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Started by upstream project "BIOFORMATS-test-repo" build number 269 originally caused by: Started by upstream project "Trigger" build number 292 originally caused by: Started by timer 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/jenkins7654250756083860392.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42545_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] 03:39:58,567 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:39:58,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:39:58,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:39:58,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:39:58,570 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:39:58,570 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:39:58,571 |-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] 03:39:58,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:39:58,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:39:58,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:39:58,572 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:39:58,572 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:39:58,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:39:58,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:39:58,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:39:58,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:39:58,751 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:39:58,751 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:39:58,751 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:39:58,751 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:39:58,751 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:39:58,753 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:39:58,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 03:39:58,761] [main] java.version = 17.0.2 [testng] 03:39:58,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:39:58,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:58,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_03-39-58.log] [testng] 03:39:58,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 03:39:58,806] [main] testng.directory = /data [testng] [2024-11-27 03:39:58,807] [main] testng.configDirectory = /config [testng] [2024-11-27 03:39:58,815] [main] testng.multiplier = 1.0 [testng] [2024-11-27 03:39:58,815] [main] testng.in-memory = false [testng] [2024-11-27 03:39:58,816] [main] testng.allow-missing = false [testng] [2024-11-27 03:39:58,816] [main] user.language = en [testng] [2024-11-27 03:39:58,816] [main] user.country = ${user.country} [testng] [2024-11-27 03:39:58,816] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 03:40:11,529] [main] ---------------------------------------- [testng] [2024-11-27 03:40:11,529] [main] Total files: 21 [testng] [2024-11-27 03:40:11,529] [main] Scan time: 12.713 s (605 ms/file) [testng] [2024-11-27 03:40:11,529] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 03:40:27,345] [pool-1-thread-1] Initializing /data/frans/CT_CRANI.hdr: [testng] 03:40:27,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:40:27,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:27,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_03-40-27.log] [testng] 03:40:27,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d69040d - End of configuration. [testng] [2024-11-27 03:40:28,075] [pool-1-thread-12] Initializing /data/frans/aal.hdr: [testng] 03:40:28,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:40:28,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:28,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_03-40-28.log] [testng] 03:40:28,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1784737c - End of configuration. [testng] [2024-11-27 03:40:28,640] [pool-1-thread-11] Initializing /data/frans/CT_APERT.hdr: [testng] 03:40:28,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:40:28,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:28,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_03-40-28.log] [testng] 03:40:28,642 |-INFO in ch.qos.logback.core.sift.SiftProcessor@111dd749 - End of configuration. [testng] [2024-11-27 03:40:29,124] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 03:40:29,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:40:29,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:29,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_03-40-29.log] [testng] 03:40:29,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595b0fa - End of configuration. [testng] [2024-11-27 03:40:29,662] [pool-1-thread-9] Initializing /data/frans/CT_CHEST.hdr: [testng] 03:40:29,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:40:29,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:29,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_03-40-29.log] [testng] 03:40:29,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36985746 - End of configuration. [testng] [2024-11-27 03:40:30,408] [pool-1-thread-8] Initializing /data/frans/ch2bet.hdr: [testng] 03:40:30,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:40:30,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:30,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_03-40-30.log] [testng] 03:40:30,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@636118fe - End of configuration. [testng] [2024-11-27 03:40:31,314] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 03:40:31,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:40:31,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:31,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_03-40-31.log] [testng] 03:40:31,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ecc8f2 - End of configuration. [testng] [2024-11-27 03:40:32,072] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 03:40:32,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:40:32,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:32,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_03-40-32.log] [testng] 03:40:32,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f0fc35 - End of configuration. [testng] [2024-11-27 03:40:32,846] [pool-1-thread-5] Initializing /data/frans/CT_KNEE.hdr: [testng] 03:40:32,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:40:32,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:32,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_03-40-32.log] [testng] 03:40:32,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f8c191d - End of configuration. [testng] [2024-11-27 03:40:33,544] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 03:40:33,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:40:33,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:33,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_03-40-33.log] [testng] 03:40:33,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e022fad - End of configuration. [testng] [2024-11-27 03:40:34,275] [pool-1-thread-3] Initializing /data/frans/CT_HAND.hdr: [testng] 03:40:34,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:40:34,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:34,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_03-40-34.log] [testng] 03:40:34,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6431fcbd - End of configuration. [testng] [2024-11-27 03:40:34,788] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 03:40:34,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:40:34,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:34,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_03-40-34.log] [testng] 03:40:34,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e4b6c74 - End of configuration. [testng] [2024-11-27 03:40:44,904] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-11-27 03:40:45,397] [pool-1-thread-12] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-11-27 03:40:45,515] [pool-1-thread-11] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-11-27 03:40:45,994] [pool-1-thread-8] Initializing /data/frans/brodmann.hdr: [testng] [2024-11-27 03:40:46,682] [pool-1-thread-6] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-11-27 03:40:47,462] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-11-27 03:40:47,962] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [2024-11-27 03:40:48,589] [pool-1-thread-5] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-11-27 03:40:49,142] [pool-1-thread-9] Initializing /data/frans/ch2.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 3 seconds Finished: SUCCESS