Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins10306184380463662934.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_20271_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 14:41:50,073 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:41:50,075 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 14:41:50,075 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:41:50,076 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:41:50,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:41:50,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:41:50,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:41:50,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:41:50,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:41:50,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:41:50,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:41:50,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:41:50,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:41:50,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:41:50,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:41:50,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:41:50,378 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:41:50,378 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:41:50,378 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:41:50,379 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:41:50,379 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 14:41:50,380 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 14:41:50,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 303 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 14:41:50,391] [main] java.version = 1.8.0_342 [testng] 14:41:50,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:41:50,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:41:50,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_14-41-50.log] [testng] 14:41:50,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 14:41:50,458] [main] testng.directory = /data [testng] [2024-07-22 14:41:50,459] [main] testng.configDirectory = /config [testng] [2024-07-22 14:41:50,481] [main] testng.multiplier = 1.0 [testng] [2024-07-22 14:41:50,482] [main] testng.in-memory = false [testng] [2024-07-22 14:41:50,482] [main] testng.allow-missing = false [testng] [2024-07-22 14:41:50,482] [main] user.language = fr [testng] [2024-07-22 14:41:50,482] [main] user.country = FR [testng] [2024-07-22 14:41:50,482] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 14:46:10,473] [main] ---------------------------------------- [testng] [2024-07-22 14:46:10,473] [main] Total files: 2169 [testng] [2024-07-22 14:46:10,474] [main] Scan time: 259.99 s (119 ms/file) [testng] [2024-07-22 14:46:10,474] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 15:05:32,413] [pool-1-thread-1] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 15:05:32,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:05:32,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:05:32,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_15-05-32.log] [testng] 15:05:32,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@413e220b - End of configuration. [testng] [2024-07-22 15:05:32,786] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 15:05:32,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:05:32,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:05:32,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_15-05-32.log] [testng] 15:05:32,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32778e4b - End of configuration. [testng] [2024-07-22 15:08:24,566] [pool-1-thread-11] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 15:08:24,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:08:24,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:24,567 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_15-08-24.log] [testng] 15:08:24,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@194cce87 - End of configuration. [testng] [2024-07-22 15:08:39,451] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 15:08:39,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:08:39,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:39,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_15-08-39.log] [testng] 15:08:39,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25ba6094 - End of configuration. [testng] [2024-07-22 15:08:49,288] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 15:08:49,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:08:49,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:49,289 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_15-08-49.log] [testng] 15:08:49,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c186fab - End of configuration. [testng] [2024-07-22 15:08:52,854] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 15:08:52,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:08:52,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:52,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_15-08-52.log] [testng] 15:08:52,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65857920 - End of configuration. [testng] [2024-07-22 15:10:41,228] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 15:10:41,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:10:41,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:10:41,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_15-10-41.log] [testng] 15:10:41,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@323d1092 - End of configuration. [testng] [2024-07-22 15:10:49,778] [pool-1-thread-6] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 15:10:49,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:10:49,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:10:49,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_15-10-49.log] [testng] 15:10:49,779 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fcbeb57 - End of configuration. [testng] [2024-07-22 15:12:01,335] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 15:12:01,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:12:01,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:12:01,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_15-12-01.log] [testng] 15:12:01,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1908382d - End of configuration. [testng] [2024-07-22 15:12:39,677] [pool-1-thread-4] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 15:12:39,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:12:39,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:12:39,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_15-12-39.log] [testng] 15:12:39,679 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73411c78 - End of configuration. [testng] [2024-07-22 15:14:00,858] [pool-1-thread-3] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 15:14:00,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:14:00,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:14:00,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_15-14-00.log] [testng] 15:14:00,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@89c3d1a - End of configuration. [testng] [2024-07-22 15:14:34,021] [pool-1-thread-2] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 15:14:34,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:14:34,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:14:34,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_15-14-34.log] [testng] 15:14:34,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23b02e73 - End of configuration. [testng] [2024-07-22 15:17:06,349] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:17:07,916] [pool-1-thread-1] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-07-22 15:17:09,200] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:17:09,900] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-07-22 15:18:15,989] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:18:16,560] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-07-22 15:19:48,384] [pool-1-thread-7] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:19:48,599] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:19:49,650] [pool-1-thread-11] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:19:51,826] [pool-1-thread-3] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:19:52,185] [pool-1-thread-5] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:19:58,677] [pool-1-thread-7] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-07-22 15:19:59,393] [pool-1-thread-7] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:19:59,937] [pool-1-thread-7] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-07-22 15:23:09,469] [pool-1-thread-4] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:23:12,888] [pool-1-thread-12] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:23:18,960] [pool-1-thread-8] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:23:25,408] [pool-1-thread-2] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:23:36,088] [pool-1-thread-6] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:24:10,050] [pool-1-thread-1] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:25:31,781] [pool-1-thread-7] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-22 15:25:39,207] [pool-1-thread-10] 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: 45 minutes 1 second Build step 'Execute shell' marked build as failure Finished: FAILURE