Started by upstream project "BIOFORMATS-test-repo" build number 181 originally caused by: Started by upstream project "Trigger" build number 202 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins7386761811492069492.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_28546_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:59:43,023 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:59:43,026 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 06:59:43,026 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:59:43,028 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:59:43,029 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:59:43,029 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:59:43,030 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:59:43,030 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:59:43,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:59:43,032 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:59:43,032 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:59:43,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:59:43,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:59:43,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:59:43,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:59:43,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:59:43,307 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:59:43,307 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:59:43,307 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:59:43,308 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:59:43,308 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 06:59:43,309 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 06:59:43,309 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 278 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-10 06:59:43,324] [main] java.version = 11.0.16 [testng] 06:59:43,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:59:43,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:43,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-10_06-59-43.log] [testng] 06:59:43,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-09-10 06:59:43,401] [main] testng.directory = /data [testng] [2024-09-10 06:59:43,401] [main] testng.configDirectory = /config [testng] [2024-09-10 06:59:43,415] [main] testng.multiplier = 1.0 [testng] [2024-09-10 06:59:43,417] [main] testng.in-memory = false [testng] [2024-09-10 06:59:43,418] [main] testng.allow-missing = false [testng] [2024-09-10 06:59:43,418] [main] user.language = en [testng] [2024-09-10 06:59:43,418] [main] user.country = ${user.country} [testng] [2024-09-10 06:59:43,418] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-10 07:00:01,505] [main] ---------------------------------------- [testng] [2024-09-10 07:00:01,506] [main] Total files: 164 [testng] [2024-09-10 07:00:01,506] [main] Scan time: 18.087 s (110 ms/file) [testng] [2024-09-10 07:00:01,506] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-10 07:00:13,597] [pool-1-thread-1] Initializing /data/openjpeg/Rome.ppm: [testng] 07:00:13,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:00:13,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:13,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-10_07-00-13.log] [testng] 07:00:13,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f69a8a7 - End of configuration. [testng] [2024-09-10 07:00:13,626] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 07:00:13,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:00:13,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:13,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-10_07-00-13.log] [testng] 07:00:13,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1d4e76 - End of configuration. [testng] [2024-09-10 07:00:13,794] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2: [testng] 07:00:13,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:00:13,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:13,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-10_07-00-13.log] [testng] 07:00:13,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c361144 - End of configuration. [testng] [2024-09-10 07:00:13,823] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] 07:00:13,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:00:13,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:13,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-10_07-00-13.log] [testng] 07:00:13,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65b3676d - End of configuration. [testng] [2024-09-10 07:00:13,899] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 07:00:13,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:00:13,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:13,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-10_07-00-13.log] [testng] 07:00:13,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77aa6680 - End of configuration. [testng] [2024-09-10 07:00:14,022] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] 07:00:14,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:00:14,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-10_07-00-14.log] [testng] 07:00:14,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a96e8e6 - End of configuration. [testng] [2024-09-10 07:00:14,043] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 07:00:14,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:00:14,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,045 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-10_07-00-14.log] [testng] 07:00:14,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@91439c8 - End of configuration. [testng] [2024-09-10 07:00:14,151] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 07:00:14,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:00:14,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-10_07-00-14.log] [testng] 07:00:14,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e99fa07 - End of configuration. [testng] [2024-09-10 07:00:14,179] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 07:00:14,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:00:14,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-10_07-00-14.log] [testng] 07:00:14,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12c66c6c - End of configuration. [testng] [2024-09-10 07:00:14,265] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 07:00:14,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:00:14,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-10_07-00-14.log] [testng] 07:00:14,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d47ae6d - End of configuration. [testng] [2024-09-10 07:00:14,285] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 07:00:14,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:00:14,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-10_07-00-14.log] [testng] 07:00:14,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14feea06 - End of configuration. [testng] [2024-09-10 07:00:14,326] [pool-1-thread-2] Initializing /data/openjpeg/Facade.bmp: [testng] 07:00:14,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:00:14,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:00:14,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-10_07-00-14.log] [testng] 07:00:14,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cf7f07f - End of configuration. [testng] [2024-09-10 07:00:16,327] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-09-10 07:00:16,373] [pool-1-thread-6] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-09-10 07:00:16,571] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-09-10 07:00:16,583] [pool-1-thread-10] Initializing /data/ome/embryo.lsm: [testng] [2024-09-10 07:00:16,617] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-09-10 07:00:16,662] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-09-10 07:00:16,857] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-09-10 07:00:17,044] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-09-10 07:00:17,093] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] [2024-09-10 07:00:17,525] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-09-10 07:00:17,708] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-09-10 07:00:17,758] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-09-10 07:00:17,767] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-09-10 07:00:17,972] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-09-10 07:00:17,979] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-09-10 07:00:18,155] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-09-10 07:00:18,429] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-09-10 07:00:18,444] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-09-10 07:00:18,511] [pool-1-thread-3] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-09-10 07:00:18,657] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-09-10 07:00:18,667] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-09-10 07:00:18,854] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-09-10 07:00:18,896] [pool-1-thread-10] Initializing /data/ome/654Atemp.stk: [testng] [2024-09-10 07:00:19,029] [pool-1-thread-3] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-09-10 07:00:20,191] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] [2024-09-10 07:00:20,273] [pool-1-thread-12] Initializing /data/ome/cb_1.r3d: [testng] [2024-09-10 07:00:20,396] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-09-10 07:00:20,428] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-09-10 07:00:20,677] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-09-10 07:00:20,751] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-09-10 07:00:20,797] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-09-10 07:00:20,852] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-09-10 07:00:20,928] [pool-1-thread-11] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-09-10 07:00:21,147] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-09-10 07:00:21,197] [pool-1-thread-7] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-09-10 07:00:21,261] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-09-10 07:00:21,338] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-09-10 07:00:22,063] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-09-10 07:00:22,173] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-09-10 07:00:22,336] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-09-10 07:00:22,371] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-09-10 07:00:22,454] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-09-10 07:00:22,617] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-09-10 07:00:22,646] [pool-1-thread-12] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-09-10 07:00:22,901] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-09-10 07:00:22,960] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-09-10 07:00:23,277] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm: time="2024-09-10T06:00:26Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE