Started by upstream project "BIOFORMATS-test-repo" build number 393
originally caused by:
Started by upstream project "Trigger" build number 418
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@19
[BIOFORMATS-test-folder@19] $ /bin/bash -xe /tmp/jenkins5234898987078008967.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_62031_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/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] 07:09:19,820 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 07:09:19,822 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service.
[testng] 07:09:19,822 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 07:09:19,823 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 07:09:19,823 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 07:09:19,823 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 07:09:19,823 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 07:09:19,823 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 07:09:19,824 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 07:09:19,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 07:09:19,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 07:09:19,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 07:09:20,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 07:09:20,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 07:09:20,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 07:09:20,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 07:09:20,086 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 07:09:20,086 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 07:09:20,087 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 07:09:20,087 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 07:09:20,087 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration.
[testng] 07:09:20,088 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point
[testng] 07:09:20,088 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 264 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-28 07:09:20,097] [main] java.version = 1.8.0_342
[testng] 07:09:20,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 07:09:20,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:09:20,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-28_07-09-20.log]
[testng] 07:09:20,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration.
[testng] [2025-03-28 07:09:20,147] [main] testng.directory = /data
[testng] [2025-03-28 07:09:20,147] [main] testng.configDirectory = /config
[testng] [2025-03-28 07:09:20,158] [main] testng.multiplier = 1.0
[testng] [2025-03-28 07:09:20,159] [main] testng.in-memory = false
[testng] [2025-03-28 07:09:20,159] [main] testng.allow-missing = false
[testng] [2025-03-28 07:09:20,159] [main] user.language = en
[testng] [2025-03-28 07:09:20,159] [main] user.country = ${user.country}
[testng] [2025-03-28 07:09:20,159] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2025-03-28 07:28:40,882] [main] ----------------------------------------
[testng] [2025-03-28 07:28:40,882] [main] Total files: 791
[testng] [2025-03-28 07:28:40,882] [main] Scan time: 1160.723 s (1467 ms/file)
[testng] [2025-03-28 07:28:40,882] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-28 07:59:18,491] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] 07:59:18,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 07:59:18,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:59:18,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-28_07-59-18.log]
[testng] 07:59:18,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73cd3a9e - End of configuration.
[testng] [2025-03-28 08:00:21,835] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] 08:00:21,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 08:00:21,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:00:21,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-28_08-00-21.log]
[testng] 08:00:21,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6764d8e7 - End of configuration.
[testng] [2025-03-28 08:00:29,314] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex:
[testng] 08:00:29,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 08:00:29,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:00:29,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-28_08-00-29.log]
[testng] 08:00:29,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26f294fe - End of configuration.
[testng] [2025-03-28 08:00:37,042] [pool-1-thread-10] Initializing /data/achim/003003000.flex:
[testng] 08:00:37,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 08:00:37,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:00:37,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-28_08-00-37.log]
[testng] 08:00:37,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ea463a - End of configuration.
[testng] [2025-03-28 08:00:44,975] [pool-1-thread-9] Initializing /data/tony/test.tiff:
[testng] 08:00:44,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 08:00:44,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:00:44,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-28_08-00-44.log]
[testng] 08:00:44,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc9b08b - End of configuration.
[testng] [2025-03-28 08:01:02,928] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] 08:01:02,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 08:01:02,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:01:02,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-28_08-01-02.log]
[testng] 08:01:02,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6231f040 - End of configuration.
[testng] [2025-03-28 08:02:22,148] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] 08:02:22,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 08:02:22,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:02:22,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-28_08-02-22.log]
[testng] 08:02:22,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@efb147f - End of configuration.
[testng] [2025-03-28 08:02:42,762] [pool-1-thread-6] Initializing /data/anatole/001004000.flex:
[testng] 08:02:42,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 08:02:42,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:02:42,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-28_08-02-42.log]
[testng] 08:02:42,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@253bff76 - End of configuration.
[testng] [2025-03-28 08:02:55,743] [pool-1-thread-5] Initializing /data/stephane/002007000.flex:
[testng] 08:02:55,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 08:02:55,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:02:55,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-28_08-02-55.log]
[testng] 08:02:55,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68948eb0 - End of configuration.
[testng] [2025-03-28 08:03:05,733] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex:
[testng] 08:03:05,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 08:03:05,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:03:05,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-28_08-03-05.log]
[testng] 08:03:05,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d2ca5d4 - End of configuration.
[testng] [2025-03-28 08:03:14,190] [pool-1-thread-3] Initializing /data/stephane/006013000.flex:
[testng] 08:03:14,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 08:03:14,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:03:14,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-28_08-03-14.log]
[testng] 08:03:14,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31a5783a - End of configuration.
[testng] [2025-03-28 08:03:23,822] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] 08:03:23,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 08:03:23,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:03:23,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-28_08-03-23.log]
[testng] 08:03:23,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@377882be - End of configuration.
[testng] [2025-03-28 08:05:35,518] [pool-1-thread-7] Initializing /data/manuel/003003001.flex:
[testng] [2025-03-28 08:05:49,720] [pool-1-thread-11] Initializing /data/tony/003003000.tiff:
[testng] [2025-03-28 08:06:12,666] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex:
[testng] [2025-03-28 08:06:18,156] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2025-03-28 08:06:41,833] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2025-03-28 08:08:30,653] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2025-03-28 08:08:42,924] [pool-1-thread-4] Initializing /data/qa-17190/002002011.flex:
[testng] [2025-03-28 08:09:13,334] [pool-1-thread-2] Initializing /data/ghislain/test.flex:
[testng] [2025-03-28 08:09:45,972] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2025-03-28 08:10:04,722] [pool-1-thread-9] Initializing /data/tony/003008000.flex:
[testng] [2025-03-28 08:10:16,822] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] [2025-03-28 08:10:29,064] [pool-1-thread-5] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2025-03-28 08:11:39,165] [pool-1-thread-7] Initializing /data/qa-7469/002002.flex:
[testng] [2025-03-28 08:11:48,270] [pool-1-thread-4] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2025-03-28 08:11:58,099] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2025-03-28 08:13:05,481] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2025-03-28 08:13:22,898] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] [2025-03-28 08:14:53,072] [pool-1-thread-5] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2025-03-28 08:16:40,284] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2025-03-28 08:17:00,809] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex:
[testng] [2025-03-28 08:17:34,373] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] [2025-03-28 08:18:12,023] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2025-03-28 08:19:26,832] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2025-03-28 08:20:38,812] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2025-03-28 08:22:42,004] [pool-1-thread-12] Initializing /data/qa-2983/004007000.flex:
[testng] [2025-03-28 08:23:04,111] [pool-1-thread-2] Initializing /data/tony/test1.flex:
[testng] [2025-03-28 08:24:13,329] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex:
[testng] [2025-03-28 08:25:04,821] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex:
[testng] [2025-03-28 08:25:43,032] [pool-1-thread-2] Initializing /data/tony/015002000.tiff:
[testng] [2025-03-28 08:26:43,093] [pool-1-thread-4] Initializing /data/tony/001001000_objects.flex:
[testng] 09:30:09,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 09:30:09,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:30:09,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-28_09-30-09.log]
[testng] 09:30:09,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e643402 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 140 minutes 52 seconds
Finished: SUCCESS