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Started by upstream project "BIOFORMATS-test-repo" build number 292 originally caused by: Started by upstream project "Trigger" build number 311 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/jenkins16672329507144716097.sh + '[' columbus = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_46096_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 00:30:37,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:37,161 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:30:37,161 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:37,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:37,162 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:37,162 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:37,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:37,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:37,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:37,163 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:37,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:37,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:37,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:37,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:37,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:37,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:37,430 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:37,430 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:37,430 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:37,431 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:37,431 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:30:37,431 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:30:37,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-16 00:30:37,441] [main] java.version = 1.8.0_342 [testng] 00:30:37,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:37,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:37,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-16_00-30-37.log] [testng] 00:30:37,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-16 00:30:37,494] [main] testng.directory = /data [testng] [2024-12-16 00:30:37,494] [main] testng.configDirectory = /config [testng] [2024-12-16 00:30:37,505] [main] testng.multiplier = 1.0 [testng] [2024-12-16 00:30:37,506] [main] testng.in-memory = false [testng] [2024-12-16 00:30:37,506] [main] testng.allow-missing = false [testng] [2024-12-16 00:30:37,506] [main] user.language = fr [testng] [2024-12-16 00:30:37,506] [main] user.country = FR [testng] [2024-12-16 00:30:37,506] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-16 01:15:34,288] [main] ---------------------------------------- [testng] [2024-12-16 01:15:34,288] [main] Total files: 4135 [testng] [2024-12-16 01:15:34,288] [main] Scan time: 2696.782 s (652 ms/file) [testng] [2024-12-16 01:15:34,288] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-16 01:17:29,057] [pool-1-thread-1] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:17:29,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:17:29,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:29,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-16_01-17-29.log] [testng] 01:17:29,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aa9855e - End of configuration. [testng] [2024-12-16 01:17:29,666] [pool-1-thread-12] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:17:29,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:17:29,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:29,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-16_01-17-29.log] [testng] 01:17:29,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75ef8b8d - End of configuration. [testng] [2024-12-16 01:17:30,248] [pool-1-thread-11] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:17:30,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:17:30,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:30,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-16_01-17-30.log] [testng] 01:17:30,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@634353f7 - End of configuration. [testng] [2024-12-16 01:17:30,855] [pool-1-thread-10] Initializing /data/public/idr0020/200972429 TOG[2702]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:17:30,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:17:30,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:30,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-16_01-17-30.log] [testng] 01:17:30,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2732cdc8 - End of configuration. [testng] [2024-12-16 01:18:39,980] [pool-1-thread-9] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:39,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:18:39,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:39,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-16_01-18-39.log] [testng] 01:18:39,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84bb96a - End of configuration. [testng] [2024-12-16 01:18:42,911] [pool-1-thread-8] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:42,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:18:42,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:42,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-16_01-18-42.log] [testng] 01:18:42,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595ecd7c - End of configuration. [testng] [2024-12-16 01:18:44,405] [pool-1-thread-7] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:44,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:18:44,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:44,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-16_01-18-44.log] [testng] 01:18:44,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4390eaf7 - End of configuration. [testng] [2024-12-16 01:18:47,819] [pool-1-thread-6] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:47,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:18:47,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:47,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-16_01-18-47.log] [testng] 01:18:47,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@588212a7 - End of configuration. [testng] [2024-12-16 01:18:49,558] [pool-1-thread-5] Initializing /data/public/zenodo-6327496/tif/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:49,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:18:49,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:49,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-16_01-18-49.log] [testng] 01:18:49,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1689345b - End of configuration. [testng] [2024-12-16 01:18:50,635] [pool-1-thread-4] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:50,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:18:50,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:50,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-16_01-18-50.log] [testng] 01:18:50,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c8304e9 - End of configuration. [testng] [2024-12-16 01:18:52,809] [pool-1-thread-3] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:52,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:18:52,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:52,810 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-16_01-18-52.log] [testng] 01:18:52,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f8145f3 - End of configuration. [testng] [2024-12-16 01:18:54,385] [pool-1-thread-2] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:18:54,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:18:54,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:54,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-16_01-18-54.log] [testng] 01:18:54,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@433253d7 - End of configuration. [testng] [2024-12-16 01:19:38,640] [pool-1-thread-5] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:19:57,663] [pool-1-thread-11] Initializing /data/public/idr0056/1983[1461]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:21:02,369] [pool-1-thread-6] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:21:04,919] [pool-1-thread-8] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:22:57,760] [pool-1-thread-6] Initializing /data/public/idr0019/22_lines_HC_EGF_200145913/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:28:03,457] [pool-1-thread-5] Initializing /data/public/zenodo-6327496/flex/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:28:52,078] [pool-1-thread-5] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:29:43,856] [pool-1-thread-5] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-12-16 01:29:53,953] [pool-1-thread-12] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 06:29:21,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:29:21,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:29:21,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-16_06-29-21.log] [testng] 06:29:21,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@175d5b6b - End of configuration. [testng] 11:41:44,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:41:44,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:41:44,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-16_11-41-44.log] [testng] 11:41:44,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4134bb30 - End of configuration. [testng] 12:06:50,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:06:50,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:50,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-16_12-06-50.log] [testng] 12:06:50,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1455a374 - 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: 696 minutes 16 seconds Finished: SUCCESS