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Started by upstream project "BIOFORMATS-test-repo" build number 2 originally caused by: Started by upstream project "Trigger" build number 3 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/jenkins6635864774677533661.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_268_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] 01:51:42,366 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:51:42,368 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:51:42,368 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:51:42,369 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:51:42,369 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:51:42,369 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:51:42,370 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:51:42,370 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:51:42,370 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:51:42,370 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:51:42,370 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:51:42,370 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:51:42,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:51:42,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:51:42,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:51:42,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:51:42,638 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:51:42,638 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:51:42,638 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:51:42,638 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:51:42,639 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:51:42,639 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:51:42,639 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-15 01:51:42,649] [main] java.version = 1.8.0_342 [testng] 01:51:42,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:51:42,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:51:42,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_01-51-42.log] [testng] 01:51:42,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-15 01:51:42,703] [main] testng.directory = /data [testng] [2024-03-15 01:51:42,704] [main] testng.configDirectory = /config [testng] [2024-03-15 01:51:42,716] [main] testng.multiplier = 1.0 [testng] [2024-03-15 01:51:42,716] [main] testng.in-memory = false [testng] [2024-03-15 01:51:42,716] [main] testng.allow-missing = false [testng] [2024-03-15 01:51:42,716] [main] user.language = en [testng] [2024-03-15 01:51:42,716] [main] user.country = ${user.country} [testng] [2024-03-15 01:51:42,717] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-15 01:51:44,783] [main] ---------------------------------------- [testng] [2024-03-15 01:51:44,784] [main] Total files: 32 [testng] [2024-03-15 01:51:44,784] [main] Scan time: 2.066 s (64 ms/file) [testng] [2024-03-15 01:51:44,784] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-15 01:52:01,035] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] 01:52:01,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:52:01,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:01,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_01-52-01.log] [testng] 01:52:01,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a8f3913 - End of configuration. [testng] [2024-03-15 01:52:01,285] [pool-1-thread-12] Initializing /data/geert/good example1.1sc.jpg: [testng] 01:52:01,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:52:01,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:01,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_01-52-01.log] [testng] 01:52:01,287 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f25a39e - End of configuration. [testng] [2024-03-15 01:52:01,411] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 01:52:01,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:52:01,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:01,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_01-52-01.log] [testng] 01:52:01,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@251a4004 - End of configuration. [testng] [2024-03-15 01:52:02,263] [pool-1-thread-10] Initializing /data/geert/good example1.1sc: [testng] 01:52:02,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:52:02,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:02,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_01-52-02.log] [testng] 01:52:02,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61c3ff9d - End of configuration. [testng] [2024-03-15 01:52:02,547] [pool-1-thread-9] Initializing /data/qa-29469/bad3.1sc: [testng] 01:52:02,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:52:02,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:02,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_01-52-02.log] [testng] 01:52:02,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fd37c58 - End of configuration. [testng] [2024-03-15 01:52:02,798] [pool-1-thread-8] Initializing /data/david/Opened in imageJ.tiff: [testng] 01:52:02,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:52:02,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:02,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_01-52-02.log] [testng] 01:52:02,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76a10ad8 - End of configuration. [testng] [2024-03-15 01:52:03,656] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 01:52:03,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:52:03,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:03,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_01-52-03.log] [testng] 01:52:03,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fa2e6fb - End of configuration. [testng] [2024-03-15 01:52:04,608] [pool-1-thread-6] Initializing /data/qa-16880/c-src v7.1sc: [testng] 01:52:04,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:52:04,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:04,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_01-52-04.log] [testng] 01:52:04,609 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61c2662 - End of configuration. [testng] [2024-03-15 01:52:04,864] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 01:52:04,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:52:04,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:04,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_01-52-04.log] [testng] 01:52:04,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61a2678a - End of configuration. [testng] [2024-03-15 01:52:05,199] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 01:52:05,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:52:05,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:05,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_01-52-05.log] [testng] 01:52:05,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@368f98dc - End of configuration. [testng] [2024-03-15 01:52:05,513] [pool-1-thread-3] Initializing /data/keith/pg020410saur3.1sc: [testng] 01:52:05,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:52:05,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:05,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_01-52-05.log] [testng] 01:52:05,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7385622 - End of configuration. [testng] [2024-03-15 01:52:05,820] [pool-1-thread-2] Initializing /data/keith/test.1sc: [testng] 01:52:05,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:52:05,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:05,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_01-52-05.log] [testng] 01:52:05,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b708be3 - End of configuration. [testng] [2024-03-15 01:52:09,213] [pool-1-thread-3] Initializing /data/adrian/test_img.1sc: [testng] [2024-03-15 01:52:09,483] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-03-15 01:52:09,760] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-03-15 01:52:10,110] [pool-1-thread-5] Initializing /data/qa-29459/bad.1sc: [testng] [2024-03-15 01:52:10,382] [pool-1-thread-12] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-03-15 01:52:11,352] [pool-1-thread-6] Initializing /data/geert/bad example1.1sc: [testng] [2024-03-15 01:52:11,639] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-03-15 01:52:12,590] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-03-15 01:52:13,703] [pool-1-thread-9] Initializing /data/samples/Criterion.1sc: [testng] [2024-03-15 01:52:17,178] [pool-1-thread-5] Initializing /data/qa-29459/bad.jpg: [testng] [2024-03-15 01:52:17,298] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-03-15 01:52:18,312] [pool-1-thread-7] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-03-15 01:52:18,423] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-03-15 01:52:18,700] [pool-1-thread-2] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-03-15 01:52:18,971] [pool-1-thread-1] Initializing /data/samples/imagesEight.1sc: [testng] [2024-03-15 01:52:19,279] [pool-1-thread-6] Initializing /data/geert/bad example1.jpg: [testng] [2024-03-15 01:52:19,402] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-03-15 01:52:19,707] [pool-1-thread-9] Initializing /data/qa-29469/good.1sc: [testng] [2024-03-15 01:52:22,193] [pool-1-thread-1] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-03-15 01:52:22,611] [pool-1-thread-5] 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: 45 seconds Finished: SUCCESS