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Started by upstream project "BIOFORMATS-test-repo" build number 262 originally caused by: Started by upstream project "Trigger" build number 286 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins9023719111960096223.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41314_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:34:35,828 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:34:35,829 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:34:35,829 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:35,830 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:35,831 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:35,831 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:35,831 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:35,831 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:35,832 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:35,833 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:35,833 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:35,833 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:35,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:35,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:36,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:36,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:36,018 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:36,018 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:36,018 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:36,019 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:36,019 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:34:36,020 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:34:36,020 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 00:34:36,029] [main] java.version = 21 [testng] 00:34:36,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:36,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:36,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_00-34-36.log] [testng] 00:34:36,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 00:34:36,074] [main] testng.directory = /data [testng] [2024-11-21 00:34:36,074] [main] testng.configDirectory = /config [testng] [2024-11-21 00:34:36,083] [main] testng.multiplier = 1.0 [testng] [2024-11-21 00:34:36,083] [main] testng.in-memory = false [testng] [2024-11-21 00:34:36,083] [main] testng.allow-missing = false [testng] [2024-11-21 00:34:36,083] [main] user.language = en [testng] [2024-11-21 00:34:36,083] [main] user.country = ${user.country} [testng] [2024-11-21 00:34:36,084] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 00:35:16,606] [main] ---------------------------------------- [testng] [2024-11-21 00:35:16,606] [main] Total files: 164 [testng] [2024-11-21 00:35:16,606] [main] Scan time: 40.522 s (247 ms/file) [testng] [2024-11-21 00:35:16,606] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 00:36:10,354] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:36:10,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:36:10,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:10,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_00-36-10.log] [testng] 00:36:10,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cedc35b - End of configuration. [testng] [2024-11-21 00:36:10,742] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] 00:36:10,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:36:10,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:10,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_00-36-10.log] [testng] 00:36:10,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6492bb3f - End of configuration. [testng] [2024-11-21 00:36:10,852] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] 00:36:10,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:36:10,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:10,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_00-36-10.log] [testng] 00:36:10,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bba0814 - End of configuration. [testng] [2024-11-21 00:36:11,336] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 00:36:11,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:36:11,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_00-36-11.log] [testng] 00:36:11,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d23af89 - End of configuration. [testng] [2024-11-21 00:36:11,427] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:36:11,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:36:11,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_00-36-11.log] [testng] 00:36:11,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@380aae2d - End of configuration. [testng] [2024-11-21 00:36:11,515] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:36:11,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:36:11,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_00-36-11.log] [testng] 00:36:11,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@167e2adc - End of configuration. [testng] [2024-11-21 00:36:11,630] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:36:11,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:36:11,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:11,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_00-36-11.log] [testng] 00:36:11,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d4ff76 - End of configuration. [testng] [2024-11-21 00:36:12,588] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] 00:36:12,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:36:12,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_00-36-12.log] [testng] 00:36:12,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36e1b1ec - End of configuration. [testng] [2024-11-21 00:36:12,942] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:36:12,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:36:12,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:12,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_00-36-12.log] [testng] 00:36:12,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c40c7b0 - End of configuration. [testng] [2024-11-21 00:36:13,058] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:36:13,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:36:13,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:13,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_00-36-13.log] [testng] 00:36:13,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ca05f - End of configuration. [testng] [2024-11-21 00:36:13,973] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] 00:36:13,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:36:13,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:13,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_00-36-13.log] [testng] 00:36:13,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ec34be - End of configuration. [testng] [2024-11-21 00:36:14,719] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 00:36:14,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:36:14,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:14,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_00-36-14.log] [testng] 00:36:14,720 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57a411f5 - End of configuration. [testng] [2024-11-21 00:36:16,775] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-21 00:36:16,841] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-11-21 00:36:17,421] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-21 00:36:17,576] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-21 00:36:18,309] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-21 00:36:18,764] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-21 00:36:22,408] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-21 00:36:22,763] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-21 00:36:23,296] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-21 00:36:23,750] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-21 00:36:24,441] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-21 00:36:24,663] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-21 00:36:24,798] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-21 00:36:24,964] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-21 00:36:25,722] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-21 00:36:39,288] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-21 00:36:40,435] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-21 00:36:41,445] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-11-21 00:36:42,313] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-21 00:36:42,443] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-21 00:36:43,507] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-21 00:36:43,665] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-21 00:36:44,964] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-21 00:36:46,048] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-21 00:36:46,692] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-21 00:36:48,395] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-21 00:36:48,990] [pool-1-thread-9] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-21 00:36:49,704] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-21 00:36:50,440] [pool-1-thread-1] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-21 00:36:52,203] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-21 00:36:53,228] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-11-21 00:36:54,737] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-21 00:36:55,582] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-21 00:36:55,997] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-21 00:36:57,026] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-21 00:36:57,132] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-11-21 00:36:57,691] [pool-1-thread-6] Initializing /data/ome/worm.tiff: [testng] [2024-11-21 00:36:59,157] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-21 00:36:59,707] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-21 00:37:00,417] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-21 00:37:00,873] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-21 00:37:01,758] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-11-21 00:37:03,661] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-21 00:37:03,858] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-21 00:37:04,419] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-21 00:37:05,231] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-21 00:37:06,554] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [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 58 seconds Finished: SUCCESS