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Started by upstream project "BIOFORMATS-test-repo" build number 362 originally caused by: Started by upstream project "Trigger" build number 388 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/jenkins2147791666472006995.sh + '[' prairie = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57752_merge_ci -v /uod/idr/repos/curated/prairie:/data -v /uod/idr-scratch/merge-ci/curated/prairie:/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] 1 warning 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] 02:57:38,289 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:57:38,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 02:57:38,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:57:38,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:57:38,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:57:38,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:57:38,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:57:38,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:57:38,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:57:38,294 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:57:38,294 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:57:38,294 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:57:38,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:57:38,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:57:38,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:57:38,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:57:38,476 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:57:38,476 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:57:38,477 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:57:38,477 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:57:38,477 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 02:57:38,478 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 02:57:38,478 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-02 02:57:38,486] [main] java.version = 17.0.2 [testng] 02:57:38,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:57:38,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:57:38,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-02_02-57-38.log] [testng] 02:57:38,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-02 02:57:38,531] [main] testng.directory = /data [testng] [2025-03-02 02:57:38,532] [main] testng.configDirectory = /config [testng] [2025-03-02 02:57:38,540] [main] testng.multiplier = 1.0 [testng] [2025-03-02 02:57:38,541] [main] testng.in-memory = false [testng] [2025-03-02 02:57:38,541] [main] testng.allow-missing = false [testng] [2025-03-02 02:57:38,541] [main] user.language = en [testng] [2025-03-02 02:57:38,542] [main] user.country = ${user.country} [testng] [2025-03-02 02:57:38,542] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-02 02:58:27,511] [main] ---------------------------------------- [testng] [2025-03-02 02:58:27,512] [main] Total files: 714 [testng] [2025-03-02 02:58:27,512] [main] Scan time: 48.969 s (68 ms/file) [testng] [2025-03-02 02:58:27,512] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 45 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-02 02:59:04,996] [pool-1-thread-1] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml: [testng] 02:59:04,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:59:04,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:04,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-02_02-59-04.log] [testng] 02:59:04,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49192bfe - End of configuration. [testng] [2025-03-02 02:59:05,888] [pool-1-thread-12] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml: [testng] 02:59:05,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:59:05,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:05,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-02_02-59-05.log] [testng] 02:59:05,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c549b5d - End of configuration. [testng] [2025-03-02 02:59:06,797] [pool-1-thread-11] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml: [testng] 02:59:06,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:59:06,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:06,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-02_02-59-06.log] [testng] 02:59:06,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@682889b1 - End of configuration. [testng] [2025-03-02 02:59:07,722] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml: [testng] 02:59:07,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:59:07,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:07,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-02_02-59-07.log] [testng] 02:59:07,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29cccf9b - End of configuration. [testng] [2025-03-02 02:59:08,527] [pool-1-thread-9] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] 02:59:08,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:59:08,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:08,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-02_02-59-08.log] [testng] 02:59:08,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4255baff - End of configuration. [testng] [2025-03-02 02:59:09,356] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml: [testng] 02:59:09,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:59:09,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:09,357 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-02_02-59-09.log] [testng] 02:59:09,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@258dabaf - End of configuration. [testng] [2025-03-02 02:59:10,210] [pool-1-thread-7] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif: [testng] 02:59:10,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:59:10,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:10,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-02_02-59-10.log] [testng] 02:59:10,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bed0785 - End of configuration. [testng] [2025-03-02 02:59:11,440] [pool-1-thread-6] Initializing /data/julie/sample1-010/sample1-010.xml: [testng] 02:59:11,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:59:11,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:11,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-02_02-59-11.log] [testng] 02:59:11,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae98d9f - End of configuration. [testng] [2025-03-02 02:59:12,293] [pool-1-thread-5] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml: [testng] 02:59:12,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:59:12,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:12,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-02_02-59-12.log] [testng] 02:59:12,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40a4edee - End of configuration. [testng] [2025-03-02 02:59:13,322] [pool-1-thread-4] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml: [testng] 02:59:13,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:59:13,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:13,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-02_02-59-13.log] [testng] 02:59:13,323 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a118fae - End of configuration. [testng] [2025-03-02 02:59:14,465] [pool-1-thread-3] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml: [testng] 02:59:14,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:59:14,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:14,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-02_02-59-14.log] [testng] 02:59:14,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@237529b2 - End of configuration. [testng] [2025-03-02 02:59:15,456] [pool-1-thread-2] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml: [testng] 02:59:15,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:59:15,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:15,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-02_02-59-15.log] [testng] 02:59:15,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2765e0c - End of configuration. [testng] [2025-03-02 02:59:23,362] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-004/pollen-004.xml: [testng] [2025-03-02 02:59:31,715] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml: [testng] [2025-03-02 02:59:36,761] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2025-03-02 02:59:39,804] [pool-1-thread-3] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml: [testng] [2025-03-02 02:59:48,123] [pool-1-thread-7] Initializing /data/julie/testslide6 2/testslide6 2.xml: [testng] [2025-03-02 02:59:58,829] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml: [testng] [2025-03-02 03:00:00,975] [pool-1-thread-9] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml: [testng] [2025-03-02 03:00:04,319] [pool-1-thread-8] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml: [testng] [2025-03-02 03:00:11,904] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml: [testng] [2025-03-02 03:00:15,768] [pool-1-thread-11] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml: [testng] [2025-03-02 03:00:31,072] [pool-1-thread-2] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml: [testng] [2025-03-02 03:01:04,930] [pool-1-thread-7] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml: [testng] [2025-03-02 03:01:10,948] [pool-1-thread-5] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif: [testng] [2025-03-02 03:01:14,103] [pool-1-thread-8] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml: [testng] [2025-03-02 03:01:20,205] [pool-1-thread-5] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml: [testng] [2025-03-02 03:01:36,146] [pool-1-thread-5] Initializing /data/julie/test slide 1_3/test slide 1_3.xml: [testng] [2025-03-02 03:01:45,208] [pool-1-thread-10] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml: [testng] [2025-03-02 03:01:46,233] [pool-1-thread-7] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml: [testng] [2025-03-02 03:01:51,805] [pool-1-thread-6] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml: [testng] [2025-03-02 03:01:58,152] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml: [testng] [2025-03-02 03:02:02,261] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml: [testng] [2025-03-02 03:02:09,127] [pool-1-thread-6] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2025-03-02 03:02:19,309] [pool-1-thread-5] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml: [testng] [2025-03-02 03:02:20,278] [pool-1-thread-10] Initializing /data/julie/sample1-010/sample1-010movie.avi: [testng] [2025-03-02 03:02:22,971] [pool-1-thread-10] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif: [testng] [2025-03-02 03:02:26,212] [pool-1-thread-6] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml: [testng] [2025-03-02 03:02:29,630] [pool-1-thread-7] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2025-03-02 03:02:32,552] [pool-1-thread-10] Initializing /data/kristin/sampleset-001/sampleset-001.xml: [testng] [2025-03-02 03:02:42,088] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml: [testng] [2025-03-02 03:02:44,911] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml: [testng] [2025-03-02 03:02:45,885] [pool-1-thread-7] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml: [testng] [2025-03-02 03:02:59,250] [pool-1-thread-5] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml: [testng] [2025-03-02 03:03:21,587] [pool-1-thread-8] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2385, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 27 minutes 55 seconds Finished: SUCCESS