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Started by upstream project "BIOFORMATS-test-repo" build number 118 originally caused by: Started by upstream project "Trigger" build number 135 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins17297740251921046769.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18366_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 test-automated: [testng] File leak detector installed [testng] 01:24:37,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:37,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:24:37,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:37,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:37,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:37,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:37,864 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:37,864 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:37,865 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:37,866 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:37,866 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:37,866 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:38,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:38,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:38,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:38,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:38,201 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:38,201 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:38,201 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:38,202 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:38,202 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:24:38,203 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:24:38,203 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 338 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-12 01:24:38,213] [main] java.version = 1.8.0_342 [testng] 01:24:38,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:38,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,262 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-12_01-24-38.log] [testng] 01:24:38,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-12 01:24:38,266] [main] testng.directory = /data [testng] [2024-07-12 01:24:38,266] [main] testng.configDirectory = /config [testng] [2024-07-12 01:24:38,278] [main] testng.multiplier = 1.0 [testng] [2024-07-12 01:24:38,278] [main] testng.in-memory = false [testng] [2024-07-12 01:24:38,278] [main] testng.allow-missing = false [testng] [2024-07-12 01:24:38,278] [main] user.language = en [testng] [2024-07-12 01:24:38,278] [main] user.country = ${user.country} [testng] [2024-07-12 01:24:38,278] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-12 01:24:38,857] [main] ---------------------------------------- [testng] [2024-07-12 01:24:38,857] [main] Total files: 31 [testng] [2024-07-12 01:24:38,857] [main] Scan time: 0.579 s (18 ms/file) [testng] [2024-07-12 01:24:38,857] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-12 01:24:42,119] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp: [testng] 01:24:42,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:42,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-12_01-24-42.log] [testng] 01:24:42,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3320d16a - End of configuration. [testng] [2024-07-12 01:24:42,151] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] 01:24:42,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:42,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-12_01-24-42.log] [testng] 01:24:42,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f0f2196 - End of configuration. [testng] [2024-07-12 01:24:42,168] [pool-1-thread-11] Initializing /data/ticket-12971/foo.bmp: [testng] 01:24:42,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:42,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-12_01-24-42.log] [testng] 01:24:42,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3df275b9 - End of configuration. [testng] [2024-07-12 01:24:42,177] [pool-1-thread-10] Initializing /data/brian/images/raw_a.bmp: [testng] 01:24:42,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:42,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-12_01-24-42.log] [testng] 01:24:42,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70350d25 - End of configuration. [testng] [2024-07-12 01:24:42,193] [pool-1-thread-9] Initializing /data/big-images/6kx6k.bmp: [testng] 01:24:42,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:42,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-12_01-24-42.log] [testng] 01:24:42,195 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7654d867 - End of configuration. [testng] [2024-07-12 01:24:42,208] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 01:24:42,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:42,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-12_01-24-42.log] [testng] 01:24:42,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28379f6f - End of configuration. [testng] [2024-07-12 01:24:42,284] [pool-1-thread-7] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 01:24:42,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:42,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,287 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-12_01-24-42.log] [testng] 01:24:42,288 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25dfb2b5 - End of configuration. [testng] [2024-07-12 01:24:42,314] [pool-1-thread-6] Initializing /data/curtis/image3.bmp: [testng] 01:24:42,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:42,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-12_01-24-42.log] [testng] 01:24:42,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37d4b1c5 - End of configuration. [testng] [2024-07-12 01:24:42,321] [pool-1-thread-5] Initializing /data/big-images/6kx6k-grey.bmp: [testng] 01:24:42,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:42,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-12_01-24-42.log] [testng] 01:24:42,323 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f80843a - End of configuration. [testng] [2024-07-12 01:24:42,332] [pool-1-thread-4] Initializing /data/big-images/8kx8k.bmp: [testng] 01:24:42,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:42,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-12_01-24-42.log] [testng] 01:24:42,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54c24575 - End of configuration. [testng] [2024-07-12 01:24:42,349] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] 01:24:42,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:42,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-12_01-24-42.log] [testng] 01:24:42,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6205bb4f - End of configuration. [testng] [2024-07-12 01:24:42,357] [pool-1-thread-2] Initializing /data/curtis/image5.bmp: [testng] 01:24:42,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:42,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-12_01-24-42.log] [testng] 01:24:42,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c64db48 - End of configuration. [testng] [2024-07-12 01:24:44,372] [pool-1-thread-12] Initializing /data/curtis/image1.bmp: [testng] [2024-07-12 01:24:44,382] [pool-1-thread-2] Initializing /data/stephane/holo0908.bmp: [testng] [2024-07-12 01:24:44,392] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] [2024-07-12 01:24:44,431] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] [2024-07-12 01:24:44,438] [pool-1-thread-8] Initializing /data/curtis/image2.bmp: [testng] [2024-07-12 01:24:44,446] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-07-12 01:24:44,455] [pool-1-thread-10] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-07-12 01:24:44,465] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2024-07-12 01:24:44,471] [pool-1-thread-1] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-07-12 01:24:45,038] [pool-1-thread-12] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-07-12 01:24:45,113] [pool-1-thread-8] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-07-12 01:24:45,307] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] [2024-07-12 01:24:45,312] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] [2024-07-12 01:24:45,321] [pool-1-thread-1] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-07-12 01:24:45,327] [pool-1-thread-11] Initializing /data/curtis/image4.bmp: [testng] [2024-07-12 01:24:45,358] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-07-12 01:24:45,719] [pool-1-thread-11] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-07-12 01:24:45,805] [pool-1-thread-1] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2024-07-12 01:24:45,865] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 30 seconds Finished: SUCCESS