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Started by upstream project "BIOFORMATS-test-repo" build number 309 originally caused by: Started by upstream project "Trigger" build number 331 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins16596957576863756969.sh + '[' columbus = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48902_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] 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] 00:26:08,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:26:08,985 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:26:08,985 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:08,986 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:08,986 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:26:08,986 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:26:08,987 |-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] 00:26:08,987 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:08,987 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:08,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:26:08,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:26:08,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:26:09,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:26:09,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:26:09,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:26:09,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:26:09,191 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:26:09,191 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:26:09,191 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:26:09,191 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:26:09,191 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:26:09,192 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:26:09,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-05 00:26:09,201] [main] java.version = 17.0.2 [testng] 00:26:09,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:26:09,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:09,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-05_00-26-09.log] [testng] 00:26:09,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-05 00:26:09,248] [main] testng.directory = /data [testng] [2025-01-05 00:26:09,248] [main] testng.configDirectory = /config [testng] [2025-01-05 00:26:09,257] [main] testng.multiplier = 1.0 [testng] [2025-01-05 00:26:09,258] [main] testng.in-memory = false [testng] [2025-01-05 00:26:09,258] [main] testng.allow-missing = false [testng] [2025-01-05 00:26:09,258] [main] user.language = en [testng] [2025-01-05 00:26:09,258] [main] user.country = ${user.country} [testng] [2025-01-05 00:26:09,258] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-05 01:12:45,958] [main] ---------------------------------------- [testng] [2025-01-05 01:12:45,958] [main] Total files: 4135 [testng] [2025-01-05 01:12:45,958] [main] Scan time: 2796.7 s (676 ms/file) [testng] [2025-01-05 01:12:45,959] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-05 01:14:32,161] [pool-1-thread-1] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:32,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:14:32,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:32,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-05_01-14-32.log] [testng] 01:14:32,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@442b3d67 - End of configuration. [testng] [2025-01-05 01:14:32,823] [pool-1-thread-12] Initializing /data/public/idr0019/22_lines_HC_EGF_200145913/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:32,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:14:32,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:32,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-05_01-14-32.log] [testng] 01:14:32,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@368ec75c - End of configuration. [testng] [2025-01-05 01:14:42,725] [pool-1-thread-11] Initializing /data/public/zenodo-6327496/tif/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:42,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:14:42,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:42,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-05_01-14-42.log] [testng] 01:14:42,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f82be93 - End of configuration. [testng] [2025-01-05 01:14:44,316] [pool-1-thread-10] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:44,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:14:44,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:44,317 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-05_01-14-44.log] [testng] 01:14:44,318 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51bea189 - End of configuration. [testng] [2025-01-05 01:14:45,084] [pool-1-thread-9] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:45,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:14:45,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:45,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-05_01-14-45.log] [testng] 01:14:45,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dffa3d - End of configuration. [testng] [2025-01-05 01:14:45,779] [pool-1-thread-8] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:45,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:14:45,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:45,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-05_01-14-45.log] [testng] 01:14:45,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aa4b958 - End of configuration. [testng] [2025-01-05 01:14:47,053] [pool-1-thread-7] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:47,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:14:47,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:47,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-05_01-14-47.log] [testng] 01:14:47,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6057f525 - End of configuration. [testng] [2025-01-05 01:14:47,845] [pool-1-thread-6] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:47,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:14:47,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:47,846 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-05_01-14-47.log] [testng] 01:14:47,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b33c67 - End of configuration. [testng] [2025-01-05 01:14:48,727] [pool-1-thread-5] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:48,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:14:48,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:48,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-05_01-14-48.log] [testng] 01:14:48,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fefc15a - End of configuration. [testng] [2025-01-05 01:14:50,271] [pool-1-thread-4] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:50,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:14:50,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:50,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-05_01-14-50.log] [testng] 01:14:50,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@340030bc - End of configuration. [testng] [2025-01-05 01:14:51,798] [pool-1-thread-3] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:51,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:14:51,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:51,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-05_01-14-51.log] [testng] 01:14:51,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56af8fea - End of configuration. [testng] [2025-01-05 01:14:52,593] [pool-1-thread-2] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:14:52,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:14:52,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:52,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-05_01-14-52.log] [testng] 01:14:52,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748d93bb - End of configuration. [testng] [2025-01-05 01:15:23,235] [pool-1-thread-5] Initializing /data/public/zenodo-6327496/flex/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:15:24,213] [pool-1-thread-11] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:15:34,652] [pool-1-thread-9] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:15:49,683] [pool-1-thread-5] Initializing /data/public/idr0020/200972429 TOG[2702]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:16:26,436] [pool-1-thread-7] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:16:27,497] [pool-1-thread-1] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:16:34,803] [pool-1-thread-3] Initializing /data/public/idr0056/1983[1461]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:17:19,061] [pool-1-thread-9] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-05 01:19:50,792] [pool-1-thread-2] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 05:17:58,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:17:58,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:17:58,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-05_05-17-58.log] [testng] 05:17:58,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c14015d - End of configuration. [testng] 05:38:35,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:38:35,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:35,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-05_05-38-35.log] [testng] 05:38:35,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@394e0104 - 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: 312 minutes 31 seconds Finished: SUCCESS