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Started by upstream project "BIOFORMATS-test-repo" build number 240 originally caused by: Started by upstream project "Trigger" build number 265 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins10179422771058807964.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37706_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:28:31,048 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:28:31,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:28:31,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:31,050 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:31,051 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:28:31,051 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:28:31,051 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:28:31,051 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:31,052 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:31,052 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:28:31,053 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:28:31,053 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:28:31,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:28:31,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:28:31,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:28:31,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:28:31,257 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:28:31,257 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:28:31,257 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:28:31,258 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:28:31,258 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:28:31,259 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:28:31,259 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-31 00:28:31,268] [main] java.version = 21 [testng] 00:28:31,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:28:31,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:31,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_00-28-31.log] [testng] 00:28:31,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-31 00:28:31,318] [main] testng.directory = /data [testng] [2024-10-31 00:28:31,318] [main] testng.configDirectory = /config [testng] [2024-10-31 00:28:31,327] [main] testng.multiplier = 1.0 [testng] [2024-10-31 00:28:31,328] [main] testng.in-memory = false [testng] [2024-10-31 00:28:31,328] [main] testng.allow-missing = false [testng] [2024-10-31 00:28:31,328] [main] user.language = en [testng] [2024-10-31 00:28:31,328] [main] user.country = ${user.country} [testng] [2024-10-31 00:28:31,328] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-31 00:29:14,825] [main] ---------------------------------------- [testng] [2024-10-31 00:29:14,825] [main] Total files: 164 [testng] [2024-10-31 00:29:14,825] [main] Scan time: 43.497 s (265 ms/file) [testng] [2024-10-31 00:29:14,826] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-31 00:30:06,221] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:30:06,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:30:06,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:06,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-31_00-30-06.log] [testng] 00:30:06,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e2fc72 - End of configuration. [testng] [2024-10-31 00:30:06,602] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] 00:30:06,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:30:06,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:06,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-31_00-30-06.log] [testng] 00:30:06,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ff55c5e - End of configuration. [testng] [2024-10-31 00:30:06,676] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] 00:30:06,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:30:06,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:06,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-31_00-30-06.log] [testng] 00:30:06,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25973bb5 - End of configuration. [testng] [2024-10-31 00:30:07,047] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 00:30:07,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:07,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:07,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-31_00-30-07.log] [testng] 00:30:07,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3499b443 - End of configuration. [testng] [2024-10-31 00:30:07,120] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:30:07,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:30:07,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:07,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-31_00-30-07.log] [testng] 00:30:07,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e878776 - End of configuration. [testng] [2024-10-31 00:30:07,209] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:30:07,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:30:07,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:07,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-31_00-30-07.log] [testng] 00:30:07,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42fa3168 - End of configuration. [testng] [2024-10-31 00:30:07,309] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:30:07,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:30:07,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:07,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-31_00-30-07.log] [testng] 00:30:07,311 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3579ff3e - End of configuration. [testng] [2024-10-31 00:30:08,151] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] 00:30:08,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:30:08,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:08,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-31_00-30-08.log] [testng] 00:30:08,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@270e021d - End of configuration. [testng] [2024-10-31 00:30:08,433] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:30:08,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:30:08,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:08,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-31_00-30-08.log] [testng] 00:30:08,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a90c1a3 - End of configuration. [testng] [2024-10-31 00:30:08,547] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:30:08,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:30:08,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:08,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-31_00-30-08.log] [testng] 00:30:08,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6425d2bd - End of configuration. [testng] [2024-10-31 00:30:09,459] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] 00:30:09,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:30:09,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:09,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-31_00-30-09.log] [testng] 00:30:09,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db551c4 - End of configuration. [testng] [2024-10-31 00:30:10,293] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 00:30:10,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:30:10,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:10,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-31_00-30-10.log] [testng] 00:30:10,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e78380 - End of configuration. [testng] [2024-10-31 00:30:12,784] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-31 00:30:12,839] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-31 00:30:13,382] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-31 00:30:13,449] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-10-31 00:30:13,974] [pool-1-thread-11] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-31 00:30:14,632] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-31 00:30:18,197] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-31 00:30:18,277] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-31 00:30:18,983] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-31 00:30:19,355] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-31 00:30:20,046] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-31 00:30:20,192] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-31 00:30:20,631] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-31 00:30:20,709] [pool-1-thread-10] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-31 00:30:21,458] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-31 00:30:34,804] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-31 00:30:35,522] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-31 00:30:35,791] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-31 00:30:35,861] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-10-31 00:30:36,846] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-31 00:30:38,167] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-31 00:30:38,264] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-31 00:30:38,836] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-31 00:30:39,344] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-31 00:30:40,023] [pool-1-thread-2] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-31 00:30:40,977] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-31 00:30:41,718] [pool-1-thread-9] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-31 00:30:42,186] [pool-1-thread-3] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-31 00:30:42,671] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-31 00:30:43,524] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-31 00:30:44,496] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-31 00:30:44,752] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-31 00:30:45,859] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-31 00:30:46,394] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-31 00:30:46,544] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-31 00:30:46,889] [pool-1-thread-9] Initializing /data/ome/embryo.lsm: [testng] [2024-10-31 00:30:47,455] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-10-31 00:30:48,188] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-31 00:30:48,506] [pool-1-thread-3] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-31 00:30:49,097] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-31 00:30:49,269] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-31 00:30:49,621] [pool-1-thread-1] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-31 00:30:49,987] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-31 00:30:50,265] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-31 00:30:50,664] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-31 00:30:51,731] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-31 00:30:52,468] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 38 seconds Finished: SUCCESS