Started by upstream project "BIOFORMATS-test-repo" build number 207 originally caused by: Started by upstream project "Trigger" build number 233 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins3427929919464799315.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32810_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] 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] 01:54:57,022 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:54:57,023 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:54:57,023 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:54:57,024 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:54:57,025 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:54:57,025 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:54:57,025 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:54:57,025 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:54:57,026 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:54:57,026 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:54:57,027 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:54:57,027 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:54:57,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:54:57,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:54:57,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:54:57,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:54:57,229 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:54:57,229 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:54:57,230 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:54:57,230 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:54:57,230 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:54:57,231 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:54:57,232 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 206 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-02 01:54:57,241] [main] java.version = 17.0.2 [testng] 01:54:57,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:54:57,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:57,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-02_01-54-57.log] [testng] 01:54:57,292 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-10-02 01:54:57,294] [main] testng.directory = /data [testng] [2024-10-02 01:54:57,294] [main] testng.configDirectory = /config [testng] [2024-10-02 01:54:57,304] [main] testng.multiplier = 1.0 [testng] [2024-10-02 01:54:57,305] [main] testng.in-memory = false [testng] [2024-10-02 01:54:57,305] [main] testng.allow-missing = false [testng] [2024-10-02 01:54:57,305] [main] user.language = en [testng] [2024-10-02 01:54:57,305] [main] user.country = ${user.country} [testng] [2024-10-02 01:54:57,305] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-02 01:56:13,812] [main] ---------------------------------------- [testng] [2024-10-02 01:56:13,812] [main] Total files: 164 [testng] [2024-10-02 01:56:13,812] [main] Scan time: 76.507 s (466 ms/file) [testng] [2024-10-02 01:56:13,812] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-02 01:58:30,852] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 01:58:30,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:58:30,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:30,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-02_01-58-30.log] [testng] 01:58:30,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f036803 - End of configuration. [testng] [2024-10-02 01:58:31,800] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:58:31,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:58:31,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:31,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-02_01-58-31.log] [testng] 01:58:31,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aca4c51 - End of configuration. [testng] [2024-10-02 01:58:32,508] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:58:32,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:58:32,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:32,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-02_01-58-32.log] [testng] 01:58:32,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72538368 - End of configuration. [testng] [2024-10-02 01:58:34,017] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:58:34,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:58:34,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:34,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-02_01-58-34.log] [testng] 01:58:34,018 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60240f0b - End of configuration. [testng] [2024-10-02 01:58:35,103] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:58:35,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:58:35,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:35,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-02_01-58-35.log] [testng] 01:58:35,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6703580a - End of configuration. [testng] [2024-10-02 01:58:35,666] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:58:35,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:58:35,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:35,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-02_01-58-35.log] [testng] 01:58:35,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55b7c62c - End of configuration. [testng] [2024-10-02 01:58:35,854] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 01:58:35,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:58:35,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:35,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-02_01-58-35.log] [testng] 01:58:35,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166a90ed - End of configuration. [testng] [2024-10-02 01:58:35,949] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:58:35,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:58:35,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:35,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-02_01-58-35.log] [testng] 01:58:35,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration. [testng] [2024-10-02 01:58:37,200] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:58:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:58:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:37,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-02_01-58-37.log] [testng] 01:58:37,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41802fc1 - End of configuration. [testng] [2024-10-02 01:58:38,786] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:58:38,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:58:38,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:38,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-02_01-58-38.log] [testng] 01:58:38,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@594515a3 - End of configuration. [testng] [2024-10-02 01:58:40,171] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 01:58:40,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:58:40,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:40,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-02_01-58-40.log] [testng] 01:58:40,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35b457b7 - End of configuration. [testng] [2024-10-02 01:58:42,850] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] 01:58:42,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:58:42,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:42,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-02_01-58-42.log] [testng] 01:58:42,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56ee7015 - End of configuration. [testng] [2024-10-02 01:58:47,973] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-02 01:58:48,107] [pool-1-thread-2] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-02 01:58:51,963] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-02 01:58:53,764] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-02 01:58:58,185] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-02 01:58:58,327] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-02 01:58:59,251] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-10-02 01:59:01,960] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-10-02 01:59:02,978] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-02 01:59:03,087] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-02 01:59:03,157] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-02 01:59:04,863] [pool-1-thread-3] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-02 01:59:07,108] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-02 01:59:07,975] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-02 01:59:10,922] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-02 01:59:11,054] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-02 01:59:11,739] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-02 01:59:11,997] [pool-1-thread-7] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-02 01:59:13,597] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-02 01:59:13,795] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-02 01:59:14,449] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-02 01:59:15,436] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-02 01:59:16,153] [pool-1-thread-8] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-02 01:59:44,320] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-02 01:59:45,290] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-02 01:59:46,222] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-02 01:59:47,142] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-02 01:59:47,351] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-02 01:59:47,437] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-02 01:59:49,736] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-10-02 01:59:50,322] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-02 01:59:50,666] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-02 01:59:51,839] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-02 01:59:53,159] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-02 01:59:53,811] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-02 01:59:54,908] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-02 01:59:55,074] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-02 01:59:55,793] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-02 01:59:57,939] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-02 01:59:58,721] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-02 01:59:59,865] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-02 02:00:01,424] [pool-1-thread-3] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-02 02:00:02,726] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-02 02:00:02,833] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-02 02:00:03,571] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-02 02:00:04,753] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-02 02:00:06,457] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 minutes 25 seconds Finished: SUCCESS