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Started by upstream project "BIOFORMATS-test-repo" build number 293 originally caused by: Started by upstream project "Trigger" build number 312 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins7206718335848233596.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46377_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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] 09:06:34,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:06:34,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 09:06:34,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:06:34,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:06:34,526 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:06:34,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:06:34,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:06:34,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:06:34,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:06:34,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:06:34,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:06:34,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:06:34,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:06:34,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:06:34,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:06:34,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:06:34,724 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:06:34,724 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:06:34,725 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:06:34,725 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:06:34,725 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 09:06:34,726 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 09:06:34,726 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-17 09:06:34,735] [main] java.version = 11.0.16 [testng] 09:06:34,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:06:34,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:34,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-17_09-06-34.log] [testng] 09:06:34,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-17 09:06:34,783] [main] testng.directory = /data [testng] [2024-12-17 09:06:34,783] [main] testng.configDirectory = /config [testng] [2024-12-17 09:06:34,793] [main] testng.multiplier = 1.0 [testng] [2024-12-17 09:06:34,794] [main] testng.in-memory = false [testng] [2024-12-17 09:06:34,794] [main] testng.allow-missing = false [testng] [2024-12-17 09:06:34,794] [main] user.language = en [testng] [2024-12-17 09:06:34,794] [main] user.country = ${user.country} [testng] [2024-12-17 09:06:34,794] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-17 10:03:07,796] [main] ---------------------------------------- [testng] [2024-12-17 10:03:07,796] [main] Total files: 826 [testng] [2024-12-17 10:03:07,796] [main] Scan time: 3393.002 s (4107 ms/file) [testng] [2024-12-17 10:03:07,796] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-17 10:05:58,360] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 10:05:58,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:05:58,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:05:58,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-17_10-05-58.log] [testng] 10:05:58,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@532a7f88 - End of configuration. [testng] [2024-12-17 10:06:02,631] [pool-1-thread-12] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 10:06:02,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:06:02,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:02,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-17_10-06-02.log] [testng] 10:06:02,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d901036 - End of configuration. [testng] [2024-12-17 10:06:13,122] [pool-1-thread-11] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 10:06:13,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:06:13,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:13,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-17_10-06-13.log] [testng] 10:06:13,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ec27c0a - End of configuration. [testng] [2024-12-17 10:06:17,246] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 10:06:17,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:06:17,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:17,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-17_10-06-17.log] [testng] 10:06:17,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4215551c - End of configuration. [testng] [2024-12-17 10:06:21,376] [pool-1-thread-9] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 10:06:21,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:06:21,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:21,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-17_10-06-21.log] [testng] 10:06:21,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79cd85b4 - End of configuration. [testng] [2024-12-17 10:06:25,563] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 10:06:25,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:06:25,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:25,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-17_10-06-25.log] [testng] 10:06:25,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49ec86a - End of configuration. [testng] [2024-12-17 10:06:29,597] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 10:06:29,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:06:29,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:29,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-17_10-06-29.log] [testng] 10:06:29,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67a4a550 - End of configuration. [testng] [2024-12-17 10:06:33,621] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 10:06:33,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:06:33,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:33,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-17_10-06-33.log] [testng] 10:06:33,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c7c5a98 - End of configuration. [testng] [2024-12-17 10:06:37,549] [pool-1-thread-5] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 10:06:37,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:06:37,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:37,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-17_10-06-37.log] [testng] 10:06:37,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61447dee - End of configuration. [testng] [2024-12-17 10:06:42,034] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 10:06:42,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:06:42,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:42,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-17_10-06-42.log] [testng] 10:06:42,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fcaa384 - End of configuration. [testng] [2024-12-17 10:06:46,061] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 10:06:46,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:06:46,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:46,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-17_10-06-46.log] [testng] 10:06:46,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28b099e6 - End of configuration. [testng] [2024-12-17 10:06:50,114] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 10:06:50,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:06:50,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:50,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-17_10-06-50.log] [testng] 10:06:50,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e014271 - End of configuration. [testng] [2024-12-17 10:07:19,739] [pool-1-thread-11] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] [2024-12-17 10:07:34,130] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-12-17 10:07:38,313] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2024-12-17 10:07:42,529] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] [2024-12-17 10:07:46,907] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 100 minutes 43 seconds Finished: SUCCESS