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Started by upstream project "BIOFORMATS-test-repo" build number 131 originally caused by: Started by upstream project "Trigger" build number 148 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins4196193280601707073.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20503_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning 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] 01:23:56,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:56,089 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:23:56,089 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:56,091 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:56,091 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:56,092 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:56,092 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:23:56,092 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:56,093 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:56,094 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:56,094 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:56,095 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:56,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:56,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:56,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:56,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:56,373 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:56,374 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:56,374 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:56,374 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:56,375 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:23:56,376 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:23:56,376 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 283 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-24 01:23:56,390] [main] java.version = 17.0.2 [testng] 01:23:56,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:56,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:56,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-24_01-23-56.log] [testng] 01:23:56,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-24 01:23:56,466] [main] testng.directory = /data [testng] [2024-07-24 01:23:56,466] [main] testng.configDirectory = /config [testng] [2024-07-24 01:23:56,479] [main] testng.multiplier = 1.0 [testng] [2024-07-24 01:23:56,480] [main] testng.in-memory = false [testng] [2024-07-24 01:23:56,480] [main] testng.allow-missing = false [testng] [2024-07-24 01:23:56,480] [main] user.language = en [testng] [2024-07-24 01:23:56,480] [main] user.country = ${user.country} [testng] [2024-07-24 01:23:56,480] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-24 01:24:17,025] [main] ---------------------------------------- [testng] [2024-07-24 01:24:17,026] [main] Total files: 164 [testng] [2024-07-24 01:24:17,026] [main] Scan time: 20.544 s (125 ms/file) [testng] [2024-07-24 01:24:17,026] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-24 01:24:27,327] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:27,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:27,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,328 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-24_01-24-27.log] [testng] 01:24:27,329 |-INFO in ch.qos.logback.core.sift.SiftProcessor@282e2d0a - End of configuration. [testng] [2024-07-24 01:24:27,359] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:24:27,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:27,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-24_01-24-27.log] [testng] 01:24:27,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76063626 - End of configuration. [testng] [2024-07-24 01:24:27,389] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:27,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:27,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-24_01-24-27.log] [testng] 01:24:27,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@af8b938 - End of configuration. [testng] [2024-07-24 01:24:27,397] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:27,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:27,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-24_01-24-27.log] [testng] 01:24:27,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20634cc8 - End of configuration. [testng] [2024-07-24 01:24:27,437] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:27,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:27,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-24_01-24-27.log] [testng] 01:24:27,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cd54bd - End of configuration. [testng] [2024-07-24 01:24:27,451] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:27,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:27,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-24_01-24-27.log] [testng] 01:24:27,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f84bd30 - End of configuration. [testng] [2024-07-24 01:24:27,468] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:24:27,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:27,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-24_01-24-27.log] [testng] 01:24:27,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d1f0080 - End of configuration. [testng] [2024-07-24 01:24:27,517] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:24:27,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:27,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-24_01-24-27.log] [testng] 01:24:27,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bee7c5e - End of configuration. [testng] [2024-07-24 01:24:27,607] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:24:27,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:27,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-24_01-24-27.log] [testng] 01:24:27,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fd6dd35 - End of configuration. [testng] [2024-07-24 01:24:27,617] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:24:27,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:27,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-24_01-24-27.log] [testng] 01:24:27,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50380ee1 - End of configuration. [testng] [2024-07-24 01:24:27,669] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:24:27,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:27,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-24_01-24-27.log] [testng] 01:24:27,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5783815f - End of configuration. [testng] [2024-07-24 01:24:27,687] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:27,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:27,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-24_01-24-27.log] [testng] 01:24:27,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7038b55 - End of configuration. [testng] [2024-07-24 01:24:28,720] [pool-1-thread-6] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-07-24 01:24:28,892] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-24 01:24:29,319] [pool-1-thread-9] Initializing /data/sdub/sdub.pattern: [testng] [2024-07-24 01:24:29,468] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-24 01:24:29,770] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-07-24 01:24:29,956] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-24 01:24:30,207] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-07-24 01:24:30,216] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-24 01:24:30,242] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-24 01:24:30,289] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-24 01:24:30,443] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-07-24 01:24:30,668] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-24 01:24:30,682] [pool-1-thread-5] Initializing /data/ome/worm.tiff: [testng] [2024-07-24 01:24:30,786] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-07-24 01:24:30,822] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-24 01:24:30,931] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-24 01:24:31,053] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-24 01:24:31,279] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-24 01:24:31,406] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-24 01:24:31,578] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-07-24 01:24:31,608] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-07-24 01:24:31,756] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-07-24 01:24:31,938] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-24 01:24:33,079] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-24 01:24:33,282] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-07-24 01:24:33,370] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-24 01:24:34,215] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-24 01:24:34,237] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-07-24 01:24:34,709] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-07-24 01:24:34,801] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-24 01:24:34,806] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-07-24 01:24:35,030] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-07-24 01:24:35,039] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-24 01:24:35,113] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-24 01:24:35,208] [pool-1-thread-9] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-24 01:24:35,266] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-24 01:24:35,346] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-24 01:24:35,444] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-24 01:24:35,609] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-24 01:24:35,689] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-24 01:24:35,710] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-24 01:24:35,764] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-24 01:24:35,926] [pool-1-thread-1] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-07-24 01:24:35,962] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-24 01:24:36,073] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-24 01:24:36,192] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-24 01:24:36,196] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-07-24 01:24:36,324] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 1, Skips: 0 [testng] =============================================== [testng] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 2 minutes 16 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE