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Started by upstream project "BIOFORMATS-test-repo" build number 270 originally caused by: Started by user devspace 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/jenkins2367094938505686768.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42621_merge_ci -v /uod/idr/repos/curated/bmp:/data -v /uod/idr-scratch/merge-ci/curated/bmp:/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] 11:40:32,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:40:32,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 11:40:32,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:40:32,810 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:40:32,810 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:40:32,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:40:32,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:40:32,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:40:32,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:40:32,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:40:32,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:40:32,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:40:32,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:40:32,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:40:32,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:40:32,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:40:32,995 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:40:32,996 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:40:32,996 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:40:32,996 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:40:32,996 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 11:40:32,997 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 11:40:32,997 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 11:40:33,006] [main] java.version = 17.0.2 [testng] 11:40:33,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:40:33,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:33,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_11-40-33.log] [testng] 11:40:33,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 11:40:33,050] [main] testng.directory = /data [testng] [2024-11-27 11:40:33,050] [main] testng.configDirectory = /config [testng] [2024-11-27 11:40:33,059] [main] testng.multiplier = 1.0 [testng] [2024-11-27 11:40:33,059] [main] testng.in-memory = false [testng] [2024-11-27 11:40:33,059] [main] testng.allow-missing = false [testng] [2024-11-27 11:40:33,059] [main] user.language = en [testng] [2024-11-27 11:40:33,059] [main] user.country = ${user.country} [testng] [2024-11-27 11:40:33,060] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 11:40:33,859] [main] ---------------------------------------- [testng] [2024-11-27 11:40:33,859] [main] Total files: 31 [testng] [2024-11-27 11:40:33,859] [main] Scan time: 0.799 s (25 ms/file) [testng] [2024-11-27 11:40:33,859] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 11:40:42,546] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] 11:40:42,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:40:42,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:42,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_11-40-42.log] [testng] 11:40:42,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a86d062 - End of configuration. [testng] [2024-11-27 11:40:42,763] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 11:40:42,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:40:42,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:42,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_11-40-42.log] [testng] 11:40:42,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1805ae45 - End of configuration. [testng] [2024-11-27 11:40:42,973] [pool-1-thread-11] Initializing /data/big-images/6kx6k-grey.bmp: [testng] 11:40:42,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:40:42,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:42,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_11-40-42.log] [testng] 11:40:42,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78879b75 - End of configuration. [testng] [2024-11-27 11:40:43,187] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] 11:40:43,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:40:43,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:43,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_11-40-43.log] [testng] 11:40:43,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c8e583d - End of configuration. [testng] [2024-11-27 11:40:43,410] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 11:40:43,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:40:43,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:43,411 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_11-40-43.log] [testng] 11:40:43,412 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59198ba9 - End of configuration. [testng] [2024-11-27 11:40:43,674] [pool-1-thread-8] Initializing /data/curtis/image2.bmp: [testng] 11:40:43,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:40:43,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:43,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_11-40-43.log] [testng] 11:40:43,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11bb4551 - End of configuration. [testng] [2024-11-27 11:40:43,909] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] 11:40:43,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:40:43,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:43,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_11-40-43.log] [testng] 11:40:43,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50ddf602 - End of configuration. [testng] [2024-11-27 11:40:44,118] [pool-1-thread-6] Initializing /data/curtis/image5.bmp: [testng] 11:40:44,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:40:44,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:44,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_11-40-44.log] [testng] 11:40:44,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3965c4cc - End of configuration. [testng] [2024-11-27 11:40:44,257] [pool-1-thread-5] Initializing /data/curtis/image3.bmp: [testng] 11:40:44,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:40:44,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:44,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_11-40-44.log] [testng] 11:40:44,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eaf757a - End of configuration. [testng] [2024-11-27 11:40:44,384] [pool-1-thread-4] Initializing /data/big-images/8kx8k-grey.bmp: [testng] 11:40:44,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:40:44,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:44,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_11-40-44.log] [testng] 11:40:44,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58ffd31b - End of configuration. [testng] [2024-11-27 11:40:44,518] [pool-1-thread-3] Initializing /data/brian/images/raw_a_rg.tiff: [testng] 11:40:44,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:40:44,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:44,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_11-40-44.log] [testng] 11:40:44,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e2e5006 - End of configuration. [testng] [2024-11-27 11:40:46,093] [pool-1-thread-2] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 11:40:46,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:40:46,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:46,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_11-40-46.log] [testng] 11:40:46,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25e0d02c - End of configuration. [testng] [2024-11-27 11:40:49,676] [pool-1-thread-2] Initializing /data/big-images/6kx6k.bmp: [testng] [2024-11-27 11:40:49,820] [pool-1-thread-8] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-11-27 11:40:49,943] [pool-1-thread-5] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-11-27 11:40:50,069] [pool-1-thread-6] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2024-11-27 11:40:50,220] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] [2024-11-27 11:40:50,384] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-11-27 11:40:50,521] [pool-1-thread-12] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-11-27 11:40:50,680] [pool-1-thread-1] Initializing /data/curtis/image4.bmp: [testng] [2024-11-27 11:40:50,828] [pool-1-thread-9] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-11-27 11:40:53,313] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] [2024-11-27 11:40:53,484] [pool-1-thread-7] Initializing /data/ticket-12971/foo.bmp: [testng] [2024-11-27 11:40:53,624] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-11-27 11:40:53,749] [pool-1-thread-10] Initializing /data/bk/ch_00.bmp: [testng] [2024-11-27 11:40:53,909] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2024-11-27 11:40:54,474] [pool-1-thread-12] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [2024-11-27 11:40:54,665] [pool-1-thread-6] Initializing /data/brian/images/raw_a.bmp: [testng] [2024-11-27 11:40:55,330] [pool-1-thread-11] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-11-27 11:40:56,057] [pool-1-thread-7] Initializing /data/curtis/image1.bmp: [testng] [2024-11-27 11:40:56,226] [pool-1-thread-1] Initializing /data/stephane/holo0908.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 50 seconds Finished: SUCCESS