Started by upstream project "BIOFORMATS-test-repo" build number 263
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins7854781623805484421.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41574_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 19:14:48,388 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 19:14:48,390 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 19:14:48,390 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 19:14:48,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 19:14:48,391 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 19:14:48,392 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 19:14:48,392 |-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] 19:14:48,392 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 19:14:48,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 19:14:48,393 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 19:14:48,394 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 19:14:48,394 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 19:14:48,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 19:14:48,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 19:14:48,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 19:14:48,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 19:14:48,617 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 19:14:48,617 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 19:14:48,617 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 19:14:48,618 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 19:14:48,618 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 19:14:48,619 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 19:14:48,619 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 226 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-21 19:14:48,629] [main] java.version = 21
[testng] 19:14:48,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 19:14:48,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:14:48,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_19-14-48.log]
[testng] 19:14:48,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-21 19:14:48,681] [main] testng.directory = /data
[testng] [2024-11-21 19:14:48,682] [main] testng.configDirectory = /config
[testng] [2024-11-21 19:14:48,691] [main] testng.multiplier = 1.0
[testng] [2024-11-21 19:14:48,692] [main] testng.in-memory = false
[testng] [2024-11-21 19:14:48,692] [main] testng.allow-missing = false
[testng] [2024-11-21 19:14:48,692] [main] user.language = en
[testng] [2024-11-21 19:14:48,692] [main] user.country = ${user.country}
[testng] [2024-11-21 19:14:48,692] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-21 19:19:24,778] [main] ----------------------------------------
[testng] [2024-11-21 19:19:24,779] [main] Total files: 2169
[testng] [2024-11-21 19:19:24,779] [main] Scan time: 276.086 s (127 ms/file)
[testng] [2024-11-21 19:19:24,779] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-21 19:50:54,649] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml:
[testng] 19:50:54,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 19:50:54,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:50:54,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_19-50-54.log]
[testng] 19:50:54,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5108a9c1 - End of configuration.
[testng] [2024-11-21 19:52:00,119] [pool-1-thread-12] Initializing /data/ruben/plate_002/experiment_descriptor.xml:
[testng] 19:52:00,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 19:52:00,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:52:00,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_19-52-00.log]
[testng] 19:52:00,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66bdfd84 - End of configuration.
[testng] [2024-11-21 19:52:04,735] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml:
[testng] 19:52:04,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 19:52:04,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:52:04,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_19-52-04.log]
[testng] 19:52:04,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24a0f30e - End of configuration.
[testng] [2024-11-21 19:54:49,619] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml:
[testng] 19:54:49,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 19:54:49,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:54:49,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_19-54-49.log]
[testng] 19:54:49,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@307e1263 - End of configuration.
[testng] [2024-11-21 19:55:29,862] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml:
[testng] 19:55:29,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 19:55:29,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:55:29,862 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_19-55-29.log]
[testng] 19:55:29,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7770823d - End of configuration.
[testng] [2024-11-21 19:55:31,433] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml:
[testng] 19:55:31,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 19:55:31,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:55:31,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_19-55-31.log]
[testng] 19:55:31,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a38c728 - End of configuration.
[testng] [2024-11-21 19:55:33,015] [pool-1-thread-7] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml:
[testng] 19:55:33,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 19:55:33,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:55:33,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_19-55-33.log]
[testng] 19:55:33,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460a78a0 - End of configuration.
[testng] [2024-11-21 19:58:30,539] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml:
[testng] 19:58:30,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 19:58:30,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:58:30,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_19-58-30.log]
[testng] 19:58:30,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46f0f637 - End of configuration.
[testng] [2024-11-21 19:58:38,926] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml:
[testng] 19:58:38,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 19:58:38,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:58:38,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_19-58-38.log]
[testng] 19:58:38,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@110f8673 - End of configuration.
[testng] [2024-11-21 20:01:32,254] [pool-1-thread-4] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml:
[testng] 20:01:32,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 20:01:32,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:01:32,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_20-01-32.log]
[testng] 20:01:32,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee831c3 - End of configuration.
[testng] [2024-11-21 20:01:42,267] [pool-1-thread-3] Initializing /data/nadine/experiment_descriptor.xml:
[testng] 20:01:42,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 20:01:42,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:01:42,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_20-01-42.log]
[testng] 20:01:42,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@737d2467 - End of configuration.
[testng] [2024-11-21 20:01:43,839] [pool-1-thread-2] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml:
[testng] 20:01:43,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 20:01:43,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:01:43,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_20-01-43.log]
[testng] 20:01:43,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ed08a2 - End of configuration.
[testng] [2024-11-21 20:02:37,212] [pool-1-thread-9] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml:
[testng] [2024-11-21 20:05:51,634] [pool-1-thread-8] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml:
[testng] [2024-11-21 20:06:59,299] [pool-1-thread-3] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml:
[testng] [2024-11-21 20:10:17,898] [pool-1-thread-12] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml:
[testng] [2024-11-21 20:13:07,322] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml:
[testng] 21:35:35,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 21:35:35,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 21:35:35,990 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_21-35-35.log]
[testng] 21:35:35,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37ed2a70 - End of configuration.
[testng] 21:45:26,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 21:45:26,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 21:45:26,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_21-45-26.log]
[testng] 21:45:26,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aaf57d2 - End of configuration.
[testng] 21:47:30,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 21:47:30,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 21:47:30,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_21-47-30.log]
[testng] 21:47:30,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c832e75 - End of configuration.
[testng] 21:50:09,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 21:50:09,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 21:50:09,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_21-50-09.log]
[testng] 21:50:09,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6886bbb - End of configuration.
[testng] 21:50:58,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 21:50:58,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 21:50:58,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_21-50-58.log]
[testng] 21:50:58,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c201f1a - End of configuration.
[testng] 21:58:57,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 21:58:57,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 21:58:57,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_21-58-57.log]
[testng] 21:58:57,693 |-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: 164 minutes 12 seconds
Finished: SUCCESS