Started by upstream project "BIOFORMATS-test-repo" build number 208
originally caused by:
Started by upstream project "Trigger" build number 234
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/jenkins12493608255983762182.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33064_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
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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 03:56:13,055 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:56:13,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 03:56:13,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:56:13,057 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:56:13,058 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:56:13,058 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:56:13,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 03:56:13,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:56:13,059 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:56:13,059 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:56:13,059 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:56:13,060 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:56:13,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:56:13,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:56:13,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:56:13,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:56:13,238 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:56:13,238 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:56:13,238 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:56:13,239 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:56:13,239 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 03:56:13,240 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 03:56:13,240 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 181 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-03 03:56:13,248] [main] java.version = 21
[testng] 03:56:13,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:56:13,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:56:13,291 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-03_03-56-13.log]
[testng] 03:56:13,292 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-10-03 03:56:13,294] [main] testng.directory = /data
[testng] [2024-10-03 03:56:13,294] [main] testng.configDirectory = /config
[testng] [2024-10-03 03:56:13,303] [main] testng.multiplier = 1.0
[testng] [2024-10-03 03:56:13,303] [main] testng.in-memory = false
[testng] [2024-10-03 03:56:13,303] [main] testng.allow-missing = false
[testng] [2024-10-03 03:56:13,304] [main] user.language = en
[testng] [2024-10-03 03:56:13,304] [main] user.country = ${user.country}
[testng] [2024-10-03 03:56:13,304] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-03 04:22:40,471] [main] ----------------------------------------
[testng] [2024-10-03 04:22:40,471] [main] Total files: 4190
[testng] [2024-10-03 04:22:40,471] [main] Scan time: 1587.167 s (378 ms/file)
[testng] [2024-10-03 04:22:40,472] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 27 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-03 04:23:46,675] [pool-1-thread-1] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce:
[testng] 04:23:46,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:23:46,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:46,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-03_04-23-46.log]
[testng] 04:23:46,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34d5b790 - End of configuration.
[testng] [2024-10-03 04:23:51,630] [pool-1-thread-12] 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] 04:23:51,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:23:51,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:51,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-03_04-23-51.log]
[testng] 04:23:51,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d6e41ba - End of configuration.
[testng] [2024-10-03 04:23:51,940] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce:
[testng] 04:23:51,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:23:51,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:51,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-03_04-23-51.log]
[testng] 04:23:51,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@638accba - End of configuration.
[testng] [2024-10-03 04:23:52,307] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce:
[testng] 04:23:52,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:23:52,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:52,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-03_04-23-52.log]
[testng] 04:23:52,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a1067a9 - End of configuration.
[testng] [2024-10-03 04:23:52,677] [pool-1-thread-9] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce:
[testng] 04:23:52,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:23:52,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:52,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-03_04-23-52.log]
[testng] 04:23:52,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72d797c8 - End of configuration.
[testng] [2024-10-03 04:23:53,082] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce:
[testng] 04:23:53,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:23:53,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:53,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-03_04-23-53.log]
[testng] 04:23:53,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f479d94 - End of configuration.
[testng] [2024-10-03 04:23:53,479] [pool-1-thread-7] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce:
[testng] 04:23:53,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:23:53,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:53,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-03_04-23-53.log]
[testng] 04:23:53,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab81b6 - End of configuration.
[testng] [2024-10-03 04:23:53,870] [pool-1-thread-6] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce:
[testng] 04:23:53,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:23:53,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:53,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-03_04-23-53.log]
[testng] 04:23:53,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f3127b7 - End of configuration.
[testng] [2024-10-03 04:23:55,694] [pool-1-thread-5] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce:
[testng] 04:23:55,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:23:55,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:55,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-03_04-23-55.log]
[testng] 04:23:55,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b5d6bf - End of configuration.
[testng] [2024-10-03 04:23:56,145] [pool-1-thread-4] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce:
[testng] 04:23:56,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:23:56,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:56,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-03_04-23-56.log]
[testng] 04:23:56,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24f0b0d8 - End of configuration.
[testng] [2024-10-03 04:23:56,527] [pool-1-thread-3] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce:
[testng] 04:23:56,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:23:56,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:56,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-03_04-23-56.log]
[testng] 04:23:56,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12104009 - End of configuration.
[testng] [2024-10-03 04:23:57,047] [pool-1-thread-2] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce:
[testng] 04:23:57,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:23:57,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:23:57,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-03_04-23-57.log]
[testng] 04:23:57,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@153110b3 - End of configuration.
[testng] [2024-10-03 04:24:39,056] [pool-1-thread-5] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce:
[testng] [2024-10-03 04:25:37,854] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce:
[testng] [2024-10-03 04:26:15,996] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] [2024-10-03 04:26:55,225] [pool-1-thread-5] Initializing /data/samples/variable-field-count/test.xdce:
[testng] [2024-10-03 04:27:09,735] [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] [2024-10-03 04:27:24,605] [pool-1-thread-5] Initializing /data/brian/livecell/H2b10xtrial.xdce:
[testng] [2024-10-03 04:38:25,660] [pool-1-thread-3] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce:
[testng] [2024-10-03 04:38:59,882] [pool-1-thread-1] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce:
[testng] [2024-10-03 04:41:03,385] [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] [2024-10-03 04:43:02,272] [pool-1-thread-3] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce:
[testng] [2024-10-03 04:51:39,409] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce:
[testng] [2024-10-03 04:54:59,139] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce:
[testng] [2024-10-03 04:55:00,626] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce:
[testng] [2024-10-03 04:55:02,935] [pool-1-thread-8] 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] [2024-10-03 04:55:07,423] [pool-1-thread-4] Initializing /data/samples/images_number_mismatch/test.xdce:
[testng] 05:52:18,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 05:52:18,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:52:18,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-03_05-52-18.log]
[testng] 05:52:18,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f71e551 - End of configuration.
[testng] 06:23:34,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 06:23:34,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:23:34,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-03_06-23-34.log]
[testng] 06:23:34,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@645d96c4 - 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: 147 minutes 24 seconds
Finished: SUCCESS