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Started by upstream project "BIOFORMATS-test-repo" build number 298 originally caused by: Started by upstream project "Trigger" build number 320 originally caused by: Started by timer 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/jenkins13166958507969742051.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47093_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] 00:29:55,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:29:55,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:29:55,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:55,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:55,853 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:29:55,853 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:29:55,854 |-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] 00:29:55,854 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:55,855 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:55,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:29:55,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:29:55,856 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:29:56,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:29:56,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:29:56,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:29:56,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:29:56,039 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:29:56,039 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:29:56,039 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:29:56,040 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:29:56,040 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:29:56,041 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:29:56,041 |-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] [2024-12-25 00:29:56,051] [main] java.version = 17.0.2 [testng] 00:29:56,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:29:56,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:56,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-25_00-29-56.log] [testng] 00:29:56,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-25 00:29:56,113] [main] testng.directory = /data [testng] [2024-12-25 00:29:56,113] [main] testng.configDirectory = /config [testng] [2024-12-25 00:29:56,121] [main] testng.multiplier = 1.0 [testng] [2024-12-25 00:29:56,122] [main] testng.in-memory = false [testng] [2024-12-25 00:29:56,122] [main] testng.allow-missing = false [testng] [2024-12-25 00:29:56,122] [main] user.language = en [testng] [2024-12-25 00:29:56,123] [main] user.country = ${user.country} [testng] [2024-12-25 00:29:56,123] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-25 00:29:57,312] [main] ---------------------------------------- [testng] [2024-12-25 00:29:57,312] [main] Total files: 31 [testng] [2024-12-25 00:29:57,312] [main] Scan time: 1.189 s (38 ms/file) [testng] [2024-12-25 00:29:57,312] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-25 00:30:03,485] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] 00:30:03,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:30:03,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:03,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-25_00-30-03.log] [testng] 00:30:03,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b12f304 - End of configuration. [testng] [2024-12-25 00:30:03,594] [pool-1-thread-12] Initializing /data/stephane/holo0908.bmp: [testng] 00:30:03,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:30:03,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:03,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-25_00-30-03.log] [testng] 00:30:03,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@354684bf - End of configuration. [testng] [2024-12-25 00:30:03,683] [pool-1-thread-11] Initializing /data/curtis/image2.bmp: [testng] 00:30:03,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:30:03,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:03,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-25_00-30-03.log] [testng] 00:30:03,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7426236b - End of configuration. [testng] [2024-12-25 00:30:03,795] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 00:30:03,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:03,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:03,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-25_00-30-03.log] [testng] 00:30:03,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d515d6a - End of configuration. [testng] [2024-12-25 00:30:03,898] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 00:30:03,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:30:03,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:03,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-25_00-30-03.log] [testng] 00:30:03,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3941ab - End of configuration. [testng] [2024-12-25 00:30:03,984] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 00:30:03,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:30:03,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:03,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-25_00-30-03.log] [testng] 00:30:03,985 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aead771 - End of configuration. [testng] [2024-12-25 00:30:04,116] [pool-1-thread-7] Initializing /data/curtis/image5.bmp: [testng] 00:30:04,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:30:04,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:04,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-25_00-30-04.log] [testng] 00:30:04,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@714f91da - End of configuration. [testng] [2024-12-25 00:30:04,282] [pool-1-thread-6] Initializing /data/brian/images/raw_a_rg.tiff: [testng] 00:30:04,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:30:04,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:04,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-25_00-30-04.log] [testng] 00:30:04,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63433986 - End of configuration. [testng] [2024-12-25 00:30:05,735] [pool-1-thread-5] Initializing /data/brian/images/raw_a.bmp: [testng] 00:30:05,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:30:05,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:05,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-25_00-30-05.log] [testng] 00:30:05,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@425061d1 - End of configuration. [testng] [2024-12-25 00:30:05,841] [pool-1-thread-4] Initializing /data/frank/cell_mask_error.bmp: [testng] 00:30:05,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:30:05,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:05,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-25_00-30-05.log] [testng] 00:30:05,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6334d8f - End of configuration. [testng] [2024-12-25 00:30:05,961] [pool-1-thread-3] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] 00:30:05,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:30:05,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:05,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-25_00-30-05.log] [testng] 00:30:05,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ee2c984 - End of configuration. [testng] [2024-12-25 00:30:06,081] [pool-1-thread-2] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] 00:30:06,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:30:06,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:06,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-25_00-30-06.log] [testng] 00:30:06,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@649845c5 - End of configuration. [testng] [2024-12-25 00:30:08,862] [pool-1-thread-7] Initializing /data/curtis/image1.bmp: [testng] [2024-12-25 00:30:09,021] [pool-1-thread-11] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-12-25 00:30:09,270] [pool-1-thread-9] Initializing /data/curtis/image4.bmp: [testng] [2024-12-25 00:30:09,381] [pool-1-thread-3] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-12-25 00:30:09,511] [pool-1-thread-8] Initializing /data/curtis/image3.bmp: [testng] [2024-12-25 00:30:09,627] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-12-25 00:30:09,763] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] [2024-12-25 00:30:09,882] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-12-25 00:30:09,993] [pool-1-thread-4] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2024-12-25 00:30:10,104] [pool-1-thread-2] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-12-25 00:30:10,249] [pool-1-thread-12] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2024-12-25 00:30:12,640] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] [2024-12-25 00:30:12,779] [pool-1-thread-7] Initializing /data/bk/ch_00.bmp: [testng] [2024-12-25 00:30:12,902] [pool-1-thread-8] Initializing /data/big-images/6kx6k.bmp: [testng] [2024-12-25 00:30:13,007] [pool-1-thread-9] Initializing /data/ticket-12971/foo.bmp: [testng] [2024-12-25 00:30:13,144] [pool-1-thread-4] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2024-12-25 00:30:13,274] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-12-25 00:30:13,405] [pool-1-thread-5] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-12-25 00:30:13,519] [pool-1-thread-1] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 42 seconds Finished: SUCCESS