![[Jenkins]](/jenkins/static/97c0ac26/images/svgs/logo.svg){kind=logo}
Started by upstream project "BIOFORMATS-test-repo" build number 317 originally caused by: Started by upstream project "Trigger" build number 339 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins15381826110941500748.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_50323_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] 02:49:18,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:49:18,652 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 02:49:18,652 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:49:18,653 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:49:18,653 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:49:18,654 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:49:18,654 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:49:18,654 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:49:18,654 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:49:18,655 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:49:18,655 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:49:18,655 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:49:18,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:49:18,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:49:18,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:49:18,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:49:18,927 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:49:18,928 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:49:18,928 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:49:18,928 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:49:18,928 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 02:49:18,929 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 02:49:18,929 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 275 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-13 02:49:18,940] [main] java.version = 1.8.0_342 [testng] 02:49:18,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:49:18,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:18,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-13_02-49-18.log] [testng] 02:49:18,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-01-13 02:49:18,995] [main] testng.directory = /data [testng] [2025-01-13 02:49:18,995] [main] testng.configDirectory = /config [testng] [2025-01-13 02:49:19,008] [main] testng.multiplier = 1.0 [testng] [2025-01-13 02:49:19,009] [main] testng.in-memory = false [testng] [2025-01-13 02:49:19,009] [main] testng.allow-missing = false [testng] [2025-01-13 02:49:19,009] [main] user.language = fr [testng] [2025-01-13 02:49:19,009] [main] user.country = FR [testng] [2025-01-13 02:49:19,009] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-13 03:12:51,346] [main] ---------------------------------------- [testng] [2025-01-13 03:12:51,346] [main] Total files: 4190 [testng] [2025-01-13 03:12:51,347] [main] Scan time: 1412.337 s (337 ms/file) [testng] [2025-01-13 03:12:51,347] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-13 03:13:58,191] [pool-1-thread-1] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 03:13:58,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:13:58,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:13:58,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-13_03-13-58.log] [testng] 03:13:58,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f26b804 - End of configuration. [testng] [2025-01-13 03:13:59,620] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: [testng] 03:13:59,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:13:59,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:13:59,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-13_03-13-59.log] [testng] 03:13:59,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eca8068 - End of configuration. [testng] [2025-01-13 03:14:00,266] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] 03:14:00,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:14:00,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:00,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-13_03-14-00.log] [testng] 03:14:00,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13dd0899 - End of configuration. [testng] [2025-01-13 03:14:00,634] [pool-1-thread-10] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] 03:14:00,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:14:00,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:00,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-13_03-14-00.log] [testng] 03:14:00,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@592039ec - End of configuration. [testng] [2025-01-13 03:14:02,954] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] 03:14:02,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:14:02,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:02,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-13_03-14-02.log] [testng] 03:14:02,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e508064 - End of configuration. [testng] [2025-01-13 03:14:03,642] [pool-1-thread-8] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 03:14:03,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:14:03,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:03,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-13_03-14-03.log] [testng] 03:14:03,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23f7161b - End of configuration. [testng] [2025-01-13 03:14:04,107] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] 03:14:04,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:14:04,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:04,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-13_03-14-04.log] [testng] 03:14:04,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30efd281 - End of configuration. [testng] [2025-01-13 03:14:04,654] [pool-1-thread-6] 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] 03:14:04,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:14:04,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:04,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-13_03-14-04.log] [testng] 03:14:04,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24303fc7 - End of configuration. [testng] [2025-01-13 03:14:05,368] [pool-1-thread-5] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] 03:14:05,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:14:05,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:05,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-13_03-14-05.log] [testng] 03:14:05,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10eeba96 - End of configuration. [testng] [2025-01-13 03:14:06,000] [pool-1-thread-4] Initializing /data/samples/variable-field-count/test.xdce: [testng] 03:14:06,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:14:06,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:06,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-13_03-14-06.log] [testng] 03:14:06,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55128a5c - End of configuration. [testng] [2025-01-13 03:14:06,702] [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] 03:14:06,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:14:06,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:06,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-13_03-14-06.log] [testng] 03:14:06,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c6cd338 - End of configuration. [testng] [2025-01-13 03:14:07,542] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] 03:14:07,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:14:07,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:14:07,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-13_03-14-07.log] [testng] 03:14:07,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4750cf0f - End of configuration. [testng] [2025-01-13 03:14:53,653] [pool-1-thread-4] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] [2025-01-13 03:16:52,319] [pool-1-thread-5] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] [2025-01-13 03:18:10,614] [pool-1-thread-8] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] [2025-01-13 03:27:24,494] [pool-1-thread-12] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] [2025-01-13 03:27:30,283] [pool-1-thread-9] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] [2025-01-13 03:27:31,562] [pool-1-thread-2] 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] [2025-01-13 03:29:20,077] [pool-1-thread-12] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2025-01-13 03:30:16,340] [pool-1-thread-5] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] [2025-01-13 03:30:17,907] [pool-1-thread-9] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2025-01-13 03:30:49,416] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] [2025-01-13 03:31:53,496] [pool-1-thread-4] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2025-01-13 03:33:00,309] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] [2025-01-13 03:42:49,278] [pool-1-thread-11] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] [2025-01-13 03:42:55,383] [pool-1-thread-7] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] [2025-01-13 03:43:00,498] [pool-1-thread-3] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] 04:29:33,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:29:33,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:29:33,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-13_04-29-33.log] [testng] 04:29:33,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fec07f6 - End of configuration. [testng] 04:37:28,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:37:28,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:37:28,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-13_04-37-28.log] [testng] 04:37:28,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45f26f13 - End of configuration. [testng] 04:54:45,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:54:45,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:54:45,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-13_04-54-45.log] [testng] 04:54:45,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@562f5cdf - 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: 125 minutes 31 seconds Finished: SUCCESS