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Started by upstream project "BIOFORMATS-test-repo" build number 240 originally caused by: Started by upstream project "Trigger" build number 265 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/jenkins4650868638211540432.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37811_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 03:12:21,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:12:21,687 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 03:12:21,687 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:12:21,688 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:12:21,688 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:12:21,689 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:12:21,689 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:12:21,689 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:12:21,689 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:12:21,690 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:12:21,690 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:12:21,690 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:12:21,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:12:21,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:12:21,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:12:21,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:12:21,872 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:12:21,872 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:12:21,872 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:12:21,872 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:12:21,872 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 03:12:21,873 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 03:12:21,873 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 184 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-31 03:12:21,882] [main] java.version = 21 [testng] 03:12:21,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:12:21,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:21,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_03-12-21.log] [testng] 03:12:21,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-31 03:12:21,928] [main] testng.directory = /data [testng] [2024-10-31 03:12:21,928] [main] testng.configDirectory = /config [testng] [2024-10-31 03:12:21,939] [main] testng.multiplier = 1.0 [testng] [2024-10-31 03:12:21,940] [main] testng.in-memory = false [testng] [2024-10-31 03:12:21,940] [main] testng.allow-missing = false [testng] [2024-10-31 03:12:21,940] [main] user.language = en [testng] [2024-10-31 03:12:21,940] [main] user.country = ${user.country} [testng] [2024-10-31 03:12:21,940] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-31 03:33:58,096] [main] ---------------------------------------- [testng] [2024-10-31 03:33:58,096] [main] Total files: 826 [testng] [2024-10-31 03:33:58,096] [main] Scan time: 1296.155 s (1569 ms/file) [testng] [2024-10-31 03:33:58,097] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-31 03:35:18,234] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 03:35:18,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:35:18,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:18,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-31_03-35-18.log] [testng] 03:35:18,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52c9aa93 - End of configuration. [testng] [2024-10-31 03:35:20,565] [pool-1-thread-12] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 03:35:20,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:35:20,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:20,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-31_03-35-20.log] [testng] 03:35:20,566 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e741ca5 - End of configuration. [testng] [2024-10-31 03:35:25,932] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 03:35:25,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:35:25,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:25,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-31_03-35-25.log] [testng] 03:35:25,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@705f4ee - End of configuration. [testng] [2024-10-31 03:35:28,139] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 03:35:28,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:35:28,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:28,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-31_03-35-28.log] [testng] 03:35:28,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5687976e - End of configuration. [testng] [2024-10-31 03:35:30,392] [pool-1-thread-9] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 03:35:30,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:35:30,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:30,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-31_03-35-30.log] [testng] 03:35:30,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fcba1b - End of configuration. [testng] [2024-10-31 03:35:37,450] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 03:35:37,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:35:37,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:37,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-31_03-35-37.log] [testng] 03:35:37,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fd8a54 - End of configuration. [testng] [2024-10-31 03:35:39,616] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 03:35:39,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:35:39,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:39,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-31_03-35-39.log] [testng] 03:35:39,617 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ff8a022 - End of configuration. [testng] [2024-10-31 03:35:41,539] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 03:35:41,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:35:41,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:41,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-31_03-35-41.log] [testng] 03:35:41,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bfb7450 - End of configuration. [testng] [2024-10-31 03:35:43,591] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 03:35:43,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:35:43,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:43,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-31_03-35-43.log] [testng] 03:35:43,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ee74a4 - End of configuration. [testng] [2024-10-31 03:35:45,770] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 03:35:45,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:35:45,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:45,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-31_03-35-45.log] [testng] 03:35:45,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1faa2417 - End of configuration. [testng] [2024-10-31 03:35:47,907] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 03:35:47,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:35:47,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:47,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-31_03-35-47.log] [testng] 03:35:47,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ce8e8f3 - End of configuration. [testng] [2024-10-31 03:35:50,075] [pool-1-thread-2] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 03:35:50,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:35:50,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:50,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-31_03-35-50.log] [testng] 03:35:50,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f21614c - End of configuration. [testng] [2024-10-31 03:36:04,595] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] [2024-10-31 03:36:06,562] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] [2024-10-31 03:36:08,382] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] [2024-10-31 03:36:10,332] [pool-1-thread-5] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] [2024-10-31 03:36:12,857] [pool-1-thread-10] 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: 37 minutes 52 seconds Finished: SUCCESS