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Started by upstream project "BIOFORMATS-test-repo" build number 30 originally caused by: Started by upstream project "Trigger" build number 33 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/jenkins4299290441075785832.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3938_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:23:38,934 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:38,936 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:23:38,936 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:38,937 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:38,937 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:38,938 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:38,938 |-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] 01:23:38,938 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:38,939 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:38,939 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:38,940 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:38,940 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:39,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:39,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:39,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:39,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:39,182 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:39,182 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:39,182 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:39,183 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:39,183 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:23:39,184 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:23:39,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 245 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-11 01:23:39,198] [main] java.version = 21 [testng] 01:23:39,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:39,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:39,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-11_01-23-39.log] [testng] 01:23:39,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-04-11 01:23:39,256] [main] testng.directory = /data [testng] [2024-04-11 01:23:39,257] [main] testng.configDirectory = /config [testng] [2024-04-11 01:23:39,268] [main] testng.multiplier = 1.0 [testng] [2024-04-11 01:23:39,269] [main] testng.in-memory = false [testng] [2024-04-11 01:23:39,269] [main] testng.allow-missing = false [testng] [2024-04-11 01:23:39,269] [main] user.language = en [testng] [2024-04-11 01:23:39,269] [main] user.country = ${user.country} [testng] [2024-04-11 01:23:39,269] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-11 01:23:59,318] [main] ---------------------------------------- [testng] [2024-04-11 01:23:59,318] [main] Total files: 164 [testng] [2024-04-11 01:23:59,319] [main] Scan time: 20.049 s (122 ms/file) [testng] [2024-04-11 01:23:59,319] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-11 01:24:10,128] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:24:10,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:10,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-11_01-24-10.log] [testng] 01:24:10,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e26f5d8 - End of configuration. [testng] [2024-04-11 01:24:10,154] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 01:24:10,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:10,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-11_01-24-10.log] [testng] 01:24:10,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bd16688 - End of configuration. [testng] [2024-04-11 01:24:10,363] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:24:10,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:10,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-11_01-24-10.log] [testng] 01:24:10,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5547168 - End of configuration. [testng] [2024-04-11 01:24:10,376] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:24:10,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:10,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-11_01-24-10.log] [testng] 01:24:10,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@384618bd - End of configuration. [testng] [2024-04-11 01:24:10,693] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:24:10,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:10,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-11_01-24-10.log] [testng] 01:24:10,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@111e45e3 - End of configuration. [testng] [2024-04-11 01:24:10,734] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:10,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:10,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-11_01-24-10.log] [testng] 01:24:10,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d4961a6 - End of configuration. [testng] [2024-04-11 01:24:10,751] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 01:24:10,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:10,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-11_01-24-10.log] [testng] 01:24:10,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43de1018 - End of configuration. [testng] [2024-04-11 01:24:10,788] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 01:24:10,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:10,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-11_01-24-10.log] [testng] 01:24:10,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be8ecaf - End of configuration. [testng] [2024-04-11 01:24:10,804] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:24:10,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:10,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-11_01-24-10.log] [testng] 01:24:10,806 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2abb9b6f - End of configuration. [testng] [2024-04-11 01:24:10,816] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:24:10,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:10,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-11_01-24-10.log] [testng] 01:24:10,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63743fe6 - End of configuration. [testng] [2024-04-11 01:24:10,899] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 01:24:10,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:10,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-11_01-24-10.log] [testng] 01:24:10,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c48d0d1 - End of configuration. [testng] [2024-04-11 01:24:10,925] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:10,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:10,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:10,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-11_01-24-10.log] [testng] 01:24:10,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31264c57 - End of configuration. [testng] [2024-04-11 01:24:12,324] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-04-11 01:24:12,330] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-11 01:24:12,341] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-11 01:24:12,460] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-04-11 01:24:12,977] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-04-11 01:24:12,985] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-11 01:24:13,679] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-11 01:24:13,997] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-04-11 01:24:14,394] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-11 01:24:14,720] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-04-11 01:24:14,757] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-04-11 01:24:14,780] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-11 01:24:14,800] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-11 01:24:15,008] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-04-11 01:24:15,145] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-11 01:24:15,352] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-11 01:24:15,369] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-04-11 01:24:15,425] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-04-11 01:24:15,486] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-04-11 01:24:15,619] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-11 01:24:15,625] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-04-11 01:24:15,690] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-11 01:24:15,793] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-04-11 01:24:15,871] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-04-11 01:24:15,907] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-11 01:24:15,980] [pool-1-thread-5] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-04-11 01:24:16,110] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-04-11 01:24:16,196] [pool-1-thread-10] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-11 01:24:17,561] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-04-11 01:24:17,884] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-11 01:24:17,933] [pool-1-thread-8] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-11 01:24:18,078] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-04-11 01:24:18,121] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-11 01:24:18,241] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-04-11 01:24:18,468] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-04-11 01:24:18,793] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-11 01:24:19,267] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-11 01:24:19,294] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-11 01:24:19,307] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-04-11 01:24:19,757] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-04-11 01:24:19,963] [pool-1-thread-5] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-04-11 01:24:20,088] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-04-11 01:24:20,143] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-11 01:24:20,158] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-11 01:24:20,327] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-11 01:24:20,454] [pool-1-thread-8] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-04-11 01:24:20,972] [pool-1-thread-12] 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 18 seconds Finished: SUCCESS