Started by upstream project "BIOFORMATS-test-repo" build number 292 originally caused by: Started by upstream project "Trigger" build number 311 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins1368327918339699922.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_46107_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] 00:42:35,586 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:42:35,588 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:42:35,588 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:42:35,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:42:35,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:42:35,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:42:35,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:42:35,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:42:35,590 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:42:35,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:42:35,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:42:35,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:42:35,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:42:35,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:42:35,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:42:35,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:42:35,839 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:42:35,839 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:42:35,839 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:42:35,840 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:42:35,840 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:42:35,840 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:42:35,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-16 00:42:35,858] [main] java.version = 1.8.0_342 [testng] 00:42:35,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:42:35,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:35,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-16_00-42-35.log] [testng] 00:42:35,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-16 00:42:35,912] [main] testng.directory = /data [testng] [2024-12-16 00:42:35,912] [main] testng.configDirectory = /config [testng] [2024-12-16 00:42:35,924] [main] testng.multiplier = 1.0 [testng] [2024-12-16 00:42:35,924] [main] testng.in-memory = false [testng] [2024-12-16 00:42:35,924] [main] testng.allow-missing = false [testng] [2024-12-16 00:42:35,924] [main] user.language = fr [testng] [2024-12-16 00:42:35,925] [main] user.country = FR [testng] [2024-12-16 00:42:35,925] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-16 00:44:14,251] [main] ---------------------------------------- [testng] [2024-12-16 00:44:14,252] [main] Total files: 164 [testng] [2024-12-16 00:44:14,252] [main] Scan time: 98.326 s (599 ms/file) [testng] [2024-12-16 00:44:14,252] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-16 00:47:06,094] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:47:06,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:47:06,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:06,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-16_00-47-06.log] [testng] 00:47:06,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17ed4889 - End of configuration. [testng] [2024-12-16 00:47:06,521] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:47:06,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:47:06,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:06,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-16_00-47-06.log] [testng] 00:47:06,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@621f0d6 - End of configuration. [testng] [2024-12-16 00:47:07,314] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:47:07,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:47:07,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:07,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-16_00-47-07.log] [testng] 00:47:07,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ecfcac - End of configuration. [testng] [2024-12-16 00:47:08,131] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:47:08,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:47:08,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:08,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-16_00-47-08.log] [testng] 00:47:08,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4a76d9 - End of configuration. [testng] [2024-12-16 00:47:09,848] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:47:09,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:47:09,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:09,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-16_00-47-09.log] [testng] 00:47:09,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f43e980 - End of configuration. [testng] [2024-12-16 00:47:10,664] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:47:10,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:47:10,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:10,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-16_00-47-10.log] [testng] 00:47:10,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ef85f50 - End of configuration. [testng] [2024-12-16 00:47:11,475] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 00:47:11,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:47:11,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:11,476 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-16_00-47-11.log] [testng] 00:47:11,477 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a341046 - End of configuration. [testng] [2024-12-16 00:47:11,635] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 00:47:11,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:47:11,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:11,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-16_00-47-11.log] [testng] 00:47:11,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d3f0f0f - End of configuration. [testng] [2024-12-16 00:47:49,851] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 00:47:49,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:47:49,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:49,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-16_00-47-49.log] [testng] 00:47:49,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c979463 - End of configuration. [testng] [2024-12-16 00:47:52,659] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 00:47:52,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:47:52,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:52,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-16_00-47-52.log] [testng] 00:47:52,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47c59bbd - End of configuration. [testng] [2024-12-16 00:47:53,103] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:47:53,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:47:53,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:53,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-16_00-47-53.log] [testng] 00:47:53,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@758b8cbc - End of configuration. [testng] [2024-12-16 00:47:53,296] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:47:53,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:47:53,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:53,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-16_00-47-53.log] [testng] 00:47:53,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b1a85e - End of configuration. [testng] [2024-12-16 00:48:00,475] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-16 00:48:01,697] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-16 00:48:03,063] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-16 00:48:03,694] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-16 00:48:09,031] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-16 00:48:09,592] [pool-1-thread-7] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-16 00:48:12,786] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-16 00:48:13,041] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-16 00:48:15,159] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-16 00:48:16,679] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-12-16 00:48:19,307] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-16 00:48:20,815] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-16 00:48:22,304] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-16 00:48:22,897] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-16 00:48:25,506] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-12-16 00:48:26,775] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-12-16 00:48:29,727] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-16 00:48:40,375] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-12-16 00:48:42,063] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-16 00:48:44,561] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-16 00:48:45,035] [pool-1-thread-4] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-16 00:48:47,947] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-16 00:48:48,255] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-16 00:48:48,911] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-16 00:48:50,006] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-16 00:48:53,520] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-16 00:48:56,118] [pool-1-thread-5] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-16 00:48:57,788] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-16 00:48:58,452] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-16 00:48:58,666] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-16 00:48:58,985] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-16 00:48:59,466] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-16 00:49:02,816] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-16 00:49:04,433] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-16 00:49:06,240] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-16 00:49:07,732] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-16 00:49:11,209] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-16 00:49:11,677] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-16 00:49:12,114] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-16 00:49:15,592] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-16 00:49:29,740] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-16 00:49:33,877] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-16 00:49:34,371] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-16 00:49:37,336] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-16 00:49:37,856] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-16 00:49:38,034] [pool-1-thread-1] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-16 00:49:40,513] [pool-1-thread-2] 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: 9 minutes 33 seconds Finished: SUCCESS