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Started by upstream project "BIOFORMATS-test-repo" build number 111 originally caused by: Started by upstream project "Trigger" build number 124 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins16239522526828183205.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17327_merge_ci -v /uod/idr/repos/curated/biorad-gel:/data -v /uod/idr-scratch/merge-ci/curated/biorad-gel:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:28:20,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:28:20,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:28:20,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:28:20,957 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:28:20,957 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:28:20,958 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:28:20,958 |-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] 02:28:20,958 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:28:20,959 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:28:20,960 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:28:20,961 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:28:20,961 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:28:21,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:28:21,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:28:21,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:28:21,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:28:21,250 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:28:21,250 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:28:21,250 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:28:21,251 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:28:21,251 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:28:21,252 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:28:21,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 293 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-04 02:28:21,263] [main] java.version = 21 [testng] 02:28:21,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:28:21,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:21,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-04_02-28-21.log] [testng] 02:28:21,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-04 02:28:21,355] [main] testng.directory = /data [testng] [2024-07-04 02:28:21,355] [main] testng.configDirectory = /config [testng] [2024-07-04 02:28:21,365] [main] testng.multiplier = 1.0 [testng] [2024-07-04 02:28:21,365] [main] testng.in-memory = false [testng] [2024-07-04 02:28:21,366] [main] testng.allow-missing = false [testng] [2024-07-04 02:28:21,366] [main] user.language = en [testng] [2024-07-04 02:28:21,366] [main] user.country = ${user.country} [testng] [2024-07-04 02:28:21,366] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-04 02:28:22,333] [main] ---------------------------------------- [testng] [2024-07-04 02:28:22,333] [main] Total files: 32 [testng] [2024-07-04 02:28:22,333] [main] Scan time: 0.967 s (30 ms/file) [testng] [2024-07-04 02:28:22,335] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-04 02:28:27,047] [pool-1-thread-1] Initializing /data/geert/bad example1.jpg: [testng] 02:28:27,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:28:27,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-04_02-28-27.log] [testng] 02:28:27,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c7d367d - End of configuration. [testng] [2024-07-04 02:28:27,113] [pool-1-thread-12] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] 02:28:27,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:28:27,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-04_02-28-27.log] [testng] 02:28:27,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b55ba8c - End of configuration. [testng] [2024-07-04 02:28:27,163] [pool-1-thread-11] Initializing /data/adrian/test_img.1sc: [testng] 02:28:27,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:28:27,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-04_02-28-27.log] [testng] 02:28:27,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79f7f579 - End of configuration. [testng] [2024-07-04 02:28:27,229] [pool-1-thread-10] Initializing /data/geert/good example1.1sc: [testng] 02:28:27,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:28:27,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-04_02-28-27.log] [testng] 02:28:27,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@696deea1 - End of configuration. [testng] [2024-07-04 02:28:27,329] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc.jpg: [testng] 02:28:27,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:28:27,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-04_02-28-27.log] [testng] 02:28:27,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@335032e7 - End of configuration. [testng] [2024-07-04 02:28:27,394] [pool-1-thread-8] Initializing /data/qa-29469/bad3.1sc: [testng] 02:28:27,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:28:27,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-04_02-28-27.log] [testng] 02:28:27,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dc837bb - End of configuration. [testng] [2024-07-04 02:28:27,508] [pool-1-thread-7] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 02:28:27,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:28:27,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-04_02-28-27.log] [testng] 02:28:27,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@117339ec - End of configuration. [testng] [2024-07-04 02:28:27,546] [pool-1-thread-6] Initializing /data/keith/pg020410saur3.1sc: [testng] 02:28:27,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:28:27,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-04_02-28-27.log] [testng] 02:28:27,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@517e671e - End of configuration. [testng] [2024-07-04 02:28:27,570] [pool-1-thread-5] Initializing /data/geert/bad example1.1sc: [testng] 02:28:27,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:28:27,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-04_02-28-27.log] [testng] 02:28:27,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ba8c9da - End of configuration. [testng] [2024-07-04 02:28:27,625] [pool-1-thread-4] Initializing /data/keith/PF020328saur v3.1sc: [testng] 02:28:27,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:28:27,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,628 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-04_02-28-27.log] [testng] 02:28:27,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a6c5585 - End of configuration. [testng] [2024-07-04 02:28:27,650] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 02:28:27,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:28:27,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-04_02-28-27.log] [testng] 02:28:27,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2937bd26 - End of configuration. [testng] [2024-07-04 02:28:27,806] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 02:28:27,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:28:27,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:27,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-04_02-28-27.log] [testng] 02:28:27,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ba6cf50 - End of configuration. [testng] [2024-07-04 02:28:30,222] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-07-04 02:28:30,372] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-07-04 02:28:30,763] [pool-1-thread-12] Initializing /data/samples/imagesEight.1sc: [testng] [2024-07-04 02:28:30,828] [pool-1-thread-7] Initializing /data/samples/Criterion.1sc: [testng] [2024-07-04 02:28:31,868] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-07-04 02:28:31,977] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-07-04 02:28:32,378] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-07-04 02:28:32,554] [pool-1-thread-9] Initializing /data/keith/test.1sc: [testng] [2024-07-04 02:28:32,848] [pool-1-thread-12] Initializing /data/keith/test2.1sc: [testng] [2024-07-04 02:28:32,954] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-07-04 02:28:33,273] [pool-1-thread-10] Initializing /data/qa-29459/bad.jpg: [testng] [2024-07-04 02:28:33,330] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-07-04 02:28:33,894] [pool-1-thread-3] Initializing /data/qa-29459/bad.1sc: [testng] [2024-07-04 02:28:34,106] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-07-04 02:28:34,507] [pool-1-thread-10] Initializing /data/qa-29469/good.1sc: [testng] [2024-07-04 02:28:34,674] [pool-1-thread-12] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-07-04 02:28:34,894] [pool-1-thread-7] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-07-04 02:28:35,041] [pool-1-thread-1] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-07-04 02:28:35,297] [pool-1-thread-8] Initializing /data/david/Opened in imageJ.tiff: [testng] [2024-07-04 02:28:35,472] [pool-1-thread-2] Initializing /data/geert/good example1.1sc.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 22 seconds Finished: SUCCESS