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Started by upstream project "BIOFORMATS-test-repo" build number 12 originally caused by: Started by upstream project "Trigger" build number 15 originally caused by: Started by timer 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/jenkins16484568314691958518.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1900_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] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:50:26,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:50:26,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:50:26,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:50:26,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:50:26,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:50:26,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:50:26,082 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:50:26,082 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:50:26,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:50:26,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:50:26,084 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:50:26,084 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:50:26,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:50:26,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:50:26,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:50:26,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:50:26,307 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:50:26,307 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:50:26,307 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:50:26,307 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:50:26,308 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:50:26,308 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:50:26,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 225 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-26 01:50:26,319] [main] java.version = 11.0.16 [testng] 01:50:26,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:50:26,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:50:26,367 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-26_01-50-26.log] [testng] 01:50:26,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-26 01:50:26,371] [main] testng.directory = /data [testng] [2024-03-26 01:50:26,371] [main] testng.configDirectory = /config [testng] [2024-03-26 01:50:26,396] [main] testng.multiplier = 1.0 [testng] [2024-03-26 01:50:26,398] [main] testng.in-memory = false [testng] [2024-03-26 01:50:26,398] [main] testng.allow-missing = false [testng] [2024-03-26 01:50:26,398] [main] user.language = en [testng] [2024-03-26 01:50:26,398] [main] user.country = ${user.country} [testng] [2024-03-26 01:50:26,398] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-26 01:54:32,034] [main] ---------------------------------------- [testng] [2024-03-26 01:54:32,034] [main] Total files: 2169 [testng] [2024-03-26 01:54:32,034] [main] Scan time: 245.636 s (113 ms/file) [testng] [2024-03-26 01:54:32,034] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-26 02:16:02,612] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:16:02,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:16:02,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:02,616 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-26_02-16-02.log] [testng] 02:16:02,617 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701c1420 - End of configuration. [testng] [2024-03-26 02:16:10,191] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 02:16:10,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:16:10,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:10,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-26_02-16-10.log] [testng] 02:16:10,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ed853ae - End of configuration. [testng] [2024-03-26 02:19:43,159] [pool-1-thread-11] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:19:43,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:19:43,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:19:43,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-26_02-19-43.log] [testng] 02:19:43,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45e599aa - End of configuration. [testng] [2024-03-26 02:20:00,123] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:20:00,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:20:00,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:00,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-26_02-20-00.log] [testng] 02:20:00,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f560006 - End of configuration. [testng] [2024-03-26 02:20:40,843] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:20:40,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:20:40,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:40,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-26_02-20-40.log] [testng] 02:20:40,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26b3a9bb - End of configuration. [testng] [2024-03-26 02:22:27,941] [pool-1-thread-7] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:22:27,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:22:27,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:27,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-26_02-22-27.log] [testng] 02:22:27,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5235277 - End of configuration. [testng] [2024-03-26 02:23:15,504] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:23:15,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:23:15,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:15,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-26_02-23-15.log] [testng] 02:23:15,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dd73262 - End of configuration. [testng] [2024-03-26 02:23:16,769] [pool-1-thread-6] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 02:23:16,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:23:16,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:16,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-26_02-23-16.log] [testng] 02:23:16,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e78f8 - End of configuration. [testng] [2024-03-26 02:26:12,127] [pool-1-thread-5] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:26:12,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:26:12,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:26:12,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-26_02-26-12.log] [testng] 02:26:12,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34f43095 - End of configuration. [testng] [2024-03-26 02:26:12,467] [pool-1-thread-4] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:26:12,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:26:12,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:26:12,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-26_02-26-12.log] [testng] 02:26:12,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5194a6 - End of configuration. [testng] [2024-03-26 02:26:16,027] [pool-1-thread-3] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:26:16,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:26:16,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:26:16,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-26_02-26-16.log] [testng] 02:26:16,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d4cec72 - End of configuration. [testng] [2024-03-26 02:30:47,912] [pool-1-thread-2] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 02:30:47,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:30:47,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:47,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-26_02-30-47.log] [testng] 02:30:47,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d1c1a4a - End of configuration. [testng] [2024-03-26 02:32:31,741] [pool-1-thread-5] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:32:33,568] [pool-1-thread-5] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-03-26 02:33:34,581] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:33:45,937] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-03-26 02:33:48,584] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:33:49,507] [pool-1-thread-9] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-03-26 02:33:53,603] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:33:54,753] [pool-1-thread-9] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-03-26 02:34:26,469] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:34:35,942] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-03-26 02:37:20,971] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:37:27,787] [pool-1-thread-4] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:37:31,678] [pool-1-thread-7] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:38:30,761] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:44:34,221] [pool-1-thread-6] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:45:09,808] [pool-1-thread-11] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:49:08,083] [pool-1-thread-5] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:57:03,629] [pool-1-thread-3] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 02:58:47,137] [pool-1-thread-12] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 03:00:05,492] [pool-1-thread-2] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 03:00:28,657] [pool-1-thread-8] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 03:01:56,527] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 17, Skips: 0 [testng] =============================================== [testng] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 71 minutes 40 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE