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Started by upstream project "BIOFORMATS-test-repo" build number 1 originally caused by: Started by upstream project "Trigger" build number 1 originally caused by: Started by user devspace 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/jenkins16697358336862195715.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/devspace/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 16:06:24,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 16:06:24,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 16:06:24,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:06:24,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:06:24,885 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 16:06:24,885 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 16:06:24,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 16:06:24,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:06:24,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:06:24,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 16:06:24,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 16:06:24,889 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 16:06:25,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 16:06:25,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 16:06:25,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 16:06:25,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 16:06:25,142 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 16:06:25,143 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 16:06:25,143 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 16:06:25,143 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 16:06:25,144 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 16:06:25,145 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 16:06:25,145 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-14 16:06:25,158] [main] java.version = 21 [testng] 16:06:25,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:06:25,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:06:25,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-14_16-06-25.log] [testng] 16:06:25,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-14 16:06:25,236] [main] testng.directory = /data [testng] [2024-03-14 16:06:25,236] [main] testng.configDirectory = /config [testng] [2024-03-14 16:06:25,250] [main] testng.multiplier = 1.0 [testng] [2024-03-14 16:06:25,252] [main] testng.in-memory = false [testng] [2024-03-14 16:06:25,252] [main] testng.allow-missing = false [testng] [2024-03-14 16:06:25,252] [main] user.language = en [testng] [2024-03-14 16:06:25,252] [main] user.country = ${user.country} [testng] [2024-03-14 16:06:25,252] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-14 16:06:48,765] [main] ---------------------------------------- [testng] [2024-03-14 16:06:48,765] [main] Total files: 164 [testng] [2024-03-14 16:06:48,765] [main] Scan time: 23.513 s (143 ms/file) [testng] [2024-03-14 16:06:48,766] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-14 16:07:03,974] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 16:07:03,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:07:03,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:03,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-14_16-07-03.log] [testng] 16:07:03,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a5d7a18 - End of configuration. [testng] [2024-03-14 16:07:04,005] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 16:07:04,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:07:04,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:04,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-14_16-07-04.log] [testng] 16:07:04,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6425d2bd - End of configuration. [testng] [2024-03-14 16:07:04,672] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 16:07:04,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 16:07:04,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:04,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-14_16-07-04.log] [testng] 16:07:04,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db551c4 - End of configuration. [testng] [2024-03-14 16:07:04,688] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 16:07:04,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 16:07:04,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:04,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-14_16-07-04.log] [testng] 16:07:04,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e78380 - End of configuration. [testng] [2024-03-14 16:07:04,994] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 16:07:04,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 16:07:04,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:04,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-14_16-07-04.log] [testng] 16:07:04,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@667846ad - End of configuration. [testng] [2024-03-14 16:07:05,081] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 16:07:05,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 16:07:05,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-14_16-07-05.log] [testng] 16:07:05,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4911acaa - End of configuration. [testng] [2024-03-14 16:07:05,116] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 16:07:05,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:07:05,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-14_16-07-05.log] [testng] 16:07:05,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c3bfb82 - End of configuration. [testng] [2024-03-14 16:07:05,128] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 16:07:05,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:07:05,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-14_16-07-05.log] [testng] 16:07:05,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fe24b48 - End of configuration. [testng] [2024-03-14 16:07:05,142] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 16:07:05,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:07:05,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-14_16-07-05.log] [testng] 16:07:05,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa39c8a - End of configuration. [testng] [2024-03-14 16:07:05,160] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 16:07:05,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:07:05,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-14_16-07-05.log] [testng] 16:07:05,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4112e0ce - End of configuration. [testng] [2024-03-14 16:07:05,263] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 16:07:05,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 16:07:05,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-14_16-07-05.log] [testng] 16:07:05,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36dccf5d - End of configuration. [testng] [2024-03-14 16:07:05,347] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 16:07:05,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 16:07:05,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:07:05,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-14_16-07-05.log] [testng] 16:07:05,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@679df212 - End of configuration. [testng] [2024-03-14 16:07:07,209] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-03-14 16:07:07,235] [pool-1-thread-7] Initializing /data/ome/654Atemp.stk: [testng] [2024-03-14 16:07:07,554] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-03-14 16:07:07,779] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-03-14 16:07:07,816] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-03-14 16:07:08,352] [pool-1-thread-4] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-03-14 16:07:08,521] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-03-14 16:07:09,523] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-03-14 16:07:09,813] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-03-14 16:07:09,933] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-03-14 16:07:10,130] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-03-14 16:07:10,328] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-03-14 16:07:10,684] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-03-14 16:07:10,755] [pool-1-thread-4] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-03-14 16:07:10,995] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-03-14 16:07:11,015] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-03-14 16:07:11,327] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-03-14 16:07:11,566] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-03-14 16:07:11,712] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] [2024-03-14 16:07:11,890] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-03-14 16:07:11,915] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-03-14 16:07:12,020] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-03-14 16:07:12,188] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-03-14 16:07:12,198] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-03-14 16:07:12,477] [pool-1-thread-8] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-03-14 16:07:12,566] [pool-1-thread-2] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-03-14 16:07:12,816] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-03-14 16:07:13,061] [pool-1-thread-4] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-03-14 16:07:15,756] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-03-14 16:07:16,020] [pool-1-thread-10] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-03-14 16:07:16,530] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2024-03-14 16:07:16,649] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-03-14 16:07:16,763] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-03-14 16:07:17,222] [pool-1-thread-10] Initializing /data/ome/embryo.lsm: [testng] [2024-03-14 16:07:17,391] [pool-1-thread-7] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-03-14 16:07:17,924] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-03-14 16:07:18,184] [pool-1-thread-12] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-03-14 16:07:18,425] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-03-14 16:07:18,673] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-03-14 16:07:18,703] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-03-14 16:07:19,055] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-03-14 16:07:19,300] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-03-14 16:07:19,442] [pool-1-thread-7] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-03-14 16:07:19,549] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-03-14 16:07:19,954] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-03-14 16:07:20,055] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-03-14 16:07:20,425] [pool-1-thread-7] 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 15 seconds Finished: SUCCESS