Started by upstream project "BIOFORMATS-test-repo" build number 262
originally caused by:
Started by upstream project "Trigger" build number 286
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins481311469903201922.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41341_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
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 00:57:03,535 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:57:03,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 00:57:03,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:57:03,537 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:57:03,537 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:57:03,538 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:57:03,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:57:03,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:57:03,539 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:57:03,539 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:57:03,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:57:03,540 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:57:03,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:57:03,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:57:03,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:57:03,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:57:03,739 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:57:03,740 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:57:03,740 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:57:03,740 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:57:03,740 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 00:57:03,741 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 00:57:03,741 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-21 00:57:03,751] [main] java.version = 21
[testng] 00:57:03,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:57:03,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:03,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_00-57-03.log]
[testng] 00:57:03,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-21 00:57:03,810] [main] testng.directory = /data
[testng] [2024-11-21 00:57:03,810] [main] testng.configDirectory = /config
[testng] [2024-11-21 00:57:03,819] [main] testng.multiplier = 1.0
[testng] [2024-11-21 00:57:03,819] [main] testng.in-memory = false
[testng] [2024-11-21 00:57:03,820] [main] testng.allow-missing = false
[testng] [2024-11-21 00:57:03,820] [main] user.language = en
[testng] [2024-11-21 00:57:03,820] [main] user.country = ${user.country}
[testng] [2024-11-21 00:57:03,820] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-21 00:58:48,363] [main] ----------------------------------------
[testng] [2024-11-21 00:58:48,363] [main] Total files: 791
[testng] [2024-11-21 00:58:48,363] [main] Scan time: 104.543 s (132 ms/file)
[testng] [2024-11-21 00:58:48,364] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-21 01:05:21,053] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] 01:05:21,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:05:21,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:21,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_01-05-21.log]
[testng] 01:05:21,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9666022 - End of configuration.
[testng] [2024-11-21 01:05:22,350] [pool-1-thread-12] Initializing /data/manuel/003003001.flex:
[testng] 01:05:22,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:05:22,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:22,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_01-05-22.log]
[testng] 01:05:22,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64386b11 - End of configuration.
[testng] [2024-11-21 01:05:23,267] [pool-1-thread-11] Initializing /data/stephane/002007000.flex:
[testng] 01:05:23,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:05:23,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:23,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_01-05-23.log]
[testng] 01:05:23,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb989b - End of configuration.
[testng] [2024-11-21 01:05:24,138] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex:
[testng] 01:05:24,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:05:24,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:24,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_01-05-24.log]
[testng] 01:05:24,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f3e8e51 - End of configuration.
[testng] [2024-11-21 01:05:24,873] [pool-1-thread-9] Initializing /data/tony/015002000.tiff:
[testng] 01:05:24,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:05:24,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:24,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_01-05-24.log]
[testng] 01:05:24,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b88358 - End of configuration.
[testng] [2024-11-21 01:05:26,495] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] 01:05:26,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:05:26,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:26,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_01-05-26.log]
[testng] 01:05:26,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@473e2494 - End of configuration.
[testng] [2024-11-21 01:05:33,142] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] 01:05:33,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:05:33,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:33,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_01-05-33.log]
[testng] 01:05:33,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a6edaaf - End of configuration.
[testng] [2024-11-21 01:05:34,060] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] 01:05:34,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:05:34,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:34,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_01-05-34.log]
[testng] 01:05:34,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aee526f - End of configuration.
[testng] [2024-11-21 01:05:39,931] [pool-1-thread-5] Initializing /data/tony/test1.flex:
[testng] 01:05:39,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:05:39,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:39,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_01-05-39.log]
[testng] 01:05:39,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d98bd7e - End of configuration.
[testng] [2024-11-21 01:05:40,812] [pool-1-thread-4] Initializing /data/tony/003008000.flex:
[testng] 01:05:40,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:05:40,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:40,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_01-05-40.log]
[testng] 01:05:40,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b45d9a - End of configuration.
[testng] [2024-11-21 01:05:41,781] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] 01:05:41,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:05:41,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:41,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_01-05-41.log]
[testng] 01:05:41,782 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f05148 - End of configuration.
[testng] [2024-11-21 01:05:42,830] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex:
[testng] 01:05:42,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:05:42,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:05:42,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_01-05-42.log]
[testng] 01:05:42,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35503e90 - End of configuration.
[testng] [2024-11-21 01:05:57,426] [pool-1-thread-9] Initializing /data/tony/test.tiff:
[testng] [2024-11-21 01:05:59,547] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-11-21 01:06:00,625] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-11-21 01:06:01,570] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-11-21 01:06:02,570] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-11-21 01:06:12,342] [pool-1-thread-3] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-11-21 01:06:14,779] [pool-1-thread-7] Initializing /data/achim/003003000.flex:
[testng] [2024-11-21 01:06:17,880] [pool-1-thread-4] Initializing /data/stephane/006013000.flex:
[testng] [2024-11-21 01:06:25,118] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] [2024-11-21 01:06:34,377] [pool-1-thread-9] Initializing /data/anatole/001004000.flex:
[testng] [2024-11-21 01:06:36,043] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-11-21 01:06:40,376] [pool-1-thread-2] Initializing /data/tamjid/006004000.flex:
[testng] [2024-11-21 01:06:41,515] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-11-21 01:06:54,020] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-11-21 01:07:03,184] [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] [2024-11-21 01:07:04,435] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2024-11-21 01:07:13,612] [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] [2024-11-21 01:07:14,945] [pool-1-thread-2] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-11-21 01:07:16,366] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-11-21 01:07:33,057] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-11-21 01:07:44,032] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-11-21 01:07:48,270] [pool-1-thread-4] Initializing /data/qa-7469/002002.flex:
[testng] [2024-11-21 01:07:51,705] [pool-1-thread-9] Initializing /data/tamjid/006003000.flex:
[testng] [2024-11-21 01:07:54,655] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex:
[testng] [2024-11-21 01:08:01,830] [pool-1-thread-11] Initializing /data/tony/003003000.tiff:
[testng] [2024-11-21 01:08:05,826] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-11-21 01:08:07,953] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] [2024-11-21 01:08:11,976] [pool-1-thread-9] Initializing /data/ghislain/test.flex:
[testng] [2024-11-21 01:08:15,526] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-11-21 01:08:21,169] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 20 minutes 43 seconds
Finished: SUCCESS