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Started by upstream project "BIOFORMATS-test-repo" build number 104 originally caused by: Started by upstream project "Trigger" build number 116 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/jenkins10948856639023208843.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16075_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:25:03,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:25:03,603 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:25:03,603 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:03,604 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:03,604 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:25:03,605 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:25:03,605 |-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] 01:25:03,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:03,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:03,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:25:03,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:25:03,607 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:25:03,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:25:03,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:25:03,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:25:03,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:25:03,825 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:25:03,826 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:25:03,826 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:25:03,826 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:25:03,826 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:25:03,827 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:25:03,827 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 222 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-27 01:25:03,837] [main] java.version = 21 [testng] 01:25:03,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:25:03,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:03,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-27_01-25-03.log] [testng] 01:25:03,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-06-27 01:25:03,893] [main] testng.directory = /data [testng] [2024-06-27 01:25:03,893] [main] testng.configDirectory = /config [testng] [2024-06-27 01:25:03,903] [main] testng.multiplier = 1.0 [testng] [2024-06-27 01:25:03,903] [main] testng.in-memory = false [testng] [2024-06-27 01:25:03,904] [main] testng.allow-missing = false [testng] [2024-06-27 01:25:03,904] [main] user.language = en [testng] [2024-06-27 01:25:03,904] [main] user.country = ${user.country} [testng] [2024-06-27 01:25:03,904] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-27 01:25:25,199] [main] ---------------------------------------- [testng] [2024-06-27 01:25:25,199] [main] Total files: 164 [testng] [2024-06-27 01:25:25,199] [main] Scan time: 21.295 s (129 ms/file) [testng] [2024-06-27 01:25:25,200] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-27 01:25:33,601] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:25:33,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:25:33,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:33,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-27_01-25-33.log] [testng] 01:25:33,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34a59cbc - End of configuration. [testng] [2024-06-27 01:25:33,620] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 01:25:33,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:25:33,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:33,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-27_01-25-33.log] [testng] 01:25:33,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ca05f - End of configuration. [testng] [2024-06-27 01:25:33,796] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:25:33,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:25:33,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:33,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-27_01-25-33.log] [testng] 01:25:33,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a90c1a3 - End of configuration. [testng] [2024-06-27 01:25:33,809] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:25:33,809 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:25:33,809 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:33,810 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-27_01-25-33.log] [testng] 01:25:33,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41e84a53 - End of configuration. [testng] [2024-06-27 01:25:34,037] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:25:34,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:25:34,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-27_01-25-34.log] [testng] 01:25:34,038 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f9a458 - End of configuration. [testng] [2024-06-27 01:25:34,062] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:25:34,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:25:34,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-27_01-25-34.log] [testng] 01:25:34,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a643f46 - End of configuration. [testng] [2024-06-27 01:25:34,083] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 01:25:34,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:25:34,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-27_01-25-34.log] [testng] 01:25:34,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c48d0d1 - End of configuration. [testng] [2024-06-27 01:25:34,092] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 01:25:34,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:25:34,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-27_01-25-34.log] [testng] 01:25:34,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@85341d5 - End of configuration. [testng] [2024-06-27 01:25:34,100] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:25:34,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:25:34,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-27_01-25-34.log] [testng] 01:25:34,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35c48f60 - End of configuration. [testng] [2024-06-27 01:25:34,111] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:25:34,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:25:34,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-27_01-25-34.log] [testng] 01:25:34,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71ee1e1a - End of configuration. [testng] [2024-06-27 01:25:34,194] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 01:25:34,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:25:34,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-27_01-25-34.log] [testng] 01:25:34,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a8e1ff - End of configuration. [testng] [2024-06-27 01:25:34,208] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:25:34,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:25:34,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:34,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-27_01-25-34.log] [testng] 01:25:34,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79529903 - End of configuration. [testng] [2024-06-27 01:25:35,768] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-06-27 01:25:35,775] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-06-27 01:25:35,783] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-06-27 01:25:35,883] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-06-27 01:25:35,999] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-06-27 01:25:36,126] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-06-27 01:25:36,205] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-06-27 01:25:36,875] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-06-27 01:25:36,964] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-06-27 01:25:37,093] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-06-27 01:25:37,174] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-06-27 01:25:37,386] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-06-27 01:25:37,409] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] [2024-06-27 01:25:37,730] [pool-1-thread-8] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-06-27 01:25:37,784] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-06-27 01:25:37,832] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-06-27 01:25:37,974] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-06-27 01:25:38,107] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-06-27 01:25:38,137] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2024-06-27 01:25:38,227] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-06-27 01:25:38,382] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-06-27 01:25:38,420] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-06-27 01:25:38,483] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-06-27 01:25:38,523] [pool-1-thread-6] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-06-27 01:25:38,529] [pool-1-thread-8] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-06-27 01:25:38,542] [pool-1-thread-12] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-06-27 01:25:38,729] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-06-27 01:25:38,825] [pool-1-thread-11] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-06-27 01:25:39,657] [pool-1-thread-1] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-06-27 01:25:39,708] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-06-27 01:25:39,981] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-06-27 01:25:40,041] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-06-27 01:25:40,080] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-06-27 01:25:40,153] [pool-1-thread-3] Initializing /data/ome/embryo.lsm: [testng] [2024-06-27 01:25:40,179] [pool-1-thread-7] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-06-27 01:25:40,553] [pool-1-thread-12] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-06-27 01:25:40,590] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-06-27 01:25:40,777] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-06-27 01:25:40,804] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-06-27 01:25:41,047] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-06-27 01:25:41,053] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-06-27 01:25:41,231] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-06-27 01:25:41,313] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-06-27 01:25:41,448] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-06-27 01:25:41,504] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-06-27 01:25:41,581] [pool-1-thread-4] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-06-27 01:25:41,675] [pool-1-thread-6] 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 4 seconds Finished: SUCCESS