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Started by upstream project "BIOFORMATS-test-repo" build number 388 originally caused by: Started by upstream project "Trigger" build number 411 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@18 [BIOFORMATS-test-folder@18] $ /bin/bash -xe /tmp/jenkins11004644550980305770.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61435_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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] 02:25:18,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:25:18,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 02:25:18,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:25:18,648 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:25:18,649 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:25:18,649 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:25:18,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:25:18,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:25:18,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:25:18,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:25:18,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:25:18,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:25:18,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:25:18,809 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:25:18,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:25:18,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:25:18,836 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:25:18,836 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:25:18,836 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:25:18,836 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:25:18,836 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 02:25:18,837 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 02:25:18,838 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-23 02:25:18,846] [main] java.version = 17.0.2 [testng] 02:25:18,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:25:18,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:25:18,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-23_02-25-18.log] [testng] 02:25:18,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-23 02:25:18,892] [main] testng.directory = /data [testng] [2025-03-23 02:25:18,892] [main] testng.configDirectory = /config [testng] [2025-03-23 02:25:18,900] [main] testng.multiplier = 1.0 [testng] [2025-03-23 02:25:18,901] [main] testng.in-memory = false [testng] [2025-03-23 02:25:18,901] [main] testng.allow-missing = false [testng] [2025-03-23 02:25:18,901] [main] user.language = en [testng] [2025-03-23 02:25:18,901] [main] user.country = ${user.country} [testng] [2025-03-23 02:25:18,901] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-23 02:26:14,846] [main] ---------------------------------------- [testng] [2025-03-23 02:26:14,846] [main] Total files: 21 [testng] [2025-03-23 02:26:14,846] [main] Scan time: 55.945 s (2664 ms/file) [testng] [2025-03-23 02:26:14,846] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-23 02:27:18,402] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 02:27:18,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:27:18,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:18,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-23_02-27-18.log] [testng] 02:27:18,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d69040d - End of configuration. [testng] [2025-03-23 02:27:21,851] [pool-1-thread-12] Initializing /data/frans/ch2bet.hdr: [testng] 02:27:21,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:27:21,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:21,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-23_02-27-21.log] [testng] 02:27:21,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51c981ae - End of configuration. [testng] [2025-03-23 02:27:25,057] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 02:27:25,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:27:25,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:25,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-23_02-27-25.log] [testng] 02:27:25,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6526877 - End of configuration. [testng] [2025-03-23 02:27:28,063] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 02:27:28,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:27:28,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:28,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-23_02-27-28.log] [testng] 02:27:28,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5389b543 - End of configuration. [testng] [2025-03-23 02:27:31,020] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 02:27:31,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:27:31,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:31,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-23_02-27-31.log] [testng] 02:27:31,021 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ed65e2 - End of configuration. [testng] [2025-03-23 02:27:33,805] [pool-1-thread-8] Initializing /data/frans/ch2.hdr: [testng] 02:27:33,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:27:33,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:33,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-23_02-27-33.log] [testng] 02:27:33,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34153be1 - End of configuration. [testng] [2025-03-23 02:27:36,712] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 02:27:36,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:27:36,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:36,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-23_02-27-36.log] [testng] 02:27:36,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35187836 - End of configuration. [testng] [2025-03-23 02:27:40,083] [pool-1-thread-6] Initializing /data/frans/CT_CRANI.hdr: [testng] 02:27:40,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:27:40,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:40,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-23_02-27-40.log] [testng] 02:27:40,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f0fc35 - End of configuration. [testng] [2025-03-23 02:27:43,211] [pool-1-thread-5] Initializing /data/frans/CT_CHEST.hdr: [testng] 02:27:43,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:27:43,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:43,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-23_02-27-43.log] [testng] 02:27:43,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f8c191d - End of configuration. [testng] [2025-03-23 02:27:46,435] [pool-1-thread-4] Initializing /data/frans/aal.hdr: [testng] 02:27:46,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:27:46,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-23_02-27-46.log] [testng] 02:27:46,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e022fad - End of configuration. [testng] [2025-03-23 02:27:49,791] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 02:27:49,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:27:49,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:49,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-23_02-27-49.log] [testng] 02:27:49,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6431fcbd - End of configuration. [testng] [2025-03-23 02:27:52,921] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 02:27:52,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:27:52,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-23_02-27-52.log] [testng] 02:27:52,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e4b6c74 - End of configuration. [testng] [2025-03-23 02:28:19,931] [pool-1-thread-1] Initializing /data/frans/CT_HAND.hdr: [testng] [2025-03-23 02:28:22,382] [pool-1-thread-3] Initializing /data/frans/CT_FOOT.hdr: [testng] [2025-03-23 02:28:25,244] [pool-1-thread-12] Initializing /data/frans/brodmann.hdr: [testng] [2025-03-23 02:28:28,125] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2025-03-23 02:28:30,976] [pool-1-thread-8] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2025-03-23 02:28:31,484] [pool-1-thread-6] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2025-03-23 02:28:34,127] [pool-1-thread-4] Initializing /data/frans/CT_APERT.hdr: [testng] [2025-03-23 02:28:36,644] [pool-1-thread-11] Initializing /data/frans/CT_KNEE.hdr: [testng] [2025-03-23 02:28:39,146] [pool-1-thread-5] Initializing /data/frans/MR_CHEST.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 46 seconds Finished: SUCCESS