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Started by upstream project "BIOFORMATS-test-repo" build number 279 originally caused by: Started by upstream project "Trigger" build number 299 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/jenkins7669930386214171521.sh + '[' visitech = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43960_merge_ci -v /uod/idr/repos/curated/visitech:/data -v /uod/idr-scratch/merge-ci/curated/visitech:/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] 00:24:36,778 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:24:36,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:24:36,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:24:36,780 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:24:36,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:24:36,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:24:36,781 |-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] 00:24:36,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:24:36,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:24:36,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:24:36,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:24:36,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:24:36,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:24:36,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:24:36,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:24:36,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:24:36,963 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:24:36,963 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:24:36,963 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:24:36,963 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:24:36,963 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:24:36,964 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:24:36,964 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-04 00:24:36,973] [main] java.version = 17.0.2 [testng] 00:24:36,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:24:36,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:37,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-04_00-24-36.log] [testng] 00:24:37,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-04 00:24:37,016] [main] testng.directory = /data [testng] [2024-12-04 00:24:37,016] [main] testng.configDirectory = /config [testng] [2024-12-04 00:24:37,024] [main] testng.multiplier = 1.0 [testng] [2024-12-04 00:24:37,025] [main] testng.in-memory = false [testng] [2024-12-04 00:24:37,025] [main] testng.allow-missing = false [testng] [2024-12-04 00:24:37,025] [main] user.language = en [testng] [2024-12-04 00:24:37,025] [main] user.country = ${user.country} [testng] [2024-12-04 00:24:37,025] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-04 00:24:49,120] [main] ---------------------------------------- [testng] [2024-12-04 00:24:49,121] [main] Total files: 45 [testng] [2024-12-04 00:24:49,121] [main] Scan time: 12.095 s (268 ms/file) [testng] [2024-12-04 00:24:49,121] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-04 00:25:08,742] [pool-1-thread-1] Initializing /data/brian/ScreenShot.jpg: [testng] 00:25:08,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:25:08,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:08,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-04_00-25-08.log] [testng] 00:25:08,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b66c7b1 - End of configuration. [testng] [2024-12-04 00:25:08,932] [pool-1-thread-12] Initializing /data/kazem/noname Report.html: [testng] 00:25:08,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:25:08,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:08,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-04_00-25-08.log] [testng] 00:25:08,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@370b0ed0 - End of configuration. [testng] [2024-12-04 00:25:09,378] [pool-1-thread-11] Initializing /data/brian/060916-01 Report.html: [testng] 00:25:09,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:25:09,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:09,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-04_00-25-09.log] [testng] 00:25:09,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b81fa55 - End of configuration. [testng] [2024-12-04 00:25:09,601] [pool-1-thread-10] Initializing /data/scott/2 channel_Z_timelaps/525.tif: [testng] 00:25:09,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:25:09,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:09,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-04_00-25-09.log] [testng] 00:25:09,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@735f1060 - End of configuration. [testng] [2024-12-04 00:25:10,726] [pool-1-thread-9] Initializing /data/brian/060916-01-561.tif: [testng] 00:25:10,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:25:10,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:10,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-04_00-25-10.log] [testng] 00:25:10,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2de2fadc - End of configuration. [testng] [2024-12-04 00:25:12,135] [pool-1-thread-8] Initializing /data/oliver/20x/488 Report.html: [testng] 00:25:12,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:25:12,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:12,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-04_00-25-12.log] [testng] 00:25:12,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77a4daaa - End of configuration. [testng] [2024-12-04 00:25:12,843] [pool-1-thread-7] Initializing /data/scott/2 Channel z timelaps original/2 channel_Z_timelaps Report.html: [testng] 00:25:12,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:25:12,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:12,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-04_00-25-12.log] [testng] 00:25:12,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46a2dac7 - End of configuration. [testng] [2024-12-04 00:25:13,072] [pool-1-thread-6] Initializing /data/scott/2 Channel Z timelaps repeat/2 channel_Z_timelaps 2 Report.html: [testng] 00:25:13,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:25:13,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:13,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-04_00-25-13.log] [testng] 00:25:13,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@395d064b - End of configuration. [testng] [2024-12-04 00:25:13,328] [pool-1-thread-5] Initializing /data/brian/060916-01-488.tif: [testng] 00:25:13,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:25:13,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:13,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-04_00-25-13.log] [testng] 00:25:13,329 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a999853 - End of configuration. [testng] [2024-12-04 00:25:14,591] [pool-1-thread-4] Initializing /data/scott/2 channel_Z_timelaps/2 channel_Z_timelaps Report.html: [testng] 00:25:14,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:25:14,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:14,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-04_00-25-14.log] [testng] 00:25:14,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a46e93 - End of configuration. [testng] [2024-12-04 00:25:15,006] [pool-1-thread-3] Initializing /data/oliver/20x/491 Report.html: [testng] 00:25:15,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:25:15,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:15,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-04_00-25-15.log] [testng] 00:25:15,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79e5368f - End of configuration. [testng] [2024-12-04 00:25:15,548] [pool-1-thread-2] Initializing /data/scott/2 Channel z no timelaps/2 chanel z no time Report.html: [testng] 00:25:15,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:25:15,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:15,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-04_00-25-15.log] [testng] 00:25:15,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ee993f2 - End of configuration. [testng] [2024-12-04 00:25:20,268] [pool-1-thread-1] Initializing /data/scott/2 channel z 6 xy stage positions/2 chanel z 3x2 GRID Report.html: [testng] [2024-12-04 00:25:22,894] [pool-1-thread-10] Initializing /data/scott/2 channel_Z_timelaps/597.tif: [testng] [2024-12-04 00:25:24,645] [pool-1-thread-9] Initializing /data/brian/070613reA1_2 Report.html: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 21 seconds Finished: SUCCESS