301] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-16 01:24:58,443] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-05-16 01:24:58,545] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-16 01:24:58,664] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-05-16 01:24:58,682] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-05-16 01:24:58,776] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-16 01:24:58,917] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-05-16 01:24:58,950] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-05-16 01:24:59,074] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-16 01:25:00,030] [pool-1-thread-3] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-16 01:25:00,249] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-16 01:25:00,335] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-16 01:25:00,541] [pool-1-thread-3] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-05-16 01:25:00,579] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-16 01:25:00,613] [pool-1-thread-4] Initializing /data/ome/embryo.lsm: [testng] [2024-05-16 01:25:00,762] [pool-1-thread-2] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-05-16 01:25:01,228] [pool-1-thread-3] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-16 01:25:01,378] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-16 01:25:01,574] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-05-16 01:25:01,768] [pool-1-thread-2] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-16 01:25:01,864] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-16 01:25:01,975] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-05-16 01:25:02,190] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-16 01:25:02,215] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-16 01:25:02,238] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-16 01:25:02,269] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-16 01:25:02,407] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-05-16 01:25:02,614] [pool-1-thread-4] Initializing /data/ome/compressed2ChZ.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 12 seconds Finished: SUCCESS