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Started by upstream project "BIOFORMATS-test-repo" build number 132 originally caused by: Started by upstream project "Trigger" build number 152 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins2024780574771866143.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20772_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 12:03:22,117 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:03:22,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 12:03:22,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:03:22,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:03:22,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:03:22,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:03:22,122 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:03:22,122 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:03:22,122 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:03:22,123 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:03:22,123 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:03:22,124 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:03:22,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:03:22,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:03:22,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:03:22,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:03:22,367 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:03:22,367 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:03:22,367 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:03:22,368 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:03:22,368 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 12:03:22,369 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 12:03:22,369 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 247 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-25 12:03:22,380] [main] java.version = 21 [testng] 12:03:22,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:03:22,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:03:22,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-25_12-03-22.log] [testng] 12:03:22,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-25 12:03:22,437] [main] testng.directory = /data [testng] [2024-07-25 12:03:22,437] [main] testng.configDirectory = /config [testng] [2024-07-25 12:03:22,481] [main] testng.multiplier = 1.0 [testng] [2024-07-25 12:03:22,482] [main] testng.in-memory = false [testng] [2024-07-25 12:03:22,482] [main] testng.allow-missing = false [testng] [2024-07-25 12:03:22,482] [main] user.language = en [testng] [2024-07-25 12:03:22,482] [main] user.country = ${user.country} [testng] [2024-07-25 12:03:22,482] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-25 12:04:06,116] [main] ---------------------------------------- [testng] [2024-07-25 12:04:06,116] [main] Total files: 826 [testng] [2024-07-25 12:04:06,116] [main] Scan time: 43.634 s (52 ms/file) [testng] [2024-07-25 12:04:06,117] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-25 12:04:09,616] [pool-1-thread-1] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 12:04:09,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:04:09,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:09,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-25_12-04-09.log] [testng] 12:04:09,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1376b50e - End of configuration. [testng] [2024-07-25 12:04:09,768] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 12:04:09,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:04:09,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:09,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-25_12-04-09.log] [testng] 12:04:09,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20abc31a - End of configuration. [testng] [2024-07-25 12:04:09,819] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 12:04:09,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:04:09,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:09,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-25_12-04-09.log] [testng] 12:04:09,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b7718bc - End of configuration. [testng] [2024-07-25 12:04:09,881] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 12:04:09,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:04:09,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:09,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-25_12-04-09.log] [testng] 12:04:09,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b9e178d - End of configuration. [testng] [2024-07-25 12:04:09,948] [pool-1-thread-9] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 12:04:09,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:04:09,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:09,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-25_12-04-09.log] [testng] 12:04:09,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7702195c - End of configuration. [testng] [2024-07-25 12:04:09,985] [pool-1-thread-8] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 12:04:09,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:04:09,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:09,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-25_12-04-09.log] [testng] 12:04:09,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7055fa48 - End of configuration. [testng] [2024-07-25 12:04:10,030] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 12:04:10,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:04:10,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:10,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-25_12-04-10.log] [testng] 12:04:10,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a167a3 - End of configuration. [testng] [2024-07-25 12:04:10,067] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 12:04:10,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:04:10,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:10,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-25_12-04-10.log] [testng] 12:04:10,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36e541a1 - End of configuration. [testng] [2024-07-25 12:04:10,112] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 12:04:10,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:04:10,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:10,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-25_12-04-10.log] [testng] 12:04:10,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@372932f4 - End of configuration. [testng] [2024-07-25 12:04:10,151] [pool-1-thread-4] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 12:04:10,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:04:10,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:10,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-25_12-04-10.log] [testng] 12:04:10,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b58e326 - End of configuration. [testng] [2024-07-25 12:04:10,193] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 12:04:10,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:04:10,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:10,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-25_12-04-10.log] [testng] 12:04:10,195 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fccf415 - End of configuration. [testng] [2024-07-25 12:04:10,244] [pool-1-thread-2] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 12:04:10,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:04:10,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:10,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-25_12-04-10.log] [testng] 12:04:10,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3929702b - End of configuration. [testng] [2024-07-25 12:04:12,392] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [2024-07-25 12:04:12,930] [pool-1-thread-7] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] [2024-07-25 12:04:13,094] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] [2024-07-25 12:04:13,149] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] [2024-07-25 12:04:13,192] [pool-1-thread-11] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.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