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Started by upstream project "BIOFORMATS-test-repo" build number 291 originally caused by: Started by upstream project "Trigger" build number 310 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins4731271378620165493.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46048_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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] 08:13:31,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:13:31,067 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 08:13:31,067 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:13:31,067 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:13:31,068 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:13:31,068 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:13:31,068 |-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] 08:13:31,068 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:13:31,069 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:13:31,069 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:13:31,070 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:13:31,070 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:13:31,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:13:31,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:13:31,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:13:31,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:13:31,245 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:13:31,245 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:13:31,245 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:13:31,245 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:13:31,246 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 08:13:31,246 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 08:13:31,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 177 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-15 08:13:31,254] [main] java.version = 17.0.2 [testng] 08:13:31,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:13:31,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:31,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-15_08-13-31.log] [testng] 08:13:31,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-15 08:13:31,299] [main] testng.directory = /data [testng] [2024-12-15 08:13:31,299] [main] testng.configDirectory = /config [testng] [2024-12-15 08:13:31,307] [main] testng.multiplier = 1.0 [testng] [2024-12-15 08:13:31,307] [main] testng.in-memory = false [testng] [2024-12-15 08:13:31,307] [main] testng.allow-missing = false [testng] [2024-12-15 08:13:31,308] [main] user.language = en [testng] [2024-12-15 08:13:31,308] [main] user.country = ${user.country} [testng] [2024-12-15 08:13:31,308] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-15 09:20:30,610] [main] ---------------------------------------- [testng] [2024-12-15 09:20:30,610] [main] Total files: 826 [testng] [2024-12-15 09:20:30,610] [main] Scan time: 4019.302 s (4865 ms/file) [testng] [2024-12-15 09:20:30,611] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-15 09:23:45,568] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 09:23:45,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:23:45,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:23:45,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-15_09-23-45.log] [testng] 09:23:45,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dd33396 - End of configuration. [testng] [2024-12-15 09:23:50,965] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 09:23:50,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:23:50,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:23:50,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-15_09-23-50.log] [testng] 09:23:50,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8660002 - End of configuration. [testng] [2024-12-15 09:23:55,911] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 09:23:55,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:23:55,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:23:55,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-15_09-23-55.log] [testng] 09:23:55,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aaf9984 - End of configuration. [testng] [2024-12-15 09:24:01,329] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 09:24:01,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:24:01,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:01,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-15_09-24-01.log] [testng] 09:24:01,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a79943 - End of configuration. [testng] [2024-12-15 09:24:06,517] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 09:24:06,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:24:06,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:06,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-15_09-24-06.log] [testng] 09:24:06,518 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f06a2b2 - End of configuration. [testng] [2024-12-15 09:24:11,401] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 09:24:11,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:24:11,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:11,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-15_09-24-11.log] [testng] 09:24:11,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbe3b09 - End of configuration. [testng] [2024-12-15 09:24:16,374] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 09:24:16,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:24:16,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:16,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-15_09-24-16.log] [testng] 09:24:16,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@361b4519 - End of configuration. [testng] [2024-12-15 09:24:21,181] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 09:24:21,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:24:21,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:21,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-15_09-24-21.log] [testng] 09:24:21,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38de452b - End of configuration. [testng] [2024-12-15 09:24:26,063] [pool-1-thread-5] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 09:24:26,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:24:26,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:26,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-15_09-24-26.log] [testng] 09:24:26,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37b8548b - End of configuration. [testng] [2024-12-15 09:24:42,825] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 09:24:42,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:24:42,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:42,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-15_09-24-42.log] [testng] 09:24:42,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7979e15f - End of configuration. [testng] [2024-12-15 09:24:48,081] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 09:24:48,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:24:48,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:48,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-15_09-24-48.log] [testng] 09:24:48,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f390755 - End of configuration. [testng] [2024-12-15 09:24:52,506] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 09:24:52,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:24:52,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:24:52,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-15_09-24-52.log] [testng] 09:24:52,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a97571 - End of configuration. [testng] [2024-12-15 09:25:29,215] [pool-1-thread-2] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] [2024-12-15 09:25:33,821] [pool-1-thread-10] Initializing /data/wis/RA_060110.051/1/acqp: [testng] [2024-12-15 09:25:45,540] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-12-15 09:25:50,126] [pool-1-thread-1] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] [2024-12-15 09:25:55,314] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 117 minutes 45 seconds Finished: SUCCESS