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Started by upstream project "BIOFORMATS-test-repo" build number 367 originally caused by: Started by upstream project "Trigger" build number 393 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins15462079057097658432.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58593_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] 09:21:05,872 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 09:21:05,874 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 09:21:05,874 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:21:05,875 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:21:05,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:21:05,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:21:05,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:21:05,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:21:05,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:21:05,876 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:21:05,876 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:21:05,877 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:21:06,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:21:06,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:21:06,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:21:06,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:21:06,119 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:21:06,119 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:21:06,119 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:21:06,120 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:21:06,120 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 09:21:06,120 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 09:21:06,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 244 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-07 09:21:06,130] [main] java.version = 1.8.0_342 [testng] 09:21:06,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:21:06,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:21:06,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-07_09-21-06.log] [testng] 09:21:06,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-07 09:21:06,178] [main] testng.directory = /data [testng] [2025-03-07 09:21:06,178] [main] testng.configDirectory = /config [testng] [2025-03-07 09:21:06,190] [main] testng.multiplier = 1.0 [testng] [2025-03-07 09:21:06,190] [main] testng.in-memory = false [testng] [2025-03-07 09:21:06,190] [main] testng.allow-missing = false [testng] [2025-03-07 09:21:06,190] [main] user.language = en [testng] [2025-03-07 09:21:06,190] [main] user.country = ${user.country} [testng] [2025-03-07 09:21:06,190] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-07 20:02:52,061] [main] ---------------------------------------- [testng] [2025-03-07 20:02:52,061] [main] Total files: 826 [testng] [2025-03-07 20:02:52,061] [main] Scan time: 38505.871 s (46617 ms/file) [testng] [2025-03-07 20:02:52,061] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-07 20:25:34,096] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 20:25:34,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 20:25:34,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:25:34,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-07_20-25-34.log] [testng] 20:25:34,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a789d1f - End of configuration. [testng] [2025-03-07 20:26:09,596] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 20:26:09,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 20:26:09,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:26:09,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-07_20-26-09.log] [testng] 20:26:09,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78150fa - End of configuration. [testng] [2025-03-07 20:26:41,818] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 20:26:41,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 20:26:41,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:26:41,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-07_20-26-41.log] [testng] 20:26:41,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bf7e863 - End of configuration. [testng] [2025-03-07 20:27:18,002] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 20:27:18,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 20:27:18,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:27:18,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-07_20-27-18.log] [testng] 20:27:18,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2010f946 - End of configuration. [testng] [2025-03-07 20:27:45,514] [pool-1-thread-9] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 20:27:45,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 20:27:45,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:27:45,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-07_20-27-45.log] [testng] 20:27:45,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10a6e5e0 - End of configuration. [testng] [2025-03-07 20:28:29,596] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 20:28:29,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 20:28:29,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:28:29,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-07_20-28-29.log] [testng] 20:28:29,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52da8f8f - End of configuration. [testng] [2025-03-07 20:29:01,637] [pool-1-thread-7] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 20:29:01,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 20:29:01,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:29:01,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-07_20-29-01.log] [testng] 20:29:01,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2896b32 - End of configuration. [testng] [2025-03-07 20:30:29,082] [pool-1-thread-6] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 20:30:29,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 20:30:29,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:30:29,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-07_20-30-29.log] [testng] 20:30:29,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9797dbd - End of configuration. [testng] [2025-03-07 20:31:34,841] [pool-1-thread-5] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 20:31:34,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 20:31:34,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:31:34,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-07_20-31-34.log] [testng] 20:31:34,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1953d584 - End of configuration. [testng] [2025-03-07 20:34:51,146] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 20:34:51,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 20:34:51,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:34:51,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-07_20-34-51.log] [testng] 20:34:51,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46652ac1 - End of configuration. [testng] [2025-03-07 20:35:20,866] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 20:35:20,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 20:35:20,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:35:20,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-07_20-35-20.log] [testng] 20:35:20,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2cae6a - End of configuration. [testng] [2025-03-07 20:35:49,997] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 20:35:49,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 20:35:49,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:35:49,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-07_20-35-49.log] [testng] 20:35:49,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@138d689f - End of configuration. [testng] [2025-03-07 20:39:54,958] [pool-1-thread-6] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] [2025-03-07 20:40:42,672] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2025-03-07 20:41:25,074] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2025-03-07 20:42:13,935] [pool-1-thread-11] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] [2025-03-07 20:43:24,889] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: Build was aborted Calling Pipeline was cancelled Finished: ABORTED