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Started by upstream project "BIOFORMATS-test-repo" build number 307 originally caused by: Started by upstream project "Trigger" build number 329 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins16435565988253252434.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48583_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/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] 00:36:31,187 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:31,188 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:36:31,188 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:31,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:31,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:31,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:31,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:36:31,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:31,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:31,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:31,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:31,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:31,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:31,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:31,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:31,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:31,456 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:31,457 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:31,457 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:31,457 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:31,457 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:36:31,458 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:36:31,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 268 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-03 00:36:31,469] [main] java.version = 1.8.0_342 [testng] 00:36:31,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:31,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:31,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-03_00-36-31.log] [testng] 00:36:31,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-03 00:36:31,524] [main] testng.directory = /data [testng] [2025-01-03 00:36:31,525] [main] testng.configDirectory = /config [testng] [2025-01-03 00:36:31,538] [main] testng.multiplier = 1.0 [testng] [2025-01-03 00:36:31,538] [main] testng.in-memory = false [testng] [2025-01-03 00:36:31,538] [main] testng.allow-missing = false [testng] [2025-01-03 00:36:31,539] [main] user.language = en [testng] [2025-01-03 00:36:31,539] [main] user.country = ${user.country} [testng] [2025-01-03 00:36:31,539] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-03 00:37:14,578] [main] ---------------------------------------- [testng] [2025-01-03 00:37:14,578] [main] Total files: 164 [testng] [2025-01-03 00:37:14,579] [main] Scan time: 43.039 s (262 ms/file) [testng] [2025-01-03 00:37:14,579] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-03 00:38:23,501] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] 00:38:23,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:38:23,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:23,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-03_00-38-23.log] [testng] 00:38:23,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@777ab9f1 - End of configuration. [testng] [2025-01-03 00:38:42,768] [pool-1-thread-12] Initializing /data/ome/worm.tiff: [testng] 00:38:42,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:38:42,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:42,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-03_00-38-42.log] [testng] 00:38:42,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8bccbff - End of configuration. [testng] [2025-01-03 00:38:46,255] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:38:46,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:38:46,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:46,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-03_00-38-46.log] [testng] 00:38:46,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ff5fd5a - End of configuration. [testng] [2025-01-03 00:38:46,294] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] 00:38:46,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:38:46,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:46,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-03_00-38-46.log] [testng] 00:38:46,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b18c545 - End of configuration. [testng] [2025-01-03 00:38:46,544] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 00:38:46,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:38:46,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:46,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-03_00-38-46.log] [testng] 00:38:46,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc0c17c - End of configuration. [testng] [2025-01-03 00:38:46,900] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] 00:38:46,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:38:46,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:46,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-03_00-38-46.log] [testng] 00:38:46,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c0d47dc - End of configuration. [testng] [2025-01-03 00:38:47,116] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:38:47,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:38:47,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:47,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-03_00-38-47.log] [testng] 00:38:47,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b7efb9a - End of configuration. [testng] [2025-01-03 00:38:47,291] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:38:47,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:38:47,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:47,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-03_00-38-47.log] [testng] 00:38:47,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b4322e7 - End of configuration. [testng] [2025-01-03 00:38:47,694] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:38:47,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:38:47,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:47,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-03_00-38-47.log] [testng] 00:38:47,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7048f5a5 - End of configuration. [testng] [2025-01-03 00:38:48,145] [pool-1-thread-4] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:38:48,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:38:48,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:48,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-03_00-38-48.log] [testng] 00:38:48,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cf456fd - End of configuration. [testng] [2025-01-03 00:38:48,620] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 00:38:48,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:38:48,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:48,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-03_00-38-48.log] [testng] 00:38:48,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c1d6d25 - End of configuration. [testng] [2025-01-03 00:38:49,047] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:38:49,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:38:49,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:49,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-03_00-38-49.log] [testng] 00:38:49,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@641003f4 - End of configuration. [testng] [2025-01-03 00:38:51,795] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2025-01-03 00:38:54,673] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-01-03 00:38:55,579] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-01-03 00:38:56,006] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-01-03 00:38:56,111] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-01-03 00:38:56,206] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-01-03 00:38:57,087] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2025-01-03 00:38:59,845] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-01-03 00:38:59,887] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-01-03 00:39:00,408] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-01-03 00:39:00,647] [pool-1-thread-11] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-01-03 00:39:01,780] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-01-03 00:39:01,859] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-01-03 00:39:01,962] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-01-03 00:39:02,846] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-01-03 00:39:03,652] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2025-01-03 00:39:05,026] [pool-1-thread-9] Initializing /data/ome/cb_1.r3d: [testng] [2025-01-03 00:39:06,467] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-01-03 00:39:07,095] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-01-03 00:39:07,815] [pool-1-thread-9] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-01-03 00:39:08,349] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-01-03 00:39:09,232] [pool-1-thread-8] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-01-03 00:39:10,509] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-01-03 00:39:10,846] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-01-03 00:39:11,587] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-01-03 00:39:11,673] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2025-01-03 00:39:11,971] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-01-03 00:39:12,582] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-01-03 00:39:12,762] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-01-03 00:39:12,997] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-01-03 00:39:13,746] [pool-1-thread-5] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-01-03 00:39:14,038] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2025-01-03 00:39:14,301] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-01-03 00:39:14,359] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2025-01-03 00:39:15,650] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-01-03 00:39:15,734] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2025-01-03 00:39:17,349] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-01-03 00:39:17,851] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-01-03 00:39:18,346] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-01-03 00:39:19,254] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-01-03 00:39:20,130] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-01-03 00:39:21,894] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-01-03 00:39:22,545] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-01-03 00:39:23,409] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-01-03 00:39:24,025] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-01-03 00:39:26,232] [pool-1-thread-12] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-01-03 00:39:26,588] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 5 seconds Finished: SUCCESS