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Started by upstream project "BIOFORMATS-test-repo" build number 285 originally caused by: Started by upstream project "Trigger" build number 304 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins10011319135113318105.sh + '[' incell = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_45049_merge_ci -v /uod/idr/repos/curated/incell:/data -v /uod/idr-scratch/merge-ci/curated/incell:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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] 03:16:21,031 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:16:21,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:16:21,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:16:21,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:16:21,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:16:21,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:16:21,036 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:16:21,036 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:16:21,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:16:21,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:16:21,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:16:21,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:16:21,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:16:21,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:16:21,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:16:21,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:16:21,372 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:16:21,372 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:16:21,372 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:16:21,372 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:16:21,372 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:16:21,373 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:16:21,373 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 336 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-09 03:16:21,384] [main] java.version = 1.8.0_342 [testng] 03:16:21,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:16:21,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:16:21,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-09_03-16-21.log] [testng] 03:16:21,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-09 03:16:21,437] [main] testng.directory = /data [testng] [2024-12-09 03:16:21,438] [main] testng.configDirectory = /config [testng] [2024-12-09 03:16:21,450] [main] testng.multiplier = 1.0 [testng] [2024-12-09 03:16:21,451] [main] testng.in-memory = false [testng] [2024-12-09 03:16:21,451] [main] testng.allow-missing = false [testng] [2024-12-09 03:16:21,451] [main] user.language = fr [testng] [2024-12-09 03:16:21,451] [main] user.country = FR [testng] [2024-12-09 03:16:21,451] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-09 03:44:55,960] [main] ---------------------------------------- [testng] [2024-12-09 03:44:55,960] [main] Total files: 4190 [testng] [2024-12-09 03:44:55,961] [main] Scan time: 1714.509 s (409 ms/file) [testng] [2024-12-09 03:44:55,961] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-09 03:45:59,539] [pool-1-thread-1] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 03:45:59,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:45:59,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:59,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-09_03-45-59.log] [testng] 03:45:59,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50c7752c - End of configuration. [testng] [2024-12-09 03:45:59,897] [pool-1-thread-12] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] 03:45:59,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:45:59,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:59,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-09_03-45-59.log] [testng] 03:45:59,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5ff865 - End of configuration. [testng] [2024-12-09 03:46:02,799] [pool-1-thread-11] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 03:46:02,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:46:02,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:02,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-09_03-46-02.log] [testng] 03:46:02,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@649bceb6 - End of configuration. [testng] [2024-12-09 03:46:04,336] [pool-1-thread-10] Initializing /data/samples/variable-field-count/test.xdce: [testng] 03:46:04,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:46:04,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:04,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-09_03-46-04.log] [testng] 03:46:04,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4225da29 - End of configuration. [testng] [2024-12-09 03:46:04,603] [pool-1-thread-9] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] 03:46:04,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:46:04,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:04,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-09_03-46-04.log] [testng] 03:46:04,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e1142a - End of configuration. [testng] [2024-12-09 03:46:04,920] [pool-1-thread-8] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] 03:46:04,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:46:04,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:04,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-09_03-46-04.log] [testng] 03:46:04,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75a12 - End of configuration. [testng] [2024-12-09 03:46:05,236] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] 03:46:05,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:46:05,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:05,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-09_03-46-05.log] [testng] 03:46:05,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4506b961 - End of configuration. [testng] [2024-12-09 03:46:06,818] [pool-1-thread-6] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] 03:46:06,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:46:06,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:06,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-09_03-46-06.log] [testng] 03:46:06,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2322deee - End of configuration. [testng] [2024-12-09 03:46:07,264] [pool-1-thread-5] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 03:46:07,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:46:07,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:07,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-09_03-46-07.log] [testng] 03:46:07,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73979ca2 - End of configuration. [testng] [2024-12-09 03:46:07,782] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] 03:46:07,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:46:07,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:07,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-09_03-46-07.log] [testng] 03:46:07,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3408be9 - End of configuration. [testng] [2024-12-09 03:46:08,197] [pool-1-thread-3] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] 03:46:08,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:46:08,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:08,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-09_03-46-08.log] [testng] 03:46:08,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eec6574 - End of configuration. [testng] [2024-12-09 03:46:09,025] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] 03:46:09,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:46:09,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:09,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-09_03-46-09.log] [testng] 03:46:09,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18757d05 - End of configuration. [testng] [2024-12-09 03:46:43,753] [pool-1-thread-8] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] [2024-12-09 03:46:45,738] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] [2024-12-09 03:47:52,227] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/txt en XML output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] [2024-12-09 03:49:26,701] [pool-1-thread-6] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-12-09 03:50:00,126] [pool-1-thread-5] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-12-09 03:51:50,550] [pool-1-thread-6] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-12-09 03:52:24,850] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] [2024-12-09 03:58:42,195] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: [testng] [2024-12-09 03:59:20,508] [pool-1-thread-9] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] [2024-12-09 04:01:50,326] [pool-1-thread-9] Initializing /data/public/idr0017/2011-11-17_X-Man_LOPAC_X01_LP_S01_1/2011-11-17 X-Man LOPAC_X03_LP_S01_1.xdce: [testng] [2024-12-09 04:02:34,620] [pool-1-thread-12] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] [2024-12-09 04:12:14,168] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] [2024-12-09 04:12:31,209] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] [2024-12-09 04:14:35,319] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] [2024-12-09 04:14:58,686] [pool-1-thread-1] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] 05:32:20,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:32:20,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:32:20,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-09_05-32-20.log] [testng] 05:32:20,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7004caf5 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1431, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 136 minutes 3 seconds Finished: SUCCESS