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Started by upstream project "BIOFORMATS-test-repo" build number 295 originally caused by: Started by upstream project "Trigger" build number 314 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins870665638927363561.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46570_merge_ci -v /uod/idr/repos/curated/leica:/data -v /uod/idr-scratch/merge-ci/curated/leica:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 00:22:04,838 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:04,839 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:22:04,839 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:04,840 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:04,840 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:04,841 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:04,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:22:04,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:04,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:04,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:04,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:04,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:04,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:04,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:05,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:05,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:05,023 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:05,023 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:05,023 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:05,024 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:05,024 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:22:05,024 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:22:05,024 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-19 00:22:05,033] [main] java.version = 21 [testng] 00:22:05,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:05,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:05,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-19_00-22-05.log] [testng] 00:22:05,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-19 00:22:05,077] [main] testng.directory = /data [testng] [2024-12-19 00:22:05,077] [main] testng.configDirectory = /config [testng] [2024-12-19 00:22:05,085] [main] testng.multiplier = 1.0 [testng] [2024-12-19 00:22:05,090] [main] testng.in-memory = false [testng] [2024-12-19 00:22:05,091] [main] testng.allow-missing = false [testng] [2024-12-19 00:22:05,091] [main] user.language = en [testng] [2024-12-19 00:22:05,091] [main] user.country = ${user.country} [testng] [2024-12-19 00:22:05,091] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-19 00:22:22,226] [main] ---------------------------------------- [testng] [2024-12-19 00:22:22,226] [main] Total files: 5651 [testng] [2024-12-19 00:22:22,226] [main] Scan time: 17.135 s (3 ms/file) [testng] [2024-12-19 00:22:22,227] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-19 00:23:05,745] [pool-1-thread-1] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:23:05,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:23:05,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:05,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-19_00-23-05.log] [testng] 00:23:05,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3878d7d1 - End of configuration. [testng] [2024-12-19 00:23:06,198] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif: [testng] 00:23:06,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:23:06,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:06,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-19_00-23-06.log] [testng] 00:23:06,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65384a2d - End of configuration. [testng] [2024-12-19 00:23:06,771] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:23:06,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:23:06,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:06,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-19_00-23-06.log] [testng] 00:23:06,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53ad284c - End of configuration. [testng] [2024-12-19 00:23:06,811] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 00:23:06,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:23:06,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:06,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-19_00-23-06.log] [testng] 00:23:06,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bc53377 - End of configuration. [testng] [2024-12-19 00:23:08,002] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:23:08,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:23:08,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:08,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-19_00-23-08.log] [testng] 00:23:08,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@609f082a - End of configuration. [testng] [2024-12-19 00:23:08,031] [pool-1-thread-8] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:23:08,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:23:08,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:08,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-19_00-23-08.log] [testng] 00:23:08,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f2e707e - End of configuration. [testng] [2024-12-19 00:23:08,315] [pool-1-thread-7] Initializing /data/andrey/10310500/10310500.lei: [testng] 00:23:08,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:23:08,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:08,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-19_00-23-08.log] [testng] 00:23:08,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@174b9422 - End of configuration. [testng] [2024-12-19 00:23:08,683] [pool-1-thread-6] Initializing /data/clay/leica_stack.tif: [testng] 00:23:08,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:23:08,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:08,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-19_00-23-08.log] [testng] 00:23:08,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42d264c - End of configuration. [testng] [2024-12-19 00:23:08,852] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] 00:23:08,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:23:08,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:08,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-19_00-23-08.log] [testng] 00:23:08,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18ff7fd6 - End of configuration. [testng] [2024-12-19 00:23:09,789] [pool-1-thread-4] Initializing /data/david/intestine/intestine.lei: [testng] 00:23:09,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:23:09,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:09,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-19_00-23-09.log] [testng] 00:23:09,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20d2e350 - End of configuration. [testng] [2024-12-19 00:23:10,039] [pool-1-thread-3] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 00:23:10,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:23:10,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:10,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-19_00-23-10.log] [testng] 00:23:10,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c7120bd - End of configuration. [testng] [2024-12-19 00:23:10,243] [pool-1-thread-2] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:23:10,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:23:10,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:10,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-19_00-23-10.log] [testng] 00:23:10,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41afb217 - End of configuration. [testng] [2024-12-19 00:23:14,740] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-12-19 00:23:15,629] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-12-19 00:23:17,827] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-12-19 00:23:20,781] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-19 00:23:21,027] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-19 00:23:22,105] [pool-1-thread-10] Initializing /data/david/megan/megan.lei: [testng] [2024-12-19 00:23:23,556] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-19 00:23:25,880] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-12-19 00:23:34,318] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-19 00:23:38,039] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-19 00:23:41,701] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-19 00:23:52,227] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-12-19 00:26:50,346] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-19 00:26:55,589] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-12-19 00:27:31,590] [pool-1-thread-6] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-12-19 00:27:33,698] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-12-19 00:27:48,764] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-19 00:27:53,789] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-19 00:28:02,431] [pool-1-thread-9] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-19 00:29:54,957] [pool-1-thread-8] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-19 00:30:43,631] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-19 00:31:40,934] [pool-1-thread-10] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-19 00:32:08,587] [pool-1-thread-11] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-12-19 00:32:46,033] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-12-19 00:32:58,617] [pool-1-thread-1] Initializing /data/oliver/o459/o459.lei: [testng] [2024-12-19 00:33:13,939] [pool-1-thread-5] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-12-19 00:33:41,199] [pool-1-thread-4] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-19 00:33:46,906] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-19 00:33:50,875] [pool-1-thread-12] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-19 00:34:03,457] [pool-1-thread-6] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-12-19 00:34:06,162] [pool-1-thread-4] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-19 00:34:20,994] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Logo.jpg: time="2024-12-19T01:00:55Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE