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Started by upstream project "BIOFORMATS-test-repo" build number 70 originally caused by: Started by upstream project "Trigger" build number 78 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7677924613008194439.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_10499_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:24:38,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:38,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:24:38,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:38,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:38,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:38,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:38,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:38,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:38,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:38,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:38,216 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:38,216 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:38,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:38,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:38,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:38,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:38,501 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:38,502 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:38,502 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:38,502 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:38,502 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:24:38,504 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:24:38,504 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 290 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-21 01:24:38,515] [main] java.version = 11.0.16 [testng] 01:24:38,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:38,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-21_01-24-38.log] [testng] 01:24:38,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-05-21 01:24:38,604] [main] testng.directory = /data [testng] [2024-05-21 01:24:38,604] [main] testng.configDirectory = /config [testng] [2024-05-21 01:24:38,618] [main] testng.multiplier = 1.0 [testng] [2024-05-21 01:24:38,620] [main] testng.in-memory = false [testng] [2024-05-21 01:24:38,620] [main] testng.allow-missing = false [testng] [2024-05-21 01:24:38,620] [main] user.language = en [testng] [2024-05-21 01:24:38,620] [main] user.country = ${user.country} [testng] [2024-05-21 01:24:38,620] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-21 01:24:58,366] [main] ---------------------------------------- [testng] [2024-05-21 01:24:58,366] [main] Total files: 164 [testng] [2024-05-21 01:24:58,366] [main] Scan time: 19.746 s (120 ms/file) [testng] [2024-05-21 01:24:58,366] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-21 01:25:06,021] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] 01:25:06,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:25:06,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-21_01-25-06.log] [testng] 01:25:06,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a8db93d - End of configuration. [testng] [2024-05-21 01:25:06,072] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] 01:25:06,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:25:06,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-21_01-25-06.log] [testng] 01:25:06,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ea673c3 - End of configuration. [testng] [2024-05-21 01:25:06,097] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:25:06,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:25:06,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-21_01-25-06.log] [testng] 01:25:06,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59f6d05d - End of configuration. [testng] [2024-05-21 01:25:06,108] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:25:06,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:25:06,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-21_01-25-06.log] [testng] 01:25:06,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20170761 - End of configuration. [testng] [2024-05-21 01:25:06,138] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:25:06,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:25:06,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-21_01-25-06.log] [testng] 01:25:06,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20f6085f - End of configuration. [testng] [2024-05-21 01:25:06,191] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:25:06,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:25:06,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-21_01-25-06.log] [testng] 01:25:06,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59d94632 - End of configuration. [testng] [2024-05-21 01:25:06,228] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:25:06,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:25:06,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-21_01-25-06.log] [testng] 01:25:06,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7db01932 - End of configuration. [testng] [2024-05-21 01:25:06,418] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] 01:25:06,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:25:06,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-21_01-25-06.log] [testng] 01:25:06,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3def125a - End of configuration. [testng] [2024-05-21 01:25:06,427] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:25:06,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:25:06,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,429 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-21_01-25-06.log] [testng] 01:25:06,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74a7c4bd - End of configuration. [testng] [2024-05-21 01:25:06,466] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:25:06,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:25:06,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-21_01-25-06.log] [testng] 01:25:06,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6909c20d - End of configuration. [testng] [2024-05-21 01:25:06,480] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:25:06,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:25:06,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-21_01-25-06.log] [testng] 01:25:06,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6705ab5b - End of configuration. [testng] [2024-05-21 01:25:06,554] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] 01:25:06,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:25:06,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:06,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-21_01-25-06.log] [testng] 01:25:06,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35d6dd18 - End of configuration. [testng] [2024-05-21 01:25:09,153] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-21 01:25:09,171] [pool-1-thread-4] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-21 01:25:09,258] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-05-21 01:25:09,264] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-05-21 01:25:09,297] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-21 01:25:09,304] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-21 01:25:09,497] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-05-21 01:25:09,508] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-21 01:25:09,871] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-05-21 01:25:09,918] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-05-21 01:25:09,948] [pool-1-thread-1] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-21 01:25:10,131] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-21 01:25:10,182] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-21 01:25:10,191] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-21 01:25:10,328] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-05-21 01:25:10,383] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-21 01:25:10,516] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-21 01:25:11,427] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-21 01:25:11,599] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-21 01:25:11,604] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-05-21 01:25:11,823] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-05-21 01:25:11,872] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-05-21 01:25:12,125] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-21 01:25:12,145] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-21 01:25:12,268] [pool-1-thread-10] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-21 01:25:12,429] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-21 01:25:12,549] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-21 01:25:12,683] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-21 01:25:12,785] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-05-21 01:25:12,990] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-05-21 01:25:13,159] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-21 01:25:13,248] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-21 01:25:13,323] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-21 01:25:13,883] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-21 01:25:13,955] [pool-1-thread-10] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-05-21 01:25:14,084] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-21 01:25:14,091] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-21 01:25:14,304] [pool-1-thread-8] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-05-21 01:25:14,483] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-21 01:25:14,560] [pool-1-thread-8] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-21 01:25:14,995] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-05-21 01:25:15,070] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-05-21 01:25:15,295] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-05-21 01:25:15,324] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-21 01:25:15,622] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-05-21 01:25:15,887] [pool-1-thread-11] Initializing /data/ome/embryo.lsm: [testng] [2024-05-21 01:25:15,992] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm: [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 13 seconds Finished: SUCCESS