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Started by upstream project "BIOFORMATS-test-repo" build number 120 originally caused by: Started by upstream project "Trigger" build number 137 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/jenkins13874196366434873189.sh + '[' i2i = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18678_merge_ci -v /uod/idr/repos/curated/i2i:/data -v /uod/idr-scratch/merge-ci/curated/i2i:/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] 01:20:22,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:22,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:22,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:22,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:22,481 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:22,481 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:22,481 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:22,482 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:22,482 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 01:20:22,483 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 01:20:22,483 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 433 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-14 01:20:22,497] [main] java.version = 17.0.2 [testng] 01:20:22,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:22,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:22,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-14_01-20-22.log] [testng] 01:20:22,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-14 01:20:22,731] [main] testng.directory = /data [testng] [2024-07-14 01:20:22,731] [main] testng.configDirectory = /config [testng] [2024-07-14 01:20:22,833] [main] testng.multiplier = 1.0 [testng] [2024-07-14 01:20:22,834] [main] testng.in-memory = false [testng] [2024-07-14 01:20:22,834] [main] testng.allow-missing = false [testng] [2024-07-14 01:20:22,834] [main] user.language = en [testng] [2024-07-14 01:20:22,834] [main] user.country = ${user.country} [testng] [2024-07-14 01:20:22,834] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-14 01:20:24,395] [main] ---------------------------------------- [testng] [2024-07-14 01:20:24,395] [main] Total files: 108 [testng] [2024-07-14 01:20:24,395] [main] Scan time: 1.561 s (14 ms/file) [testng] [2024-07-14 01:20:24,395] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 103 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-14 01:20:32,998] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000048_491-TIRF_000.tif: [testng] 01:20:32,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:20:32,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,001 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-14_01-20-33.log] [testng] 01:20:33,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2e68 - End of configuration. [testng] [2024-07-14 01:20:33,160] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000078_491-TIRF_000.tif: [testng] 01:20:33,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:20:33,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-14_01-20-33.log] [testng] 01:20:33,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78733ad1 - End of configuration. [testng] [2024-07-14 01:20:33,235] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000073_491-TIRF_000.tif: [testng] 01:20:33,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:20:33,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-14_01-20-33.log] [testng] 01:20:33,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@361567d0 - End of configuration. [testng] [2024-07-14 01:20:33,310] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000009_491-TIRF_000.tif: [testng] 01:20:33,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:20:33,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-14_01-20-33.log] [testng] 01:20:33,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ad371e8 - End of configuration. [testng] [2024-07-14 01:20:33,357] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000067_491-TIRF_000.tif: [testng] 01:20:33,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:20:33,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-14_01-20-33.log] [testng] 01:20:33,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56373f36 - End of configuration. [testng] [2024-07-14 01:20:33,399] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000077_491-TIRF_000.tif: [testng] 01:20:33,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:20:33,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-14_01-20-33.log] [testng] 01:20:33,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56875248 - End of configuration. [testng] [2024-07-14 01:20:33,445] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000035_491-TIRF_000.tif: [testng] 01:20:33,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:20:33,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-14_01-20-33.log] [testng] 01:20:33,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52eb4f8c - End of configuration. [testng] [2024-07-14 01:20:33,502] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000059_491-TIRF_000.tif: [testng] 01:20:33,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:20:33,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-14_01-20-33.log] [testng] 01:20:33,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@564cfb2a - End of configuration. [testng] [2024-07-14 01:20:33,562] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000036_491-TIRF_000.tif: [testng] 01:20:33,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:20:33,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-14_01-20-33.log] [testng] 01:20:33,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@565b8177 - End of configuration. [testng] [2024-07-14 01:20:33,606] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000052_491-TIRF_000.tif: [testng] 01:20:33,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:20:33,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-14_01-20-33.log] [testng] 01:20:33,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19e04b61 - End of configuration. [testng] [2024-07-14 01:20:33,647] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000047_491-TIRF_000.tif: [testng] 01:20:33,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:20:33,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-14_01-20-33.log] [testng] 01:20:33,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e741ca5 - End of configuration. [testng] [2024-07-14 01:20:33,692] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000043_491-TIRF_000.tif: [testng] 01:20:33,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:20:33,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:33,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-14_01-20-33.log] [testng] 01:20:33,693 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7b5593 - End of configuration. [testng] [2024-07-14 01:20:37,259] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000003_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,322] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000017_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,390] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000064_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,453] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_i2i_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.i2i: [testng] [2024-07-14 01:20:37,505] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000010_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,586] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000051_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,643] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000015_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,709] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000025_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,747] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000038_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,780] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000055_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,816] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000079_491-TIRF_000.tif: [testng] [2024-07-14 01:20:37,872] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000080_491-TIRF_000.tif: [testng] [2024-07-14 01:20:38,765] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000032_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,012] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000001_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,168] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000016_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,394] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000074_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,428] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000070_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,469] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000096_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,513] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000013_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,555] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000000_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,601] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000028_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,658] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000066_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,710] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000054_491-TIRF_000.tif: [testng] [2024-07-14 01:20:39,759] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000002_491-TIRF_000.tif: [testng] [2024-07-14 01:20:40,468] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000050_491-TIRF_000.tif: [testng] [2024-07-14 01:20:40,815] [pool-1-thread-5] Initializing /data/sample 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files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000018_491-TIRF_000.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 5459, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 32 seconds Finished: SUCCESS