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Started by upstream project "BIOFORMATS-test-repo" build number 398 originally caused by: Started by upstream project "Trigger" build number 484 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@17 [BIOFORMATS-test-folder@17] $ /bin/bash -xe /tmp/jenkins15779684950553064971.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_62909_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] 07:37:30,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 07:37:30,608 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 07:37:30,608 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:37:30,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:37:30,609 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:37:30,609 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:37:30,610 |-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] 07:37:30,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:37:30,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:37:30,611 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:37:30,611 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:37:30,611 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:37:30,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:37:30,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:37:30,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:37:30,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:37:30,802 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:37:30,802 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:37:30,803 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:37:30,803 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:37:30,803 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 07:37:30,804 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 07:37:30,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-05-18 07:37:30,813] [main] java.version = 17.0.2 [testng] 07:37:30,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:37:30,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:37:30,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-18_07-37-30.log] [testng] 07:37:30,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-05-18 07:37:30,859] [main] testng.directory = /data [testng] [2025-05-18 07:37:30,860] [main] testng.configDirectory = /config [testng] [2025-05-18 07:37:30,868] [main] testng.multiplier = 1.0 [testng] [2025-05-18 07:37:30,869] [main] testng.in-memory = false [testng] [2025-05-18 07:37:30,869] [main] testng.allow-missing = false [testng] [2025-05-18 07:37:30,869] [main] user.language = en [testng] [2025-05-18 07:37:30,869] [main] user.country = ${user.country} [testng] [2025-05-18 07:37:30,869] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-05-18 07:39:24,098] [main] ---------------------------------------- [testng] [2025-05-18 07:39:24,098] [main] Total files: 21 [testng] [2025-05-18 07:39:24,098] [main] Scan time: 113.228 s (5391 ms/file) [testng] [2025-05-18 07:39:24,098] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-05-18 07:41:40,558] [pool-1-thread-1] Initializing /data/frans/CT_FOOT.hdr: [testng] 07:41:40,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:41:40,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:41:40,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-05-18_07-41-40.log] [testng] 07:41:40,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@716ca73d - End of configuration. [testng] [2025-05-18 07:41:49,348] [pool-1-thread-12] Initializing /data/frans/ch2bet.hdr: [testng] 07:41:49,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:41:49,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:41:49,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-05-18_07-41-49.log] [testng] 07:41:49,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45cc5755 - End of configuration. [testng] [2025-05-18 07:41:57,705] [pool-1-thread-11] Initializing /data/frans/CT_HAND.hdr: [testng] 07:41:57,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:41:57,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:41:57,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-05-18_07-41-57.log] [testng] 07:41:57,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a87c2f2 - End of configuration. [testng] [2025-05-18 07:42:00,874] [pool-1-thread-10] Initializing /data/frans/CT_CRANI.hdr: [testng] 07:42:00,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:42:00,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:00,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-05-18_07-42-00.log] [testng] 07:42:00,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16e5ae62 - End of configuration. [testng] [2025-05-18 07:42:10,079] [pool-1-thread-9] Initializing /data/frans/betmask.hdr: [testng] 07:42:10,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:42:10,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:10,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-05-18_07-42-10.log] [testng] 07:42:10,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46233177 - End of configuration. [testng] [2025-05-18 07:42:18,991] [pool-1-thread-8] Initializing /data/frans/CT_KNEE.hdr: [testng] 07:42:18,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:42:18,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:18,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-05-18_07-42-18.log] [testng] 07:42:18,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f27a87d - End of configuration. [testng] [2025-05-18 07:42:28,075] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 07:42:28,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:42:28,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:28,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-05-18_07-42-28.log] [testng] 07:42:28,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2147e37e - End of configuration. [testng] [2025-05-18 07:42:35,305] [pool-1-thread-6] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 07:42:35,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:42:35,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:35,306 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-05-18_07-42-35.log] [testng] 07:42:35,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d39b66d - End of configuration. [testng] [2025-05-18 07:42:42,226] [pool-1-thread-5] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 07:42:42,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:42:42,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:42,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-05-18_07-42-42.log] [testng] 07:42:42,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ce9a97 - End of configuration. [testng] [2025-05-18 07:42:50,557] [pool-1-thread-4] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 07:42:50,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:42:50,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:50,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-05-18_07-42-50.log] [testng] 07:42:50,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@516639ac - End of configuration. [testng] [2025-05-18 07:42:57,586] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 07:42:57,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:42:57,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:42:57,587 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-05-18_07-42-57.log] [testng] 07:42:57,587 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7239982c - End of configuration. [testng] [2025-05-18 07:43:04,195] [pool-1-thread-2] Initializing /data/frans/CT_WHOLE.hdr: [testng] 07:43:04,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:43:04,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:04,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-05-18_07-43-04.log] [testng] 07:43:04,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd5d8d8 - End of configuration. [testng] [2025-05-18 07:43:55,336] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2025-05-18 07:44:01,124] [pool-1-thread-7] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [2025-05-18 07:44:06,742] [pool-1-thread-12] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2025-05-18 07:44:07,870] [pool-1-thread-4] Initializing /data/frans/MR_CHEST.hdr: [testng] [2025-05-18 07:44:13,963] [pool-1-thread-2] Initializing /data/frans/brodmann.hdr: [testng] [2025-05-18 07:44:19,937] [pool-1-thread-10] Initializing /data/frans/aal.hdr: [testng] [2025-05-18 07:44:25,112] [pool-1-thread-1] Initializing /data/frans/CT_APERT.hdr: [testng] [2025-05-18 07:44:31,012] [pool-1-thread-8] Initializing /data/frans/ch2.hdr: [testng] [2025-05-18 07:44:36,660] [pool-1-thread-11] Initializing /data/frans/CT_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: 8 minutes 9 seconds Finished: SUCCESS