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Started by upstream project "BIOFORMATS-test-repo" build number 191 originally caused by: Started by upstream project "Trigger" build number 213 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/jenkins1875215309635337639.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30230_merge_ci -v /uod/idr/repos/curated/tillvision:/data -v /uod/idr-scratch/merge-ci/curated/tillvision:/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] 01:52:03,203 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:52:03,205 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:52:03,205 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:52:03,207 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:52:03,207 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:52:03,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:52:03,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:52:03,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:52:03,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:52:03,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:52:03,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:52:03,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:52:03,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:52:03,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:52:03,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:52:03,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:52:03,450 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:52:03,450 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:52:03,450 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:52:03,451 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:52:03,451 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:52:03,452 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:52:03,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 243 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-17 01:52:03,462] [main] java.version = 11.0.16 [testng] 01:52:03,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:52:03,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:03,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-17_01-52-03.log] [testng] 01:52:03,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-09-17 01:52:03,517] [main] testng.directory = /data [testng] [2024-09-17 01:52:03,517] [main] testng.configDirectory = /config [testng] [2024-09-17 01:52:03,529] [main] testng.multiplier = 1.0 [testng] [2024-09-17 01:52:03,530] [main] testng.in-memory = false [testng] [2024-09-17 01:52:03,531] [main] testng.allow-missing = false [testng] [2024-09-17 01:52:03,531] [main] user.language = en [testng] [2024-09-17 01:52:03,531] [main] user.country = ${user.country} [testng] [2024-09-17 01:52:03,531] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-17 01:52:08,677] [main] ---------------------------------------- [testng] [2024-09-17 01:52:08,677] [main] Total files: 46 [testng] [2024-09-17 01:52:08,678] [main] Scan time: 5.146 s (111 ms/file) [testng] [2024-09-17 01:52:08,678] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-17 01:52:26,835] [pool-1-thread-1] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 01:52:26,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:52:26,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:26,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-17_01-52-26.log] [testng] 01:52:26,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e3d7ef - End of configuration. [testng] [2024-09-17 01:52:27,099] [pool-1-thread-12] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:52:27,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:52:27,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:27,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-17_01-52-27.log] [testng] 01:52:27,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b7d39fa - End of configuration. [testng] [2024-09-17 01:52:27,224] [pool-1-thread-11] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:52:27,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:52:27,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:27,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-17_01-52-27.log] [testng] 01:52:27,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8f4faa - End of configuration. [testng] [2024-09-17 01:52:27,345] [pool-1-thread-10] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:52:27,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:52:27,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:27,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-17_01-52-27.log] [testng] 01:52:27,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27d529e0 - End of configuration. [testng] [2024-09-17 01:52:27,369] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] 01:52:27,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:52:27,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:27,370 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-17_01-52-27.log] [testng] 01:52:27,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c3b9b85 - End of configuration. [testng] [2024-09-17 01:52:27,417] [pool-1-thread-8] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:52:27,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:52:27,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:27,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-17_01-52-27.log] [testng] 01:52:27,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68084013 - End of configuration. [testng] [2024-09-17 01:52:28,736] [pool-1-thread-7] Initializing /data/imagesc-84715/working.vws: [testng] 01:52:28,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:52:28,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:28,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-17_01-52-28.log] [testng] 01:52:28,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ec3a828 - End of configuration. [testng] [2024-09-17 01:52:29,157] [pool-1-thread-6] Initializing /data/andreas/090811E1.vws: [testng] 01:52:29,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:52:29,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:29,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-17_01-52-29.log] [testng] 01:52:29,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4855f9e9 - End of configuration. [testng] [2024-09-17 01:52:31,541] [pool-1-thread-5] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:52:31,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:52:31,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:31,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-17_01-52-31.log] [testng] 01:52:31,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a237670 - End of configuration. [testng] [2024-09-17 01:52:31,647] [pool-1-thread-4] Initializing /data/samples/fibre.vws: [testng] 01:52:31,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:52:31,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:31,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-17_01-52-31.log] [testng] 01:52:31,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a91343e - End of configuration. [testng] [2024-09-17 01:52:31,673] [pool-1-thread-3] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 01:52:31,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:52:31,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:31,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-17_01-52-31.log] [testng] 01:52:31,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78879b75 - End of configuration. [testng] [2024-09-17 01:52:32,353] [pool-1-thread-2] Initializing /data/imagesc-84715/not working.vws: [testng] 01:52:32,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:52:32,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:32,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-17_01-52-32.log] [testng] 01:52:32,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@362a0c31 - End of configuration. [testng] [2024-09-17 01:52:34,114] [pool-1-thread-4] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2024-09-17 01:52:37,886] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-09-17 01:52:38,261] [pool-1-thread-11] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-09-17 01:52:41,670] [pool-1-thread-12] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-09-17 01:52:41,940] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-09-17 01:52:43,240] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] [2024-09-17 01:52:44,160] [pool-1-thread-5] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-09-17 01:52:44,780] [pool-1-thread-2] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-09-17 01:52:44,863] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-09-17 01:52:44,955] [pool-1-thread-10] Initializing /data/gerhard/test.vws: [testng] [2024-09-17 01:52:45,278] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-09-17 01:52:45,791] [pool-1-thread-1] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-09-17 01:52:46,085] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 43 seconds Finished: SUCCESS