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Started by upstream project "BIOFORMATS-test-repo" build number 87 originally caused by: Started by upstream project "Trigger" build number 98 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins139643617258186339.sh + '[' i2i = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_13266_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] 01:21:32,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:32,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:32,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:32,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:32,827 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:32,828 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:32,828 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:32,829 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:32,829 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 01:21:32,830 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 01:21:32,830 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 457 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-09 01:21:32,845] [main] java.version = 17.0.2 [testng] 01:21:32,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:32,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:33,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-09_01-21-32.log] [testng] 01:21:33,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-09 01:21:33,064] [main] testng.directory = /data [testng] [2024-06-09 01:21:33,065] [main] testng.configDirectory = /config [testng] [2024-06-09 01:21:33,089] [main] testng.multiplier = 1.0 [testng] [2024-06-09 01:21:33,090] [main] testng.in-memory = false [testng] [2024-06-09 01:21:33,090] [main] testng.allow-missing = false [testng] [2024-06-09 01:21:33,090] [main] user.language = en [testng] [2024-06-09 01:21:33,091] [main] user.country = ${user.country} [testng] [2024-06-09 01:21:33,091] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-09 01:21:35,009] [main] ---------------------------------------- [testng] [2024-06-09 01:21:35,009] [main] Total files: 108 [testng] [2024-06-09 01:21:35,009] [main] Scan time: 1.918 s (17 ms/file) [testng] [2024-06-09 01:21:35,009] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 103 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-09 01:21:44,912] [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] 01:21:44,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:44,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:44,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-09_01-21-44.log] [testng] 01:21:44,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5df5d258 - End of configuration. [testng] [2024-06-09 01:21:45,131] [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] 01:21:45,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:45,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-09_01-21-45.log] [testng] 01:21:45,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7099abd7 - End of configuration. [testng] [2024-06-09 01:21:45,204] [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] 01:21:45,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:45,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-09_01-21-45.log] [testng] 01:21:45,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ac9189b - End of configuration. [testng] [2024-06-09 01:21:45,296] [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] 01:21:45,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:45,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-09_01-21-45.log] [testng] 01:21:45,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cbb7096 - End of configuration. [testng] [2024-06-09 01:21:45,342] [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] 01:21:45,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:45,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,343 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-09_01-21-45.log] [testng] 01:21:45,344 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2653f72b - End of configuration. [testng] [2024-06-09 01:21:45,391] [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] 01:21:45,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:45,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-09_01-21-45.log] [testng] 01:21:45,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d654a70 - End of configuration. [testng] [2024-06-09 01:21:45,468] [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] 01:21:45,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:45,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-09_01-21-45.log] [testng] 01:21:45,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e519c94 - End of configuration. [testng] [2024-06-09 01:21:45,535] [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] 01:21:45,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:45,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-09_01-21-45.log] [testng] 01:21:45,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b507987 - End of configuration. [testng] [2024-06-09 01:21:45,584] [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] 01:21:45,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:45,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-09_01-21-45.log] [testng] 01:21:45,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15755609 - End of configuration. [testng] [2024-06-09 01:21:45,619] [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] 01:21:45,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:45,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-09_01-21-45.log] [testng] 01:21:45,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bf40750 - End of configuration. [testng] [2024-06-09 01:21:45,656] [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] 01:21:45,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:45,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-09_01-21-45.log] [testng] 01:21:45,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30eed605 - End of configuration. [testng] [2024-06-09 01:21:45,702] [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] 01:21:45,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:45,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-09_01-21-45.log] [testng] 01:21:45,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2103e842 - End of configuration. [testng] [2024-06-09 01:21:49,444] [pool-1-thread-10] 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] [2024-06-09 01:21:49,493] [pool-1-thread-12] 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] [2024-06-09 01:21:49,554] [pool-1-thread-6] 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] [2024-06-09 01:21:49,612] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_i2i_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.i2i: [testng] [2024-06-09 01:21:49,635] [pool-1-thread-4] 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] [2024-06-09 01:21:49,673] [pool-1-thread-5] 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] [2024-06-09 01:21:49,726] [pool-1-thread-2] 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] [2024-06-09 01:21:49,771] [pool-1-thread-1] 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] [2024-06-09 01:21:49,818] [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] [2024-06-09 01:21:49,871] [pool-1-thread-9] 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] [2024-06-09 01:21:49,916] [pool-1-thread-11] 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] [2024-06-09 01:21:49,988] [pool-1-thread-7] 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] [2024-06-09 01:21:50,969] [pool-1-thread-3] 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] [2024-06-09 01:21:51,551] [pool-1-thread-1] 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] [2024-06-09 01:21:51,673] [pool-1-thread-5] 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] [2024-06-09 01:21:51,790] [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] [2024-06-09 01:21:51,869] [pool-1-thread-9] 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] [2024-06-09 01:21:51,919] [pool-1-thread-12] 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] [2024-06-09 01:21:51,965] [pool-1-thread-6] 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] [2024-06-09 01:21:52,015] [pool-1-thread-11] 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] [2024-06-09 01:21:52,072] [pool-1-thread-8] 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] [2024-06-09 01:21:52,134] [pool-1-thread-10] 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] [2024-06-09 01:21:52,253] [pool-1-thread-4] 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] [2024-06-09 01:21:52,353] [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] [2024-06-09 01:21:52,941] [pool-1-thread-3] 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] [2024-06-09 01:21:53,384] [pool-1-thread-9] Initializing /data/sample 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files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000062_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: 35 seconds Finished: SUCCESS