Started by upstream project "BIOFORMATS-test-repo" build number 133 originally caused by: Started by upstream project "Trigger" build number 153 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins14206959468308568013.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20935_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 test-automated: [testng] File leak detector installed [testng] 02:39:08,623 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:39:08,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:39:08,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:39:08,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:39:08,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:39:08,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:39:08,627 |-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] 02:39:08,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:39:08,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:39:08,628 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:39:08,628 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:39:08,628 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:39:08,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:39:08,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:39:09,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:39:09,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:39:09,035 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:39:09,035 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:39:09,035 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:39:09,036 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:39:09,036 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:39:09,037 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:39:09,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 410 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-26 02:39:09,046] [main] java.version = 1.8.0_342 [testng] 02:39:09,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:39:09,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:09,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-26_02-39-09.log] [testng] 02:39:09,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-26 02:39:09,111] [main] testng.directory = /data [testng] [2024-07-26 02:39:09,111] [main] testng.configDirectory = /config [testng] [2024-07-26 02:39:09,161] [main] testng.multiplier = 1.0 [testng] [2024-07-26 02:39:09,161] [main] testng.in-memory = false [testng] [2024-07-26 02:39:09,161] [main] testng.allow-missing = false [testng] [2024-07-26 02:39:09,161] [main] user.language = en [testng] [2024-07-26 02:39:09,161] [main] user.country = ${user.country} [testng] [2024-07-26 02:39:09,161] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-26 02:39:09,972] [main] ---------------------------------------- [testng] [2024-07-26 02:39:09,972] [main] Total files: 32 [testng] [2024-07-26 02:39:09,972] [main] Scan time: 0.811 s (25 ms/file) [testng] [2024-07-26 02:39:09,972] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-26 02:39:13,479] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] 02:39:13,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:39:13,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-26_02-39-13.log] [testng] 02:39:13,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b062c73 - End of configuration. [testng] [2024-07-26 02:39:13,568] [pool-1-thread-12] Initializing /data/geert/good example1.1sc.jpg: [testng] 02:39:13,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:39:13,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-26_02-39-13.log] [testng] 02:39:13,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17707e43 - End of configuration. [testng] [2024-07-26 02:39:13,587] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 02:39:13,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:39:13,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-26_02-39-13.log] [testng] 02:39:13,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d1e3bd5 - End of configuration. [testng] [2024-07-26 02:39:13,649] [pool-1-thread-10] Initializing /data/geert/good example1.1sc: [testng] 02:39:13,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:39:13,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-26_02-39-13.log] [testng] 02:39:13,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35412dbf - End of configuration. [testng] [2024-07-26 02:39:13,733] [pool-1-thread-9] Initializing /data/qa-29469/bad3.1sc: [testng] 02:39:13,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:39:13,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-26_02-39-13.log] [testng] 02:39:13,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20ebd8c4 - End of configuration. [testng] [2024-07-26 02:39:13,768] [pool-1-thread-8] Initializing /data/david/Opened in imageJ.tiff: [testng] 02:39:13,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:39:13,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-26_02-39-13.log] [testng] 02:39:13,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5595581d - End of configuration. [testng] [2024-07-26 02:39:13,803] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 02:39:13,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:39:13,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-26_02-39-13.log] [testng] 02:39:13,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a2f5d6 - End of configuration. [testng] [2024-07-26 02:39:13,855] [pool-1-thread-6] Initializing /data/qa-16880/c-src v7.1sc: [testng] 02:39:13,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:39:13,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-26_02-39-13.log] [testng] 02:39:13,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a7f36ef - End of configuration. [testng] [2024-07-26 02:39:13,883] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 02:39:13,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:39:13,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-26_02-39-13.log] [testng] 02:39:13,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25dd2fc3 - End of configuration. [testng] [2024-07-26 02:39:13,901] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 02:39:13,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:39:13,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-26_02-39-13.log] [testng] 02:39:13,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b9769dc - End of configuration. [testng] [2024-07-26 02:39:13,928] [pool-1-thread-3] Initializing /data/keith/pg020410saur3.1sc: [testng] 02:39:13,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:39:13,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-26_02-39-13.log] [testng] 02:39:13,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dc45a40 - End of configuration. [testng] [2024-07-26 02:39:13,941] [pool-1-thread-2] Initializing /data/keith/test.1sc: [testng] 02:39:13,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:39:13,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:13,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-26_02-39-13.log] [testng] 02:39:13,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c60221d - End of configuration. [testng] [2024-07-26 02:39:15,571] [pool-1-thread-2] Initializing /data/adrian/test_img.1sc: [testng] [2024-07-26 02:39:15,598] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] [2024-07-26 02:39:15,624] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-07-26 02:39:15,674] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-07-26 02:39:15,712] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-07-26 02:39:15,741] [pool-1-thread-6] Initializing /data/qa-29459/bad.1sc: [testng] [2024-07-26 02:39:15,794] [pool-1-thread-12] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-07-26 02:39:15,822] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc: [testng] [2024-07-26 02:39:16,145] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-07-26 02:39:16,193] [pool-1-thread-7] Initializing /data/qa-29459/bad.jpg: [testng] [2024-07-26 02:39:16,510] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-07-26 02:39:16,564] [pool-1-thread-11] Initializing /data/geert/bad example1.jpg: [testng] [2024-07-26 02:39:16,774] [pool-1-thread-12] Initializing /data/samples/imagesEight.1sc: [testng] [2024-07-26 02:39:16,925] [pool-1-thread-7] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-07-26 02:39:17,090] [pool-1-thread-12] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-07-26 02:39:17,109] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-07-26 02:39:17,283] [pool-1-thread-5] Initializing /data/qa-29469/good.1sc: [testng] [2024-07-26 02:39:17,583] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-07-26 02:39:17,664] [pool-1-thread-11] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-07-26 02:39:17,849] [pool-1-thread-10] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 17 seconds Finished: SUCCESS