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Started by upstream project "BIOFORMATS-test-repo" build number 132 originally caused by: Started by upstream project "Trigger" build number 152 originally caused by: Started by user devspace 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/jenkins16104886460544389842.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20667_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 11:01:20,799 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:01:20,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 11:01:20,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:01:20,803 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:01:20,804 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:01:20,804 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:01:20,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:01:20,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:01:20,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:01:20,806 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:01:20,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:01:20,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:01:21,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:01:21,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:01:21,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:01:21,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:01:21,085 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:01:21,086 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:01:21,086 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:01:21,086 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:01:21,087 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 11:01:21,088 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 11:01:21,088 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 283 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-25 11:01:21,102] [main] java.version = 21 [testng] 11:01:21,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:01:21,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:21,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-25_11-01-21.log] [testng] 11:01:21,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-25 11:01:21,185] [main] testng.directory = /data [testng] [2024-07-25 11:01:21,185] [main] testng.configDirectory = /config [testng] [2024-07-25 11:01:21,201] [main] testng.multiplier = 1.0 [testng] [2024-07-25 11:01:21,202] [main] testng.in-memory = false [testng] [2024-07-25 11:01:21,202] [main] testng.allow-missing = false [testng] [2024-07-25 11:01:21,202] [main] user.language = en [testng] [2024-07-25 11:01:21,202] [main] user.country = ${user.country} [testng] [2024-07-25 11:01:21,202] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-25 11:01:42,669] [main] ---------------------------------------- [testng] [2024-07-25 11:01:42,670] [main] Total files: 164 [testng] [2024-07-25 11:01:42,670] [main] Scan time: 21.467 s (130 ms/file) [testng] [2024-07-25 11:01:42,670] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-25 11:01:51,008] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 11:01:51,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:01:51,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-25_11-01-51.log] [testng] 11:01:51,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6963d493 - End of configuration. [testng] [2024-07-25 11:01:51,026] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 11:01:51,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:01:51,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-25_11-01-51.log] [testng] 11:01:51,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@111e45e3 - End of configuration. [testng] [2024-07-25 11:01:51,252] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 11:01:51,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:01:51,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,254 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-25_11-01-51.log] [testng] 11:01:51,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d4961a6 - End of configuration. [testng] [2024-07-25 11:01:51,268] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 11:01:51,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:01:51,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-25_11-01-51.log] [testng] 11:01:51,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27672ca5 - End of configuration. [testng] [2024-07-25 11:01:51,520] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 11:01:51,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:01:51,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-25_11-01-51.log] [testng] 11:01:51,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d0b7986 - End of configuration. [testng] [2024-07-25 11:01:51,542] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 11:01:51,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:01:51,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-25_11-01-51.log] [testng] 11:01:51,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f162f5c - End of configuration. [testng] [2024-07-25 11:01:51,559] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 11:01:51,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:01:51,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-25_11-01-51.log] [testng] 11:01:51,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5095471d - End of configuration. [testng] [2024-07-25 11:01:51,621] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 11:01:51,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:01:51,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-25_11-01-51.log] [testng] 11:01:51,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43de1018 - End of configuration. [testng] [2024-07-25 11:01:51,634] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 11:01:51,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:01:51,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-25_11-01-51.log] [testng] 11:01:51,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be8ecaf - End of configuration. [testng] [2024-07-25 11:01:51,644] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 11:01:51,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:01:51,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-25_11-01-51.log] [testng] 11:01:51,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7880b379 - End of configuration. [testng] [2024-07-25 11:01:51,726] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 11:01:51,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:01:51,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-25_11-01-51.log] [testng] 11:01:51,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ea9de2 - End of configuration. [testng] [2024-07-25 11:01:51,743] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 11:01:51,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:01:51,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:01:51,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-25_11-01-51.log] [testng] 11:01:51,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c148d0d - End of configuration. [testng] [2024-07-25 11:01:53,394] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-07-25 11:01:53,404] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-25 11:01:53,527] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-07-25 11:01:53,800] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-25 11:01:53,808] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-25 11:01:54,028] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-25 11:01:54,125] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-25 11:01:55,129] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-25 11:01:55,143] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-25 11:01:55,400] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-07-25 11:01:55,470] [pool-1-thread-12] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-25 11:01:55,566] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-25 11:01:55,760] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] [2024-07-25 11:01:55,789] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-07-25 11:01:56,204] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-25 11:01:56,212] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-25 11:01:56,232] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-25 11:01:56,296] [pool-1-thread-7] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-25 11:01:56,361] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] [2024-07-25 11:01:56,507] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-25 11:01:56,619] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-07-25 11:01:56,625] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-25 11:01:56,751] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-25 11:01:56,757] [pool-1-thread-10] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-25 11:01:56,805] [pool-1-thread-8] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-25 11:01:56,852] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-07-25 11:01:56,916] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-07-25 11:01:57,055] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-25 11:01:58,003] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-25 11:01:58,043] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-25 11:01:58,376] [pool-1-thread-12] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-25 11:01:58,487] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-07-25 11:01:58,511] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-25 11:01:58,579] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-07-25 11:01:58,602] [pool-1-thread-2] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-07-25 11:01:59,074] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-25 11:01:59,131] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-25 11:01:59,261] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-07-25 11:01:59,413] [pool-1-thread-2] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-25 11:01:59,664] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-07-25 11:01:59,681] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-07-25 11:01:59,815] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-25 11:01:59,938] [pool-1-thread-12] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-25 11:02:00,104] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-25 11:02:00,258] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-25 11:02:00,331] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-07-25 11:02:00,513] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 8 seconds Finished: SUCCESS