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Started by upstream project "BIOFORMATS-test-repo" build number 185 originally caused by: Started by upstream project "Trigger" build number 207 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins12901191135132217415.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29285_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] 16:19:17,450 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 16:19:17,455 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 16:19:17,455 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:19:17,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:19:17,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 16:19:17,461 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 16:19:17,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 4 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 16:19:17,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:19:17,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:19:17,465 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 16:19:17,465 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 16:19:17,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 16:19:17,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 16:19:17,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 16:19:17,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 16:19:17,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 16:19:17,753 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 16:19:17,753 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 16:19:17,753 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 16:19:17,753 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 16:19:17,753 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 16:19:17,754 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 16:19:17,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 290 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-11 16:19:17,766] [main] java.version = 17.0.2 [testng] 16:19:17,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:19:17,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:17,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-11_16-19-17.log] [testng] 16:19:17,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-11 16:19:17,872] [main] testng.directory = /data [testng] [2024-09-11 16:19:17,873] [main] testng.configDirectory = /config [testng] [2024-09-11 16:19:17,891] [main] testng.multiplier = 1.0 [testng] [2024-09-11 16:19:17,892] [main] testng.in-memory = false [testng] [2024-09-11 16:19:17,893] [main] testng.allow-missing = false [testng] [2024-09-11 16:19:17,893] [main] user.language = en [testng] [2024-09-11 16:19:17,893] [main] user.country = ${user.country} [testng] [2024-09-11 16:19:17,893] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-11 16:19:19,484] [main] ---------------------------------------- [testng] [2024-09-11 16:19:19,485] [main] Total files: 21 [testng] [2024-09-11 16:19:19,485] [main] Scan time: 1.591 s (75 ms/file) [testng] [2024-09-11 16:19:19,485] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-11 16:19:21,693] [pool-1-thread-1] Initializing /data/frans/CT_CHEST.hdr: [testng] 16:19:21,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:19:21,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:21,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-11_16-19-21.log] [testng] 16:19:21,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c50f48c - End of configuration. [testng] [2024-09-11 16:19:21,807] [pool-1-thread-12] Initializing /data/frans/CT_CRANI.hdr: [testng] 16:19:21,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:19:21,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:21,810 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-11_16-19-21.log] [testng] 16:19:21,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@498c306 - End of configuration. [testng] [2024-09-11 16:19:21,874] [pool-1-thread-11] Initializing /data/frans/CT_APERT.hdr: [testng] 16:19:21,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 16:19:21,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:21,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-11_16-19-21.log] [testng] 16:19:21,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9d771a - End of configuration. [testng] [2024-09-11 16:19:21,978] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 16:19:21,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 16:19:21,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:21,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-11_16-19-21.log] [testng] 16:19:21,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196433ac - End of configuration. [testng] [2024-09-11 16:19:22,017] [pool-1-thread-9] Initializing /data/frans/CT_FOOT.hdr: [testng] 16:19:22,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 16:19:22,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-11_16-19-22.log] [testng] 16:19:22,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc69d2c - End of configuration. [testng] [2024-09-11 16:19:22,082] [pool-1-thread-8] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 16:19:22,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 16:19:22,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-11_16-19-22.log] [testng] 16:19:22,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c975e5e - End of configuration. [testng] [2024-09-11 16:19:22,142] [pool-1-thread-7] Initializing /data/frans/ch2.hdr: [testng] 16:19:22,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:19:22,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-11_16-19-22.log] [testng] 16:19:22,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46d8464b - End of configuration. [testng] [2024-09-11 16:19:22,178] [pool-1-thread-6] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 16:19:22,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:19:22,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-11_16-19-22.log] [testng] 16:19:22,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e8e6e1d - End of configuration. [testng] [2024-09-11 16:19:22,225] [pool-1-thread-5] Initializing /data/frans/MR_CHEST.hdr: [testng] 16:19:22,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:19:22,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-11_16-19-22.log] [testng] 16:19:22,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@249c208d - End of configuration. [testng] [2024-09-11 16:19:22,266] [pool-1-thread-4] Initializing /data/frans/CT_WHOLE.hdr: [testng] 16:19:22,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:19:22,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-11_16-19-22.log] [testng] 16:19:22,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b790ac5 - End of configuration. [testng] [2024-09-11 16:19:22,309] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 16:19:22,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 16:19:22,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-11_16-19-22.log] [testng] 16:19:22,311 |-INFO in ch.qos.logback.core.sift.SiftProcessor@220a3cb6 - End of configuration. [testng] [2024-09-11 16:19:22,351] [pool-1-thread-2] Initializing /data/frans/CT_HAND.hdr: [testng] 16:19:22,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 16:19:22,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:19:22,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-11_16-19-22.log] [testng] 16:19:22,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7655bcc9 - End of configuration. [testng] [2024-09-11 16:19:24,835] [pool-1-thread-8] Initializing /data/frans/brodmann.hdr: [testng] [2024-09-11 16:19:24,905] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-09-11 16:19:24,954] [pool-1-thread-12] Initializing /data/frans/ch2bet.hdr: [testng] [2024-09-11 16:19:24,980] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr: [testng] [2024-09-11 16:19:25,077] [pool-1-thread-2] Initializing /data/frans/aal.hdr: [testng] [2024-09-11 16:19:25,149] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-09-11 16:19:25,174] [pool-1-thread-11] Initializing /data/frans/betmask.hdr: [testng] [2024-09-11 16:19:25,202] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-09-11 16:19:25,267] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 seconds Finished: SUCCESS