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Started by upstream project "BIOFORMATS-test-repo" build number 239 originally caused by: Started by upstream project "Trigger" build number 264 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/jenkins14141146149970062599.sh + '[' columbus = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37531_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] 00:32:46,257 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:32:46,258 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:32:46,258 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:46,259 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:46,260 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:32:46,260 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:32:46,260 |-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] 00:32:46,260 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:46,261 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:46,262 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:32:46,262 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:32:46,262 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:32:46,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:32:46,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:32:46,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:32:46,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:32:46,457 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:32:46,457 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:32:46,457 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:32:46,458 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:32:46,458 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:32:46,459 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:32:46,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-30 00:32:46,468] [main] java.version = 17.0.2 [testng] 00:32:46,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:32:46,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:46,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_00-32-46.log] [testng] 00:32:46,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-30 00:32:46,514] [main] testng.directory = /data [testng] [2024-10-30 00:32:46,514] [main] testng.configDirectory = /config [testng] [2024-10-30 00:32:46,524] [main] testng.multiplier = 1.0 [testng] [2024-10-30 00:32:46,524] [main] testng.in-memory = false [testng] [2024-10-30 00:32:46,524] [main] testng.allow-missing = false [testng] [2024-10-30 00:32:46,524] [main] user.language = en [testng] [2024-10-30 00:32:46,525] [main] user.country = ${user.country} [testng] [2024-10-30 00:32:46,525] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-30 01:44:49,183] [main] ---------------------------------------- [testng] [2024-10-30 01:44:49,184] [main] Total files: 4135 [testng] [2024-10-30 01:44:49,184] [main] Scan time: 4322.658 s (1045 ms/file) [testng] [2024-10-30 01:44:49,184] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-30 01:45:56,633] [pool-1-thread-1] Initializing /data/public/idr0020/200972429 TOG[2702]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:45:56,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:45:56,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:56,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_01-45-56.log] [testng] 01:45:56,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc9fc56 - End of configuration. [testng] [2024-10-30 01:46:15,119] [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] 01:46:15,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:46:15,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:15,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-30_01-46-15.log] [testng] 01:46:15,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8cafe4 - End of configuration. [testng] [2024-10-30 01:46:16,143] [pool-1-thread-11] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6_rep[7273]/2024-01-23T115103+1100[7778]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:16,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:46:16,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:16,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-30_01-46-16.log] [testng] 01:46:16,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dbcf442 - End of configuration. [testng] [2024-10-30 01:46:16,760] [pool-1-thread-10] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:16,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:46:16,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:16,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_01-46-16.log] [testng] 01:46:16,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c88d79d - End of configuration. [testng] [2024-10-30 01:46:17,876] [pool-1-thread-9] Initializing /data/public/idr0056/1983[1461]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:17,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:46:17,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:17,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-30_01-46-17.log] [testng] 01:46:17,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@401df70b - End of configuration. [testng] [2024-10-30 01:46:45,529] [pool-1-thread-8] Initializing /data/public/idr0019/22_lines_HC_EGF_200145913/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:45,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:46:45,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:45,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-30_01-46-45.log] [testng] 01:46:45,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36ab2a2a - End of configuration. [testng] [2024-10-30 01:46:53,576] [pool-1-thread-7] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:53,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:46:53,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:53,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-30_01-46-53.log] [testng] 01:46:53,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@93d1b98 - End of configuration. [testng] [2024-10-30 01:46:54,867] [pool-1-thread-6] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w64c3t1f1p6x63[7275]/2024-01-23T121859+1100[7780]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:54,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:46:54,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:54,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_01-46-54.log] [testng] 01:46:54,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e800c9f - End of configuration. [testng] [2024-10-30 01:46:55,391] [pool-1-thread-5] Initializing /data/public/zenodo-6327496/flex/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:55,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:46:55,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:55,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-30_01-46-55.log] [testng] 01:46:55,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13e8abbb - End of configuration. [testng] [2024-10-30 01:46:55,968] [pool-1-thread-4] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:55,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:46:55,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:55,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-30_01-46-55.log] [testng] 01:46:55,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@643e733a - End of configuration. [testng] [2024-10-30 01:46:56,441] [pool-1-thread-3] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:56,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:46:56,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:56,442 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_01-46-56.log] [testng] 01:46:56,442 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37ba8f6a - End of configuration. [testng] [2024-10-30 01:46:56,981] [pool-1-thread-2] Initializing /data/public/zenodo-6327496/tif/MeasurementIndex.ColumbusIDX.xml: [testng] 01:46:56,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:46:56,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:56,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-30_01-46-56.log] [testng] 01:46:56,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bce9cdc - End of configuration. [testng] [2024-10-30 01:47:16,825] [pool-1-thread-5] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:47:18,880] [pool-1-thread-2] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p1[7272]/2024-01-23T120450+1100[7777]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:47:42,699] [pool-1-thread-11] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w1c3t4f5p6[7268]/2024-01-23T114912+1100[7773]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:48:04,844] [pool-1-thread-2] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:48:06,018] [pool-1-thread-5] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f1p6[7271]/2024-01-23T120146+1100[7776]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:48:12,989] [pool-1-thread-11] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c1t4f5p6[7269]/2024-01-23T115618+1100[7774]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:48:22,585] [pool-1-thread-2] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t4f5p6[7274]/2024-01-23T111314+1100[7779]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:48:58,523] [pool-1-thread-11] Initializing /data/tim/multi-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] [2024-10-30 01:49:46,045] [pool-1-thread-11] Initializing /data/tim/single-plane/ImportedHarmonyArchives[3602]/240113_TRB_w2c3t1f5p6[7270]/2024-01-23T115956+1100[7775]/MeasurementIndex.ColumbusIDX.xml: [testng] 05:06:13,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:06:13,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:06:13,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_05-06-13.log] [testng] 05:06:13,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43858d12 - End of configuration. [testng] 05:23:01,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:23:01,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:01,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_05-23-01.log] [testng] 05:23:01,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@296ddfc7 - 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: 290 minutes 20 seconds Finished: SUCCESS