Started by upstream project "BIOFORMATS-test-repo" build number 255
originally caused by:
Started by upstream project "Trigger" build number 279
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins2646648244925910145.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_40262_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 03:06:56,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:06:56,542 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 03:06:56,542 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:06:56,543 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:06:56,543 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:06:56,543 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:06:56,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 03:06:56,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:06:56,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:06:56,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:06:56,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:06:56,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:06:56,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:06:56,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:06:56,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:06:56,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:06:56,776 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:06:56,776 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:06:56,776 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:06:56,776 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:06:56,777 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 03:06:56,777 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 03:06:56,777 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 233 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-14 03:06:56,787] [main] java.version = 21
[testng] 03:06:56,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:06:56,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:06:56,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-14_03-06-56.log]
[testng] 03:06:56,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-14 03:06:56,841] [main] testng.directory = /data
[testng] [2024-11-14 03:06:56,841] [main] testng.configDirectory = /config
[testng] [2024-11-14 03:06:56,854] [main] testng.multiplier = 1.0
[testng] [2024-11-14 03:06:56,855] [main] testng.in-memory = false
[testng] [2024-11-14 03:06:56,855] [main] testng.allow-missing = false
[testng] [2024-11-14 03:06:56,855] [main] user.language = en
[testng] [2024-11-14 03:06:56,855] [main] user.country = ${user.country}
[testng] [2024-11-14 03:06:56,855] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-14 03:11:17,304] [main] ----------------------------------------
[testng] [2024-11-14 03:11:17,305] [main] Total files: 2169
[testng] [2024-11-14 03:11:17,305] [main] Scan time: 260.449 s (120 ms/file)
[testng] [2024-11-14 03:11:17,306] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-14 03:28:22,537] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml:
[testng] 03:28:22,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:28:22,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:28:22,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-14_03-28-22.log]
[testng] 03:28:22,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bf0833b - End of configuration.
[testng] [2024-11-14 03:29:16,013] [pool-1-thread-12] Initializing /data/ruben/plate_002/experiment_descriptor.xml:
[testng] 03:29:16,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:29:16,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:29:16,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-14_03-29-16.log]
[testng] 03:29:16,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22da5fc4 - End of configuration.
[testng] [2024-11-14 03:29:18,823] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml:
[testng] 03:29:18,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:29:18,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:29:18,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-14_03-29-18.log]
[testng] 03:29:18,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30eed605 - End of configuration.
[testng] [2024-11-14 03:30:56,931] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml:
[testng] 03:30:56,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:30:56,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:30:56,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-14_03-30-56.log]
[testng] 03:30:56,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@771c5da1 - End of configuration.
[testng] [2024-11-14 03:31:30,904] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml:
[testng] 03:31:30,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:31:30,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:30,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-14_03-31-30.log]
[testng] 03:31:30,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46f0f637 - End of configuration.
[testng] [2024-11-14 03:31:31,835] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml:
[testng] 03:31:31,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:31:31,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:31,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-14_03-31-31.log]
[testng] 03:31:31,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee831c3 - End of configuration.
[testng] [2024-11-14 03:31:32,873] [pool-1-thread-7] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml:
[testng] 03:31:32,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:31:32,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:32,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-14_03-31-32.log]
[testng] 03:31:32,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@737d2467 - End of configuration.
[testng] [2024-11-14 03:34:13,380] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml:
[testng] 03:34:13,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:34:13,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:34:13,382 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-14_03-34-13.log]
[testng] 03:34:13,382 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ed08a2 - End of configuration.
[testng] [2024-11-14 03:34:23,466] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml:
[testng] 03:34:23,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:34:23,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:34:23,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-14_03-34-23.log]
[testng] 03:34:23,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64830adf - End of configuration.
[testng] [2024-11-14 03:37:01,433] [pool-1-thread-4] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml:
[testng] 03:37:01,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:37:01,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:37:01,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-14_03-37-01.log]
[testng] 03:37:01,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57dae4d6 - End of configuration.
[testng] [2024-11-14 03:37:07,075] [pool-1-thread-3] Initializing /data/nadine/experiment_descriptor.xml:
[testng] 03:37:07,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:37:07,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:37:07,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-14_03-37-07.log]
[testng] 03:37:07,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1efc830f - End of configuration.
[testng] [2024-11-14 03:37:08,072] [pool-1-thread-2] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml:
[testng] 03:37:08,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:37:08,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:37:08,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-14_03-37-08.log]
[testng] 03:37:08,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6338a4ea - End of configuration.
[testng] [2024-11-14 03:37:39,835] [pool-1-thread-9] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml:
[testng] [2024-11-14 03:40:53,084] [pool-1-thread-8] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml:
[testng] [2024-11-14 03:41:44,390] [pool-1-thread-3] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml:
[testng] [2024-11-14 03:45:30,942] [pool-1-thread-12] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml:
[testng] [2024-11-14 03:46:45,613] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml:
[testng] 04:55:59,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:55:59,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:59,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-14_04-55-59.log]
[testng] 04:55:59,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fee79a9 - End of configuration.
[testng] 04:58:03,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:58:03,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:58:03,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-14_04-58-03.log]
[testng] 04:58:03,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a47234b - End of configuration.
[testng] 04:59:49,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:59:49,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:59:49,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-14_04-59-49.log]
[testng] 04:59:49,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51bac128 - End of configuration.
[testng] 05:00:21,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 05:00:21,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:00:21,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-14_05-00-21.log]
[testng] 05:00:21,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ef05e2 - End of configuration.
[testng] 05:05:57,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 05:05:57,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:05:57,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-14_05-05-57.log]
[testng] 05:05:57,970 |-INFO in ch.qos.logback.core.sift.SiftProcessor@280b0df9 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 119 minutes 4 seconds
Finished: SUCCESS