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Started by upstream project "BIOFORMATS-test-repo" build number 229 originally caused by: Started by upstream project "Trigger" build number 254 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins18426980039728561487.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36006_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] 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] 04:05:22,223 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:05:22,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 04:05:22,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:05:22,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:05:22,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:05:22,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:05:22,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:05:22,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:05:22,227 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:05:22,227 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:05:22,228 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:05:22,228 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:05:22,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:05:22,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:05:22,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:05:22,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:05:22,425 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:05:22,425 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:05:22,425 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:05:22,426 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:05:22,426 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 04:05:22,426 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 04:05:22,426 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-20 04:05:22,435] [main] java.version = 17.0.2 [testng] 04:05:22,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:05:22,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:22,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-20_04-05-22.log] [testng] 04:05:22,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-20 04:05:22,486] [main] testng.directory = /data [testng] [2024-10-20 04:05:22,486] [main] testng.configDirectory = /config [testng] [2024-10-20 04:05:22,495] [main] testng.multiplier = 1.0 [testng] [2024-10-20 04:05:22,496] [main] testng.in-memory = false [testng] [2024-10-20 04:05:22,496] [main] testng.allow-missing = false [testng] [2024-10-20 04:05:22,496] [main] user.language = en [testng] [2024-10-20 04:05:22,496] [main] user.country = ${user.country} [testng] [2024-10-20 04:05:22,496] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-20 04:26:35,617] [main] ---------------------------------------- [testng] [2024-10-20 04:26:35,617] [main] Total files: 826 [testng] [2024-10-20 04:26:35,617] [main] Scan time: 1273.121 s (1541 ms/file) [testng] [2024-10-20 04:26:35,617] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-20 04:27:56,986] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 04:27:56,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:27:56,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:27:56,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-20_04-27-56.log] [testng] 04:27:56,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b365d79 - End of configuration. [testng] [2024-10-20 04:27:58,984] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 04:27:58,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:27:58,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:27:58,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-20_04-27-58.log] [testng] 04:27:58,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@692d5e0b - End of configuration. [testng] [2024-10-20 04:28:00,912] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 04:28:00,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:28:00,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:00,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-20_04-28-00.log] [testng] 04:28:00,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@686787ad - End of configuration. [testng] [2024-10-20 04:28:02,926] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 04:28:02,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:28:02,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:02,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-20_04-28-02.log] [testng] 04:28:02,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e0638d - End of configuration. [testng] [2024-10-20 04:28:04,906] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 04:28:04,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:28:04,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:04,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-20_04-28-04.log] [testng] 04:28:04,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409059a8 - End of configuration. [testng] [2024-10-20 04:28:06,877] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 04:28:06,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:28:06,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:06,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-20_04-28-06.log] [testng] 04:28:06,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31949e61 - End of configuration. [testng] [2024-10-20 04:28:08,815] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 04:28:08,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:28:08,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:08,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-20_04-28-08.log] [testng] 04:28:08,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2878c1ae - End of configuration. [testng] [2024-10-20 04:28:10,791] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 04:28:10,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:28:10,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:10,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-20_04-28-10.log] [testng] 04:28:10,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6057f525 - End of configuration. [testng] [2024-10-20 04:28:12,743] [pool-1-thread-5] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 04:28:12,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:28:12,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:12,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-20_04-28-12.log] [testng] 04:28:12,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b33c67 - End of configuration. [testng] [2024-10-20 04:28:19,318] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 04:28:19,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:28:19,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:19,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-20_04-28-19.log] [testng] 04:28:19,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fefc15a - End of configuration. [testng] [2024-10-20 04:28:21,301] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 04:28:21,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:28:21,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:21,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-20_04-28-21.log] [testng] 04:28:21,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@340030bc - End of configuration. [testng] [2024-10-20 04:28:23,271] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 04:28:23,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:28:23,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:23,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-20_04-28-23.log] [testng] 04:28:23,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56af8fea - End of configuration. [testng] [2024-10-20 04:28:36,769] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] [2024-10-20 04:28:38,730] [pool-1-thread-3] Initializing /data/wis/RA_060110.051/1/acqp: [testng] [2024-10-20 04:28:43,721] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-10-20 04:28:45,665] [pool-1-thread-4] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] [2024-10-20 04:28:47,859] [pool-1-thread-7] 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: 39 minutes 46 seconds Finished: SUCCESS