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Started by upstream project "BIOFORMATS-test-repo" build number 118 originally caused by: Started by upstream project "Trigger" build number 135 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/jenkins15219872499014682166.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18371_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 test-automated: [testng] File leak detector installed [testng] 01:26:05,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:26:05,889 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:26:05,889 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:05,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:05,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:26:05,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:26:05,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:26:05,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:05,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:05,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:26:05,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:26:05,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:26:06,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:26:06,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:26:06,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:26:06,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:26:06,198 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:26:06,199 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:26:06,199 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:26:06,199 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:26:06,199 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:26:06,200 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:26:06,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 308 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-12 01:26:06,212] [main] java.version = 1.8.0_342 [testng] 01:26:06,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:26:06,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:06,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-12_01-26-06.log] [testng] 01:26:06,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-12 01:26:06,276] [main] testng.directory = /data [testng] [2024-07-12 01:26:06,277] [main] testng.configDirectory = /config [testng] [2024-07-12 01:26:06,292] [main] testng.multiplier = 1.0 [testng] [2024-07-12 01:26:06,292] [main] testng.in-memory = false [testng] [2024-07-12 01:26:06,292] [main] testng.allow-missing = false [testng] [2024-07-12 01:26:06,292] [main] user.language = en [testng] [2024-07-12 01:26:06,292] [main] user.country = ${user.country} [testng] [2024-07-12 01:26:06,292] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-12 01:26:30,542] [main] ---------------------------------------- [testng] [2024-07-12 01:26:30,542] [main] Total files: 164 [testng] [2024-07-12 01:26:30,542] [main] Scan time: 24.25 s (147 ms/file) [testng] [2024-07-12 01:26:30,542] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-12 01:26:41,551] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:26:41,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:26:41,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-12_01-26-41.log] [testng] 01:26:41,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10973371 - End of configuration. [testng] [2024-07-12 01:26:41,596] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 01:26:41,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:26:41,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-12_01-26-41.log] [testng] 01:26:41,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4d094e - End of configuration. [testng] [2024-07-12 01:26:41,616] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 01:26:41,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:26:41,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-12_01-26-41.log] [testng] 01:26:41,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aa35c0c - End of configuration. [testng] [2024-07-12 01:26:41,657] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] 01:26:41,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:26:41,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-12_01-26-41.log] [testng] 01:26:41,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b91422 - End of configuration. [testng] [2024-07-12 01:26:41,703] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 01:26:41,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:26:41,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-12_01-26-41.log] [testng] 01:26:41,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30ca7afd - End of configuration. [testng] [2024-07-12 01:26:41,724] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:26:41,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:26:41,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-12_01-26-41.log] [testng] 01:26:41,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41ad31dc - End of configuration. [testng] [2024-07-12 01:26:41,796] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:26:41,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:26:41,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-12_01-26-41.log] [testng] 01:26:41,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b107a52 - End of configuration. [testng] [2024-07-12 01:26:41,839] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 01:26:41,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:26:41,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-12_01-26-41.log] [testng] 01:26:41,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb21b7f - End of configuration. [testng] [2024-07-12 01:26:41,849] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:26:41,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:26:41,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,850 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-12_01-26-41.log] [testng] 01:26:41,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51133498 - End of configuration. [testng] [2024-07-12 01:26:41,863] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 01:26:41,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:26:41,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-12_01-26-41.log] [testng] 01:26:41,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76088e72 - End of configuration. [testng] [2024-07-12 01:26:41,887] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] 01:26:41,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:26:41,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-12_01-26-41.log] [testng] 01:26:41,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2690dc60 - End of configuration. [testng] [2024-07-12 01:26:41,910] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:26:41,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:26:41,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:41,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-12_01-26-41.log] [testng] 01:26:41,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69edda6c - End of configuration. [testng] [2024-07-12 01:26:45,019] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-12 01:26:45,045] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-07-12 01:26:45,203] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-12 01:26:45,434] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-12 01:26:45,476] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-07-12 01:26:45,498] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-12 01:26:46,391] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-07-12 01:26:46,449] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-12 01:26:46,459] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-07-12 01:26:46,581] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-12 01:26:46,675] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-07-12 01:26:47,054] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-12 01:26:47,062] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern: [testng] [2024-07-12 01:26:47,398] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-07-12 01:26:47,483] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-07-12 01:26:48,019] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-12 01:26:48,030] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-07-12 01:26:48,123] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-12 01:26:48,133] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-12 01:26:48,142] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-12 01:26:48,206] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-12 01:26:48,260] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-07-12 01:26:48,312] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-07-12 01:26:48,566] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-12 01:26:48,761] [pool-1-thread-3] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-07-12 01:26:48,800] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-12 01:26:49,439] [pool-1-thread-7] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-12 01:26:49,563] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-12 01:26:49,768] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-12 01:26:49,899] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-07-12 01:26:50,045] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-07-12 01:26:50,055] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-07-12 01:26:50,119] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-07-12 01:26:50,176] [pool-1-thread-10] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-12 01:26:51,679] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-12 01:26:51,762] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-07-12 01:26:52,269] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-07-12 01:26:52,304] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-07-12 01:26:52,313] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-12 01:26:52,455] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-12 01:26:52,573] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-07-12 01:26:52,639] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-12 01:26:52,673] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-12 01:26:52,703] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-07-12 01:26:53,020] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-12 01:26:53,400] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-12 01:26:53,423] [pool-1-thread-1] Initializing /data/ome/t1_pos1-0_5x.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 31 seconds Finished: SUCCESS