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Started by upstream project "BIOFORMATS-test-repo" build number 366 originally caused by: Started by upstream project "Trigger" build number 392 originally caused by: Started by timer 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/jenkins17695605474791229197.sh + '[' columbus = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58312_merge_ci -v /uod/idr/repos/curated/columbus:/data -v /uod/idr-scratch/merge-ci/curated/columbus:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:28:32,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:28:32,812 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 00:28:32,812 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:32,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:32,813 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:28:32,814 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:28:32,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:28:32,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:32,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:32,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:28:32,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:28:32,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:28:32,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:28:32,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:28:32,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:28:32,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:28:32,995 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:28:32,995 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:28:32,995 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:28:32,995 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:28:32,995 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration. [testng] 00:28:32,996 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point [testng] 00:28:32,996 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-06 00:28:33,005] [main] java.version = 21 [testng] 00:28:33,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:28:33,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:33,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-06_00-28-33.log] [testng] 00:28:33,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-03-06 00:28:33,051] [main] testng.directory = /data [testng] [2025-03-06 00:28:33,051] [main] testng.configDirectory = /config [testng] [2025-03-06 00:28:33,059] [main] testng.multiplier = 1.0 [testng] [2025-03-06 00:28:33,060] [main] testng.in-memory = false [testng] [2025-03-06 00:28:33,060] [main] testng.allow-missing = false [testng] [2025-03-06 00:28:33,060] [main] user.language = en [testng] [2025-03-06 00:28:33,060] [main] user.country = ${user.country} [testng] [2025-03-06 00:28:33,060] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-06 01:11:52,769] [main] ---------------------------------------- [testng] [2025-03-06 01:11:52,770] [main] Total files: 4135 [testng] [2025-03-06 01:11:52,770] [main] Scan time: 2599.709 s (628 ms/file) [testng] [2025-03-06 01:11:52,770] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-06 01:13:56,231] [pool-1-thread-1] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:13:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:13:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:56,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-06_01-13-56.log] [testng] 01:13:56,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dbef0f5 - End of configuration. [testng] [2025-03-06 01:13:56,931] [pool-1-thread-12] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:13:56,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:13:56,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:56,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-06_01-13-56.log] [testng] 01:13:56,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dcf08ec - End of configuration. [testng] [2025-03-06 01:13:58,072] [pool-1-thread-11] Initializing /data/public/idr0020/200972429 TOG[2702]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:13:58,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:13:58,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:58,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-06_01-13-58.log] [testng] 01:13:58,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16110c29 - End of configuration. [testng] [2025-03-06 01:14:39,065] [pool-1-thread-10] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:39,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:14:39,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:39,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-06_01-14-39.log] [testng] 01:14:39,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@102ebc8c - End of configuration. [testng] [2025-03-06 01:14:39,958] [pool-1-thread-9] Initializing /data/public/zenodo-6327496/tif/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:39,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:14:39,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:39,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-06_01-14-39.log] [testng] 01:14:39,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cedd991 - End of configuration. [testng] [2025-03-06 01:14:40,904] [pool-1-thread-8] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:40,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:14:40,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:40,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-06_01-14-40.log] [testng] 01:14:40,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4988f60c - End of configuration. [testng] [2025-03-06 01:14:42,210] [pool-1-thread-7] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:42,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:14:42,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:42,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-06_01-14-42.log] [testng] 01:14:42,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33677d08 - End of configuration. [testng] [2025-03-06 01:14:43,173] [pool-1-thread-6] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:43,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:14:43,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:43,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-06_01-14-43.log] [testng] 01:14:43,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@954fb2a - End of configuration. [testng] [2025-03-06 01:14:44,148] [pool-1-thread-5] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:44,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:14:44,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:44,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-06_01-14-44.log] [testng] 01:14:44,149 |-INFO in ch.qos.logback.core.sift.SiftProcessor@316ac66a - End of configuration. [testng] [2025-03-06 01:14:45,181] [pool-1-thread-4] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:45,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:14:45,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:45,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-06_01-14-45.log] [testng] 01:14:45,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2683eba3 - End of configuration. [testng] [2025-03-06 01:14:46,170] [pool-1-thread-3] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:46,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:14:46,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:46,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-06_01-14-46.log] [testng] 01:14:46,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aa957aa - End of configuration. [testng] [2025-03-06 01:14:47,241] [pool-1-thread-2] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:47,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:14:47,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:47,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-06_01-14-47.log] [testng] 01:14:47,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35fe2a4b - End of configuration. [testng] [2025-03-06 01:15:15,478] [pool-1-thread-9] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:15:42,960] [pool-1-thread-9] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:15:47,335] [pool-1-thread-10] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:15:49,263] [pool-1-thread-6] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:15:53,802] [pool-1-thread-2] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:16:30,658] [pool-1-thread-9] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:17:02,562] [pool-1-thread-6] Initializing /data/public/idr0019/22_lines_HC_EGF_200145913/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:17:25,973] [pool-1-thread-2] Initializing /data/public/zenodo-6327496/flex/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-03-06 01:17:53,760] [pool-1-thread-2] Initializing /data/public/idr0056/1983[1461]/MeasurementIndex.ColumbusIDX.xml: [testng] 07:58:45,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:58:45,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:58:45,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-06_07-58-45.log] [testng] 07:58:45,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2023e85f - End of configuration. [testng] 08:19:14,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:19:14,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:19:14,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-06_08-19-14.log] [testng] 08:19:14,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52dfd7f5 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 470 minutes 44 seconds Finished: SUCCESS