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Started by upstream project "BIOFORMATS-test-repo" build number 105 originally caused by: Started by upstream project "Trigger" build number 117 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins2297353372853371714.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16344_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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 test-automated: [testng] File leak detector installed [testng] 02:39:00,885 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:39:00,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:39:00,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:39:00,888 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:39:00,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:39:00,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:39:00,889 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:39:00,889 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:39:00,889 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:39:00,890 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:39:00,890 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:39:00,890 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:39:01,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:39:01,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:39:01,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:39:01,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:39:01,173 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:39:01,174 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:39:01,174 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:39:01,174 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:39:01,174 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:39:01,175 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:39:01,175 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-28 02:39:01,185] [main] java.version = 1.8.0_342 [testng] 02:39:01,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:39:01,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:01,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-28_02-39-01.log] [testng] 02:39:01,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-28 02:39:01,247] [main] testng.directory = /data [testng] [2024-06-28 02:39:01,247] [main] testng.configDirectory = /config [testng] [2024-06-28 02:39:01,263] [main] testng.multiplier = 1.0 [testng] [2024-06-28 02:39:01,264] [main] testng.in-memory = false [testng] [2024-06-28 02:39:01,264] [main] testng.allow-missing = false [testng] [2024-06-28 02:39:01,264] [main] user.language = en [testng] [2024-06-28 02:39:01,264] [main] user.country = ${user.country} [testng] [2024-06-28 02:39:01,264] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-28 02:39:44,424] [main] ---------------------------------------- [testng] [2024-06-28 02:39:44,424] [main] Total files: 826 [testng] [2024-06-28 02:39:44,424] [main] Scan time: 43.16 s (52 ms/file) [testng] [2024-06-28 02:39:44,424] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-28 02:39:47,794] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 02:39:47,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:39:47,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:47,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-28_02-39-47.log] [testng] 02:39:47,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e81600c - End of configuration. [testng] [2024-06-28 02:39:47,851] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 02:39:47,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:39:47,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:47,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-28_02-39-47.log] [testng] 02:39:47,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cff6066 - End of configuration. [testng] [2024-06-28 02:39:47,900] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 02:39:47,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:39:47,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:47,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-28_02-39-47.log] [testng] 02:39:47,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5da663d5 - End of configuration. [testng] [2024-06-28 02:39:47,952] [pool-1-thread-10] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 02:39:47,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:39:47,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:47,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-28_02-39-47.log] [testng] 02:39:47,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57eb3371 - End of configuration. [testng] [2024-06-28 02:39:48,055] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 02:39:48,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:39:48,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-28_02-39-48.log] [testng] 02:39:48,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60dce90e - End of configuration. [testng] [2024-06-28 02:39:48,099] [pool-1-thread-8] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 02:39:48,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:39:48,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-28_02-39-48.log] [testng] 02:39:48,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4243b70b - End of configuration. [testng] [2024-06-28 02:39:48,226] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 02:39:48,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:39:48,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-28_02-39-48.log] [testng] 02:39:48,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a65593 - End of configuration. [testng] [2024-06-28 02:39:48,284] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 02:39:48,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:39:48,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-28_02-39-48.log] [testng] 02:39:48,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62a25055 - End of configuration. [testng] [2024-06-28 02:39:48,319] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 02:39:48,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:39:48,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,320 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-28_02-39-48.log] [testng] 02:39:48,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71647c70 - End of configuration. [testng] [2024-06-28 02:39:48,356] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 02:39:48,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:39:48,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,357 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-28_02-39-48.log] [testng] 02:39:48,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a77b19b - End of configuration. [testng] [2024-06-28 02:39:48,396] [pool-1-thread-3] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 02:39:48,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:39:48,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-28_02-39-48.log] [testng] 02:39:48,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79a032fb - End of configuration. [testng] [2024-06-28 02:39:48,422] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 02:39:48,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:39:48,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:48,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-28_02-39-48.log] [testng] 02:39:48,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28da782d - End of configuration. [testng] [2024-06-28 02:39:50,373] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2024-06-28 02:39:50,426] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [2024-06-28 02:39:50,466] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] [2024-06-28 02:39:50,511] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] [2024-06-28 02:39:50,550] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 12 seconds Finished: SUCCESS