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Started by upstream project "BIOFORMATS-test-repo" build number 294 originally caused by: Started by upstream project "Trigger" build number 313 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/jenkins16873872036787039248.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46437_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] 00:54:02,918 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:54:02,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:54:02,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:54:02,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:54:02,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:54:02,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:54:02,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:54:02,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:54:02,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:54:02,922 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:54:02,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:54:02,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:54:03,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:54:03,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:54:03,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:54:03,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:54:03,115 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:54:03,116 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:54:03,116 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:54:03,116 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:54:03,116 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:54:03,117 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:54:03,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-18 00:54:03,126] [main] java.version = 17.0.2 [testng] 00:54:03,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:54:03,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:03,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_00-54-03.log] [testng] 00:54:03,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-18 00:54:03,176] [main] testng.directory = /data [testng] [2024-12-18 00:54:03,176] [main] testng.configDirectory = /config [testng] [2024-12-18 00:54:03,185] [main] testng.multiplier = 1.0 [testng] [2024-12-18 00:54:03,186] [main] testng.in-memory = false [testng] [2024-12-18 00:54:03,186] [main] testng.allow-missing = false [testng] [2024-12-18 00:54:03,186] [main] user.language = en [testng] [2024-12-18 00:54:03,186] [main] user.country = ${user.country} [testng] [2024-12-18 00:54:03,186] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-18 00:55:47,766] [main] ---------------------------------------- [testng] [2024-12-18 00:55:47,766] [main] Total files: 164 [testng] [2024-12-18 00:55:47,767] [main] Scan time: 104.58 s (637 ms/file) [testng] [2024-12-18 00:55:47,767] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-18 00:58:55,944] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:58:55,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:58:55,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:55,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_00-58-55.log] [testng] 00:58:55,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28d720b6 - End of configuration. [testng] [2024-12-18 00:58:56,879] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:58:56,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:58:56,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:56,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_00-58-56.log] [testng] 00:58:56,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e6c1b29 - End of configuration. [testng] [2024-12-18 00:58:57,636] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] 00:58:57,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:58:57,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:57,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_00-58-57.log] [testng] 00:58:57,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54249d81 - End of configuration. [testng] [2024-12-18 00:58:58,729] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:58:58,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:58:58,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:58,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_00-58-58.log] [testng] 00:58:58,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7940257c - End of configuration. [testng] [2024-12-18 00:58:58,938] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:58:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:58:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:58,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_00-58-58.log] [testng] 00:58:58,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40dfd862 - End of configuration. [testng] [2024-12-18 00:58:59,058] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:58:59,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:58:59,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:59,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_00-58-59.log] [testng] 00:58:59,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1970e753 - End of configuration. [testng] [2024-12-18 00:58:59,165] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:58:59,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:58:59,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:59,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_00-58-59.log] [testng] 00:58:59,169 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45014310 - End of configuration. [testng] [2024-12-18 00:59:01,511] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:59:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:59:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:59:01,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_00-59-01.log] [testng] 00:59:01,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68dcba6d - End of configuration. [testng] [2024-12-18 00:59:02,302] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:59:02,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:59:02,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:59:02,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_00-59-02.log] [testng] 00:59:02,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4744ae1b - End of configuration. [testng] [2024-12-18 00:59:04,033] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] 00:59:04,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:59:04,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:59:04,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_00-59-04.log] [testng] 00:59:04,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4df0432c - End of configuration. [testng] [2024-12-18 00:59:14,745] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:59:14,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:59:14,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:59:14,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_00-59-14.log] [testng] 00:59:14,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ac1715e - End of configuration. [testng] [2024-12-18 00:59:16,031] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:59:16,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:59:16,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:59:16,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_00-59-16.log] [testng] 00:59:16,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f24812e - End of configuration. [testng] [2024-12-18 00:59:21,373] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-18 00:59:22,057] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-18 00:59:22,778] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-18 00:59:25,039] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-18 00:59:26,771] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-12-18 00:59:27,969] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-18 00:59:28,366] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-18 00:59:29,274] [pool-1-thread-12] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-18 00:59:32,340] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-18 00:59:32,965] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-18 00:59:34,576] [pool-1-thread-3] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-18 00:59:34,835] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-18 00:59:37,257] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-12-18 00:59:39,825] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-18 00:59:43,580] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-18 00:59:44,450] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-18 00:59:44,712] [pool-1-thread-5] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-18 00:59:44,878] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-18 00:59:46,963] [pool-1-thread-2] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-18 00:59:47,518] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-18 00:59:48,979] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-18 00:59:51,912] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-18 00:59:54,087] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-18 00:59:54,545] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-18 00:59:55,046] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-18 00:59:55,930] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-18 00:59:56,473] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-18 00:59:58,974] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-12-18 01:00:01,041] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-18 01:00:01,587] [pool-1-thread-11] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-18 01:00:01,784] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-18 01:00:02,630] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-18 01:00:50,612] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-12-18 01:00:54,935] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-18 01:00:59,133] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-18 01:00:59,504] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-18 01:01:01,217] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-18 01:01:01,427] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-18 01:01:06,757] [pool-1-thread-12] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-18 01:01:09,006] [pool-1-thread-6] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-18 01:01:11,276] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-18 01:01:12,571] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-18 01:01:16,138] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-18 01:01:17,395] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-18 01:01:17,667] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-18 01:01:19,665] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-12-18 01:01:22,856] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 31 seconds Finished: SUCCESS