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Started by upstream project "BIOFORMATS-test-repo" build number 314 originally caused by: Started by upstream project "Trigger" build number 336 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins14620420783341079709.sh + '[' columbus = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49727_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 test-automated: [testng] File leak detector installed [testng] 01:20:56,839 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:20:56,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:20:56,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:56,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:56,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:20:56,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:20:56,843 |-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] 01:20:56,843 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:56,843 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:56,843 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:20:56,843 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:20:56,844 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:20:57,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:57,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:57,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:57,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:57,125 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:57,125 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:57,125 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:57,125 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:57,125 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:20:57,126 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:20:57,126 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 283 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-10 01:20:57,137] [main] java.version = 1.8.0_342 [testng] 01:20:57,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:57,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:57,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_01-20-57.log] [testng] 01:20:57,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-10 01:20:57,194] [main] testng.directory = /data [testng] [2025-01-10 01:20:57,194] [main] testng.configDirectory = /config [testng] [2025-01-10 01:20:57,207] [main] testng.multiplier = 1.0 [testng] [2025-01-10 01:20:57,208] [main] testng.in-memory = false [testng] [2025-01-10 01:20:57,208] [main] testng.allow-missing = false [testng] [2025-01-10 01:20:57,208] [main] user.language = en [testng] [2025-01-10 01:20:57,208] [main] user.country = ${user.country} [testng] [2025-01-10 01:20:57,208] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-10 02:06:16,325] [main] ---------------------------------------- [testng] [2025-01-10 02:06:16,325] [main] Total files: 4135 [testng] [2025-01-10 02:06:16,325] [main] Scan time: 2719.117 s (657 ms/file) [testng] [2025-01-10 02:06:16,325] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-10 02:07:54,554] [pool-1-thread-1] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:07:54,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:07:54,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:54,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-10_02-07-54.log] [testng] 02:07:54,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7be3b86c - End of configuration. [testng] [2025-01-10 02:07:55,400] [pool-1-thread-12] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:07:55,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:07:55,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:55,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-10_02-07-55.log] [testng] 02:07:55,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ef3297c - End of configuration. [testng] [2025-01-10 02:07:55,947] [pool-1-thread-11] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:07:55,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:07:55,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:55,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-10_02-07-55.log] [testng] 02:07:55,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a2b89f8 - End of configuration. [testng] [2025-01-10 02:07:56,445] [pool-1-thread-10] Initializing /data/public/idr0056/1983[1461]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:07:56,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:07:56,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:56,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-10_02-07-56.log] [testng] 02:07:56,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58146bb6 - End of configuration. [testng] [2025-01-10 02:08:29,420] [pool-1-thread-9] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:29,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:08:29,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:29,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-10_02-08-29.log] [testng] 02:08:29,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@783eb488 - End of configuration. [testng] [2025-01-10 02:08:29,877] [pool-1-thread-8] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:29,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:08:29,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:29,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-10_02-08-29.log] [testng] 02:08:29,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75c64b6e - End of configuration. [testng] [2025-01-10 02:08:30,376] [pool-1-thread-7] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:30,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:08:30,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:30,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-10_02-08-30.log] [testng] 02:08:30,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40666c2e - End of configuration. [testng] [2025-01-10 02:08:31,002] [pool-1-thread-6] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:31,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:08:31,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:31,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-10_02-08-31.log] [testng] 02:08:31,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f71512f - End of configuration. [testng] [2025-01-10 02:08:31,438] [pool-1-thread-5] Initializing /data/public/idr0020/200972429 TOG[2702]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:31,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:08:31,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:31,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-10_02-08-31.log] [testng] 02:08:31,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e5a7cdb - End of configuration. [testng] [2025-01-10 02:08:56,372] [pool-1-thread-4] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:56,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:08:56,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:56,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-10_02-08-56.log] [testng] 02:08:56,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bcfd952 - End of configuration. [testng] [2025-01-10 02:08:57,132] [pool-1-thread-3] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:57,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:08:57,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:57,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-10_02-08-57.log] [testng] 02:08:57,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fb47276 - End of configuration. [testng] [2025-01-10 02:08:58,068] [pool-1-thread-2] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] 02:08:58,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:08:58,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:58,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-10_02-08-58.log] [testng] 02:08:58,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76e45786 - End of configuration. [testng] [2025-01-10 02:09:28,892] [pool-1-thread-8] Initializing /data/public/zenodo-6327496/flex/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:09:58,042] [pool-1-thread-8] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:10:03,266] [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] [2025-01-10 02:10:04,785] [pool-1-thread-6] Initializing /data/public/idr0019/22_lines_HC_EGF_200145913/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:10:14,460] [pool-1-thread-1] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:10:17,696] [pool-1-thread-3] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:11:00,503] [pool-1-thread-1] Initializing /data/public/zenodo-6327496/tif/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:11:23,592] [pool-1-thread-1] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] [2025-01-10 02:12:29,338] [pool-1-thread-1] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] 05:38:20,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:38:20,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:20,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-10_05-38-20.log] [testng] 05:38:20,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ca1bc88 - End of configuration. [testng] 06:02:19,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:02:19,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:02:19,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_06-02-19.log] [testng] 06:02:19,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10b063fd - 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: 281 minutes 28 seconds Finished: SUCCESS