![[Jenkins]](/jenkins/static/f6f303f9/images/svgs/logo.svg){kind=logo}
Started by upstream project "BIOFORMATS-test-repo" build number 259 originally caused by: Started by upstream project "Trigger" build number 283 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins130114867626665916.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_40912_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] 02:48:31,794 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:48:31,796 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 02:48:31,796 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:48:31,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:48:31,797 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:48:31,797 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:48:31,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:48:31,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:48:31,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:48:31,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:48:31,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:48:31,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:48:32,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:48:32,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:48:32,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:48:32,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:48:32,055 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:48:32,055 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:48:32,055 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:48:32,055 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:48:32,055 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 02:48:32,056 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 02:48:32,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-18 02:48:32,066] [main] java.version = 1.8.0_342 [testng] 02:48:32,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:48:32,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:32,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_02-48-32.log] [testng] 02:48:32,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-18 02:48:32,121] [main] testng.directory = /data [testng] [2024-11-18 02:48:32,122] [main] testng.configDirectory = /config [testng] [2024-11-18 02:48:32,135] [main] testng.multiplier = 1.0 [testng] [2024-11-18 02:48:32,135] [main] testng.in-memory = false [testng] [2024-11-18 02:48:32,135] [main] testng.allow-missing = false [testng] [2024-11-18 02:48:32,136] [main] user.language = fr [testng] [2024-11-18 02:48:32,136] [main] user.country = FR [testng] [2024-11-18 02:48:32,136] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-18 03:16:12,768] [main] ---------------------------------------- [testng] [2024-11-18 03:16:12,768] [main] Total files: 4190 [testng] [2024-11-18 03:16:12,769] [main] Scan time: 1660.632 s (396 ms/file) [testng] [2024-11-18 03:16:12,769] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-18 03:17:20,244] [pool-1-thread-1] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 03:17:20,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:17:20,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:20,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-18_03-17-20.log] [testng] 03:17:20,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@799ccc2a - End of configuration. [testng] [2024-11-18 03:17:20,571] [pool-1-thread-12] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] 03:17:20,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:17:20,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:20,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-18_03-17-20.log] [testng] 03:17:20,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e7c66ad - End of configuration. [testng] [2024-11-18 03:17:23,479] [pool-1-thread-11] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 03:17:23,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:17:23,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:23,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-18_03-17-23.log] [testng] 03:17:23,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31a91711 - End of configuration. [testng] [2024-11-18 03:17:25,198] [pool-1-thread-10] Initializing /data/samples/variable-field-count/test.xdce: [testng] 03:17:25,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:17:25,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:25,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-18_03-17-25.log] [testng] 03:17:25,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43272970 - End of configuration. [testng] [2024-11-18 03:17:25,471] [pool-1-thread-9] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] 03:17:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:17:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:25,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-18_03-17-25.log] [testng] 03:17:25,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7877c301 - End of configuration. [testng] [2024-11-18 03:17:25,813] [pool-1-thread-8] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] 03:17:25,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:17:25,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:25,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-18_03-17-25.log] [testng] 03:17:25,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a7d3ea - End of configuration. [testng] [2024-11-18 03:17:26,150] [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] 03:17:26,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:17:26,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:26,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-18_03-17-26.log] [testng] 03:17:26,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f03edb1 - End of configuration. [testng] [2024-11-18 03:17:26,846] [pool-1-thread-6] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] 03:17:26,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:17:26,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:26,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-18_03-17-26.log] [testng] 03:17:26,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a73205 - End of configuration. [testng] [2024-11-18 03:17:27,201] [pool-1-thread-5] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 03:17:27,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:17:27,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:27,202 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-18_03-17-27.log] [testng] 03:17:27,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3749ff2f - End of configuration. [testng] [2024-11-18 03:17:27,616] [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] 03:17:27,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:17:27,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:27,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-18_03-17-27.log] [testng] 03:17:27,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73f5536c - End of configuration. [testng] [2024-11-18 03:17:28,038] [pool-1-thread-3] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] 03:17:28,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:17:28,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:28,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-18_03-17-28.log] [testng] 03:17:28,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@256dbd9 - End of configuration. [testng] [2024-11-18 03:17:28,889] [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] 03:17:28,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:17:28,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:28,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-18_03-17-28.log] [testng] 03:17:28,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27ae2383 - End of configuration. [testng] [2024-11-18 03:17:58,757] [pool-1-thread-8] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] [2024-11-18 03:18:01,769] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] [2024-11-18 03:19:13,496] [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] [2024-11-18 03:21:03,387] [pool-1-thread-6] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-11-18 03:21:30,981] [pool-1-thread-5] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-11-18 03:23:29,521] [pool-1-thread-6] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-11-18 03:24:11,403] [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] [2024-11-18 03:31:22,590] [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] [2024-11-18 03:32:04,995] [pool-1-thread-9] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] [2024-11-18 03:34:08,332] [pool-1-thread-12] 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] [2024-11-18 03:34:43,883] [pool-1-thread-9] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] [2024-11-18 03:44:57,478] [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] [2024-11-18 03:45:01,776] [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] [2024-11-18 03:46:38,419] [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] [2024-11-18 03:46:50,066] [pool-1-thread-1] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] 04:58:46,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:58:46,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:58:46,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_04-58-46.log] [testng] 04:58:46,832 |-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: 130 minutes 17 seconds Finished: SUCCESS