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Started by upstream project "BIOFORMATS-test-repo" build number 131 originally caused by: Started by upstream project "Trigger" build number 148 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins6834944438831378768.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20599_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] 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] 02:16:38,899 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:16:38,900 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:16:38,900 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:38,901 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:38,901 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:16:38,902 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:16:38,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:16:38,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:38,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:38,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:16:38,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:16:38,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:16:39,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:16:39,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:16:39,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:16:39,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:16:39,130 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:16:39,130 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:16:39,130 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:16:39,131 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:16:39,131 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:16:39,132 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:16:39,132 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 230 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-24 02:16:39,141] [main] java.version = 17.0.2 [testng] 02:16:39,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:16:39,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:39,187 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-24_02-16-39.log] [testng] 02:16:39,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-24 02:16:39,191] [main] testng.directory = /data [testng] [2024-07-24 02:16:39,191] [main] testng.configDirectory = /config [testng] [2024-07-24 02:16:39,200] [main] testng.multiplier = 1.0 [testng] [2024-07-24 02:16:39,201] [main] testng.in-memory = false [testng] [2024-07-24 02:16:39,201] [main] testng.allow-missing = false [testng] [2024-07-24 02:16:39,201] [main] user.language = en [testng] [2024-07-24 02:16:39,201] [main] user.country = ${user.country} [testng] [2024-07-24 02:16:39,201] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-24 02:21:35,119] [main] ---------------------------------------- [testng] [2024-07-24 02:21:35,119] [main] Total files: 2169 [testng] [2024-07-24 02:21:35,120] [main] Scan time: 295.918 s (136 ms/file) [testng] [2024-07-24 02:21:35,120] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-24 02:37:59,411] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:37:59,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:37:59,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:59,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-24_02-37-59.log] [testng] 02:37:59,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b5379db - End of configuration. [testng] [2024-07-24 02:39:57,437] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:39:57,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:39:57,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:57,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-24_02-39-57.log] [testng] 02:39:57,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7211b1de - End of configuration. [testng] [2024-07-24 02:40:03,425] [pool-1-thread-11] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:40:03,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:40:03,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:03,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-24_02-40-03.log] [testng] 02:40:03,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e6535fe - End of configuration. [testng] [2024-07-24 02:40:05,103] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 02:40:05,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:40:05,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:05,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-24_02-40-05.log] [testng] 02:40:05,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75615228 - End of configuration. [testng] [2024-07-24 02:40:05,352] [pool-1-thread-9] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:40:05,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:40:05,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:05,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-24_02-40-05.log] [testng] 02:40:05,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bce76b3 - End of configuration. [testng] [2024-07-24 02:40:22,177] [pool-1-thread-8] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:40:22,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:40:22,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:22,178 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-24_02-40-22.log] [testng] 02:40:22,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cbb3301 - End of configuration. [testng] [2024-07-24 02:40:29,463] [pool-1-thread-7] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:40:29,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:40:29,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:29,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-24_02-40-29.log] [testng] 02:40:29,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cda7e6 - End of configuration. [testng] [2024-07-24 02:41:20,948] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 02:41:20,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:41:20,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:20,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-24_02-41-20.log] [testng] 02:41:20,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5394169b - End of configuration. [testng] [2024-07-24 02:44:27,736] [pool-1-thread-5] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 02:44:27,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:44:27,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:27,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-24_02-44-27.log] [testng] 02:44:27,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3100407b - End of configuration. [testng] [2024-07-24 02:45:32,108] [pool-1-thread-4] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:45:32,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:45:32,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:45:32,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-24_02-45-32.log] [testng] 02:45:32,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6971659a - End of configuration. [testng] [2024-07-24 02:45:51,332] [pool-1-thread-3] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:45:51,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:45:51,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:45:51,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-24_02-45-51.log] [testng] 02:45:51,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ccd0ddd - End of configuration. [testng] [2024-07-24 02:46:36,700] [pool-1-thread-2] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:46:36,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:46:36,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:36,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-24_02-46-36.log] [testng] 02:46:36,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f068e2 - End of configuration. [testng] [2024-07-24 02:47:59,103] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:48:00,167] [pool-1-thread-10] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-07-24 02:48:01,527] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:48:02,396] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-07-24 02:48:03,180] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:48:03,713] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-07-24 02:49:30,110] [pool-1-thread-11] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:49:39,060] [pool-1-thread-8] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:49:39,880] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-07-24 02:52:02,460] [pool-1-thread-8] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-07-24 02:52:11,653] [pool-1-thread-12] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:11,897] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:11,950] [pool-1-thread-4] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:12,561] [pool-1-thread-5] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:12,607] [pool-1-thread-7] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:12,986] [pool-1-thread-3] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:21,245] [pool-1-thread-8] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:41,367] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:52:47,533] [pool-1-thread-6] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:54:14,218] [pool-1-thread-2] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:54:19,527] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 02:56:09,833] [pool-1-thread-11] 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: 40 minutes 14 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE