Started by upstream project "BIOFORMATS-test-repo" build number 245 originally caused by: Started by upstream project "Trigger" build number 269 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/jenkins13972831038937640893.sh + '[' samples = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_38526_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 -Duser.language=fr -Duser.country=FR 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] 00:55:32,092 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:55:32,094 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:55:32,094 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:32,095 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:32,096 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:55:32,096 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:55:32,096 |-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] 00:55:32,096 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:32,097 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:32,097 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:55:32,097 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:55:32,097 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:55:32,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:55:32,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:55:32,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:55:32,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:55:32,367 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:55:32,368 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:55:32,368 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:55:32,368 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:55:32,368 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:55:32,369 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:55:32,369 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 272 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-04 00:55:32,379] [main] java.version = 1.8.0_342 [testng] 00:55:32,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:55:32,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:32,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-04_00-55-32.log] [testng] 00:55:32,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-04 00:55:32,443] [main] testng.directory = /data [testng] [2024-11-04 00:55:32,443] [main] testng.configDirectory = /config [testng] [2024-11-04 00:55:32,459] [main] testng.multiplier = 1.0 [testng] [2024-11-04 00:55:32,459] [main] testng.in-memory = false [testng] [2024-11-04 00:55:32,459] [main] testng.allow-missing = false [testng] [2024-11-04 00:55:32,459] [main] user.language = fr [testng] [2024-11-04 00:55:32,459] [main] user.country = FR [testng] [2024-11-04 00:55:32,459] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-04 00:58:07,457] [main] ---------------------------------------- [testng] [2024-11-04 00:58:07,458] [main] Total files: 164 [testng] [2024-11-04 00:58:07,458] [main] Scan time: 154.998 s (945 ms/file) [testng] [2024-11-04 00:58:07,458] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-04 01:02:45,257] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:02:45,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:02:45,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:45,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-04_01-02-45.log] [testng] 01:02:45,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@255876ce - End of configuration. [testng] [2024-11-04 01:02:45,525] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:02:45,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:02:45,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:45,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-04_01-02-45.log] [testng] 01:02:45,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10628999 - End of configuration. [testng] [2024-11-04 01:02:47,002] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:02:47,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:02:47,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:47,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-04_01-02-47.log] [testng] 01:02:47,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4a76d9 - End of configuration. [testng] [2024-11-04 01:02:48,885] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 01:02:48,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:02:48,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:48,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-04_01-02-48.log] [testng] 01:02:48,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@237f2a7b - End of configuration. [testng] [2024-11-04 01:02:50,465] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 01:02:50,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:02:50,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:50,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-04_01-02-50.log] [testng] 01:02:50,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35c60d8e - End of configuration. [testng] [2024-11-04 01:02:51,100] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 01:02:51,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:02:51,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:51,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-04_01-02-51.log] [testng] 01:02:51,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32ad4035 - End of configuration. [testng] [2024-11-04 01:02:52,670] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 01:02:52,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:02:52,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:52,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-04_01-02-52.log] [testng] 01:02:52,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78a515a2 - End of configuration. [testng] [2024-11-04 01:02:53,151] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 01:02:53,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:02:53,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:53,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-04_01-02-53.log] [testng] 01:02:53,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4663b67c - End of configuration. [testng] [2024-11-04 01:04:28,745] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 01:04:28,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:04:28,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:04:28,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-04_01-04-28.log] [testng] 01:04:28,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b6b16b - End of configuration. [testng] [2024-11-04 01:04:34,304] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 01:04:34,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:04:34,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:04:34,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-04_01-04-34.log] [testng] 01:04:34,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2269473a - End of configuration. [testng] [2024-11-04 01:04:34,890] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 01:04:34,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:04:34,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:04:34,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-04_01-04-34.log] [testng] 01:04:34,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1300d672 - End of configuration. [testng] [2024-11-04 01:04:35,339] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:04:35,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:04:35,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:04:35,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-04_01-04-35.log] [testng] 01:04:35,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43f4bd6 - End of configuration. [testng] [2024-11-04 01:04:46,035] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-04 01:04:48,933] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-04 01:04:50,940] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-04 01:04:53,729] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-04 01:04:54,435] [pool-1-thread-12] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-04 01:04:56,935] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-04 01:05:04,841] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-04 01:05:05,263] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-04 01:05:10,807] [pool-1-thread-3] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-04 01:05:14,630] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-11-04 01:05:20,502] [pool-1-thread-2] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-04 01:05:23,064] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-04 01:05:23,319] [pool-1-thread-4] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-04 01:05:24,482] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-04 01:05:26,935] [pool-1-thread-9] Initializing /data/ome/C1.lsm: [testng] [2024-11-04 01:05:31,881] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-11-04 01:05:36,852] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-11-04 01:05:43,966] [pool-1-thread-7] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-04 01:05:48,405] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-04 01:05:50,515] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-04 01:05:50,726] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-04 01:05:51,592] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-11-04 01:05:55,378] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-04 01:05:56,402] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-04 01:06:02,251] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-04 01:06:09,802] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-04 01:06:14,467] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-04 01:06:16,760] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-04 01:06:17,132] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-04 01:06:17,795] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-04 01:06:18,301] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-04 01:06:19,059] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-04 01:06:21,406] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-04 01:06:26,738] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-04 01:06:29,925] [pool-1-thread-12] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-04 01:06:31,111] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-04 01:06:41,321] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-04 01:06:46,164] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-04 01:06:49,145] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-04 01:06:57,893] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-04 01:07:36,883] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-04 01:07:40,113] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-04 01:07:43,704] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-04 01:07:44,116] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-04 01:07:45,155] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-04 01:07:46,803] [pool-1-thread-11] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-04 01:07:50,585] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 18 minutes 41 seconds Finished: SUCCESS