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Started by upstream project "BIOFORMATS-test-repo" build number 194 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins3692373706260388068.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30647_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 11:01:03,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:01:03,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:01:03,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:01:03,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:01:03,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:01:03,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:01:03,505 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:01:03,505 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:01:03,506 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:01:03,506 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:01:03,506 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@428640fa - End of configuration. [testng] 11:01:03,507 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6bd61f98 - Registering current configuration as safe fallback point [testng] 11:01:03,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@48aca48b - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 387 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 11:01:03,516] [main] java.version = 21 [testng] 11:01:03,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:01:03,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:03,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_11-01-03.log] [testng] 11:01:03,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 11:01:03,804] [main] testng.directory = /data [testng] [2024-09-19 11:01:03,805] [main] testng.configDirectory = /config [testng] [2024-09-19 11:01:03,893] [main] testng.multiplier = 1.0 [testng] [2024-09-19 11:01:03,894] [main] testng.in-memory = false [testng] [2024-09-19 11:01:03,894] [main] testng.allow-missing = false [testng] [2024-09-19 11:01:03,895] [main] user.language = en [testng] [2024-09-19 11:01:03,895] [main] user.country = ${user.country} [testng] [2024-09-19 11:01:03,895] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 11:02:04,475] [main] ---------------------------------------- [testng] [2024-09-19 11:02:04,476] [main] Total files: 5651 [testng] [2024-09-19 11:02:04,476] [main] Scan time: 60.58 s (10 ms/file) [testng] [2024-09-19 11:02:04,476] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 11:03:33,621] [pool-1-thread-1] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 11:03:33,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:03:33,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:33,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_11-03-33.log] [testng] 11:03:33,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34abadde - End of configuration. [testng] [2024-09-19 11:03:33,950] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] 11:03:33,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:03:33,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:33,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_11-03-33.log] [testng] 11:03:33,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44bfc280 - End of configuration. [testng] [2024-09-19 11:03:35,010] [pool-1-thread-11] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 11:03:35,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:03:35,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:35,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_11-03-35.log] [testng] 11:03:35,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@230670f0 - End of configuration. [testng] [2024-09-19 11:03:35,342] [pool-1-thread-10] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 11:03:35,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:03:35,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:35,343 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_11-03-35.log] [testng] 11:03:35,343 |-INFO in ch.qos.logback.core.sift.SiftProcessor@517731df - End of configuration. [testng] [2024-09-19 11:03:35,750] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 11:03:35,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:03:35,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:35,751 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_11-03-35.log] [testng] 11:03:35,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c6aeb08 - End of configuration. [testng] [2024-09-19 11:03:36,736] [pool-1-thread-8] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 11:03:36,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:03:36,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:36,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_11-03-36.log] [testng] 11:03:36,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49a123d1 - End of configuration. [testng] [2024-09-19 11:03:37,645] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 11:03:37,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:03:37,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:37,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_11-03-37.log] [testng] 11:03:37,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f02de79 - End of configuration. [testng] [2024-09-19 11:03:37,780] [pool-1-thread-6] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 11:03:37,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:03:37,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:37,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_11-03-37.log] [testng] 11:03:37,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d520a9f - End of configuration. [testng] [2024-09-19 11:03:38,280] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 11:03:38,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:03:38,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:38,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_11-03-38.log] [testng] 11:03:38,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b076663 - End of configuration. [testng] [2024-09-19 11:03:38,413] [pool-1-thread-4] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 11:03:38,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:03:38,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:38,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_11-03-38.log] [testng] 11:03:38,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@560e6e03 - End of configuration. [testng] [2024-09-19 11:03:39,216] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 11:03:39,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:03:39,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:39,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_11-03-39.log] [testng] 11:03:39,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78c9f8d1 - End of configuration. [testng] [2024-09-19 11:03:39,289] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 11:03:39,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:03:39,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:03:39,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_11-03-39.log] [testng] 11:03:39,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c89057a - End of configuration. [testng] [2024-09-19 11:03:44,611] [pool-1-thread-3] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-09-19 11:03:45,955] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-09-19 11:03:47,405] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-09-19 11:03:50,573] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-09-19 11:03:53,582] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-09-19 11:03:56,630] [pool-1-thread-1] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-09-19 11:04:03,309] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-09-19 11:04:06,494] [pool-1-thread-8] Initializing /data/david/megan/megan.lei: [testng] [2024-09-19 11:04:13,004] [pool-1-thread-6] Initializing /data/clay/leica_stack.lei: [testng] [2024-09-19 11:04:27,710] [pool-1-thread-6] Initializing /data/clay/leica_stack.tif: [testng] [2024-09-19 11:04:33,461] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-09-19 11:06:42,514] [pool-1-thread-4] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-09-19 11:06:46,058] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-09-19 11:06:52,976] [pool-1-thread-2] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-09-19 11:08:21,125] [pool-1-thread-11] Initializing /data/samples/Leica_sample.lei: [testng] [2024-09-19 11:08:31,796] [pool-1-thread-11] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-09-19 11:08:34,137] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-09-19 11:08:36,157] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-09-19 11:10:05,652] [pool-1-thread-6] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-09-19 11:10:20,948] [pool-1-thread-8] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-09-19 11:11:08,809] [pool-1-thread-5] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-09-19 11:11:17,939] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-09-19 11:11:44,366] [pool-1-thread-3] Initializing /data/david/intestine/intestine.lei: [testng] [2024-09-19 11:12:04,329] [pool-1-thread-4] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-09-19 11:12:15,710] [pool-1-thread-12] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-09-19 11:12:18,131] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-09-19 11:12:30,248] [pool-1-thread-6] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-09-19 11:12:37,936] [pool-1-thread-6] Initializing /data/oliver/o459/o459.lei: [testng] [2024-09-19 11:13:45,369] [pool-1-thread-9] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-09-19 11:14:41,209] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-09-19 11:14:43,825] [pool-1-thread-1] Initializing /data/julie/c164_1.tif: [testng] [2024-09-19 11:14:47,614] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei: [testng] 12:15:18,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:15:18,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:18,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_12-15-18.log] [testng] 12:15:18,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b364f47 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 74 minutes 33 seconds Finished: SUCCESS