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Started by upstream project "BIOFORMATS-test-repo" build number 117 originally caused by: Started by upstream project "Trigger" build number 134 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/jenkins17482444855672902970.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18294_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:17:32,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:17:32,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:17:32,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:17:32,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:17:32,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:17:32,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:17:32,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:17:32,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:17:32,983 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:17:32,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:17:32,984 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:17:32,984 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:17:33,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:17:33,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:17:33,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:17:33,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:17:33,177 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:17:33,177 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:17:33,177 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:17:33,177 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:17:33,177 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:17:33,178 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:17:33,178 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-11 02:17:33,187] [main] java.version = 21 [testng] 02:17:33,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:17:33,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:33,232 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-11_02-17-33.log] [testng] 02:17:33,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-11 02:17:33,235] [main] testng.directory = /data [testng] [2024-07-11 02:17:33,235] [main] testng.configDirectory = /config [testng] [2024-07-11 02:17:33,244] [main] testng.multiplier = 1.0 [testng] [2024-07-11 02:17:33,245] [main] testng.in-memory = false [testng] [2024-07-11 02:17:33,245] [main] testng.allow-missing = false [testng] [2024-07-11 02:17:33,245] [main] user.language = en [testng] [2024-07-11 02:17:33,245] [main] user.country = ${user.country} [testng] [2024-07-11 02:17:33,245] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-11 02:17:42,017] [main] ---------------------------------------- [testng] [2024-07-11 02:17:42,017] [main] Total files: 68 [testng] [2024-07-11 02:17:42,017] [main] Scan time: 8.772 s (129 ms/file) [testng] [2024-07-11 02:17:42,018] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-11 02:18:07,469] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/R18Demo.ims: [testng] 02:18:07,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:18:07,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-11_02-18-07.log] [testng] 02:18:07,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a28c50c - End of configuration. [testng] [2024-07-11 02:18:07,515] [pool-1-thread-12] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] 02:18:07,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:18:07,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-11_02-18-07.log] [testng] 02:18:07,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27b20340 - End of configuration. [testng] [2024-07-11 02:18:07,598] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] 02:18:07,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:18:07,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-11_02-18-07.log] [testng] 02:18:07,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@470d15a - End of configuration. [testng] [2024-07-11 02:18:07,626] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] 02:18:07,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:18:07,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-11_02-18-07.log] [testng] 02:18:07,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c5f17a3 - End of configuration. [testng] [2024-07-11 02:18:07,660] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] 02:18:07,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:18:07,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-11_02-18-07.log] [testng] 02:18:07,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ec42212 - End of configuration. [testng] [2024-07-11 02:18:07,708] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0015.ims: [testng] 02:18:07,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:18:07,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-11_02-18-07.log] [testng] 02:18:07,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ebefaf - End of configuration. [testng] [2024-07-11 02:18:07,725] [pool-1-thread-7] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] 02:18:07,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:18:07,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-11_02-18-07.log] [testng] 02:18:07,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7253a6a1 - End of configuration. [testng] [2024-07-11 02:18:07,771] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0009.ims: [testng] 02:18:07,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:18:07,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-11_02-18-07.log] [testng] 02:18:07,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fb03b1 - End of configuration. [testng] [2024-07-11 02:18:07,785] [pool-1-thread-5] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 02:18:07,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:18:07,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-11_02-18-07.log] [testng] 02:18:07,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9a64ed - End of configuration. [testng] [2024-07-11 02:18:07,824] [pool-1-thread-4] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 02:18:07,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:18:07,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-11_02-18-07.log] [testng] 02:18:07,826 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40742e38 - End of configuration. [testng] [2024-07-11 02:18:07,862] [pool-1-thread-3] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] 02:18:07,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:18:07,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-11_02-18-07.log] [testng] 02:18:07,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e32f9bf - End of configuration. [testng] [2024-07-11 02:18:07,893] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims: [testng] 02:18:07,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:18:07,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:07,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-11_02-18-07.log] [testng] 02:18:07,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42789927 - End of configuration. [testng] [2024-07-11 02:18:09,881] [pool-1-thread-1] Initializing /data/chris/supMovie3.ims: [testng] [2024-07-11 02:18:09,946] [pool-1-thread-6] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] [2024-07-11 02:18:09,993] [pool-1-thread-8] Initializing /data/qa-17515/Organoid=1.ims: [testng] [2024-07-11 02:18:10,086] [pool-1-thread-4] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-07-11 02:18:10,180] [pool-1-thread-7] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] [2024-07-11 02:18:10,238] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0006.ims: [testng] [2024-07-11 02:18:10,622] [pool-1-thread-11] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] [2024-07-11 02:18:10,811] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: [testng] [2024-07-11 02:18:11,358] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0012.ims: [testng] [2024-07-11 02:18:11,412] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0007.ims: [testng] [2024-07-11 02:18:11,805] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0002.ims: [testng] [2024-07-11 02:18:11,845] [pool-1-thread-12] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] [2024-07-11 02:18:12,234] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] [2024-07-11 02:18:12,295] [pool-1-thread-4] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] [2024-07-11 02:18:12,608] [pool-1-thread-7] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] [2024-07-11 02:18:12,717] [pool-1-thread-6] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [2024-07-11 02:18:13,237] [pool-1-thread-9] Initializing /data/generated/MF-2CH-Z-T.ims: [testng] [2024-07-11 02:18:13,435] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0011.ims: [testng] [2024-07-11 02:18:13,479] [pool-1-thread-10] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] [2024-07-11 02:18:13,599] [pool-1-thread-9] Initializing /data/public/eliana/retina_large.ims: [testng] [2024-07-11 02:18:13,842] [pool-1-thread-12] Initializing /data/kay/Imaris503_test_Kay.ims: [testng] [2024-07-11 02:18:13,899] [pool-1-thread-6] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF.ims: [testng] [2024-07-11 02:18:14,265] [pool-1-thread-10] Initializing /data/public/davemason/TransFactors_2C_SRRF.ims: [testng] [2024-07-11 02:18:14,295] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0013.ims: [testng] [2024-07-11 02:18:14,377] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PyramidalCell.ims: [testng] [2024-07-11 02:18:14,575] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal_IMS3.ims: [testng] [2024-07-11 02:18:14,876] [pool-1-thread-1] Initializing /data/qa-17839/Fusion _Stack.ims: [testng] [2024-07-11 02:18:15,352] [pool-1-thread-2] Initializing /data/generated/10-31_E_t0008.ims: [testng] [2024-07-11 02:18:15,671] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] [2024-07-11 02:18:16,337] [pool-1-thread-11] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] [2024-07-11 02:18:16,587] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0003.ims: [testng] [2024-07-11 02:18:16,890] [pool-1-thread-11] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] [2024-07-11 02:18:25,267] [pool-1-thread-5] Initializing /data/generated/10-31_E_t0004.ims: [testng] [2024-07-11 02:18:25,548] [pool-1-thread-5] Initializing /data/generated/10-31_E_t0000.ims: [testng] [2024-07-11 02:18:25,683] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0001.ims: [testng] [2024-07-11 02:18:25,782] [pool-1-thread-5] Initializing /data/generated/10-31_E_t0014.ims: [testng] [2024-07-11 02:18:25,948] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0010.ims: [testng] [2024-07-11 02:18:26,099] [pool-1-thread-5] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3180, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 7 seconds Finished: SUCCESS