Started by upstream project "BIOFORMATS-test-repo" build number 225
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins4486252006003788670.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_35481_merge_ci -v /uod/idr/repos/curated/vectra-qptiff:/data -v /uod/idr-scratch/merge-ci/curated/vectra-qptiff:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 12:31:40,645 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 12:31:40,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 12:31:40,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:31:40,648 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:31:40,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 12:31:40,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 12:31:40,649 |-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] 12:31:40,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:31:40,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:31:40,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 12:31:40,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 12:31:40,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 12:31:40,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 12:31:40,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 12:31:40,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 12:31:40,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 12:31:40,826 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 12:31:40,826 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 12:31:40,826 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 12:31:40,827 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 12:31:40,827 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 12:31:40,828 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 12:31:40,828 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 179 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-17 12:31:40,836] [main] java.version = 21
[testng] 12:31:40,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 12:31:40,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:31:40,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_12-31-40.log]
[testng] 12:31:40,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-10-17 12:31:40,881] [main] testng.directory = /data
[testng] [2024-10-17 12:31:40,881] [main] testng.configDirectory = /config
[testng] [2024-10-17 12:31:40,890] [main] testng.multiplier = 1.0
[testng] [2024-10-17 12:31:40,890] [main] testng.in-memory = false
[testng] [2024-10-17 12:31:40,890] [main] testng.allow-missing = false
[testng] [2024-10-17 12:31:40,890] [main] user.language = en
[testng] [2024-10-17 12:31:40,890] [main] user.country = ${user.country}
[testng] [2024-10-17 12:31:40,890] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-17 12:31:50,547] [main] ----------------------------------------
[testng] [2024-10-17 12:31:50,547] [main] Total files: 15
[testng] [2024-10-17 12:31:50,547] [main] Scan time: 9.657 s (643 ms/file)
[testng] [2024-10-17 12:31:50,548] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 14 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-17 12:33:14,347] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif:
[testng] 12:33:14,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 12:33:14,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:14,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_12-33-14.log]
[testng] 12:33:14,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9f41134 - End of configuration.
[testng] [2024-10-17 12:33:18,611] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif:
[testng] 12:33:18,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 12:33:18,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:18,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_12-33-18.log]
[testng] 12:33:18,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e89db4 - End of configuration.
[testng] [2024-10-17 12:33:23,174] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif:
[testng] 12:33:23,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 12:33:23,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:23,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_12-33-23.log]
[testng] 12:33:23,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bcaffbc - End of configuration.
[testng] [2024-10-17 12:33:27,621] [pool-1-thread-10] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff:
[testng] 12:33:27,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 12:33:27,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:27,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_12-33-27.log]
[testng] 12:33:27,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31b89335 - End of configuration.
[testng] [2024-10-17 12:33:32,545] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif:
[testng] 12:33:32,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 12:33:32,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:32,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_12-33-32.log]
[testng] 12:33:32,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11f4514a - End of configuration.
[testng] [2024-10-17 12:33:36,263] [pool-1-thread-8] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif:
[testng] 12:33:36,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 12:33:36,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:36,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_12-33-36.log]
[testng] 12:33:36,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30e7a52e - End of configuration.
[testng] [2024-10-17 12:33:40,747] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff:
[testng] 12:33:40,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 12:33:40,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:40,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_12-33-40.log]
[testng] 12:33:40,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fe64e41 - End of configuration.
[testng] [2024-10-17 12:33:45,712] [pool-1-thread-6] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff:
[testng] 12:33:45,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 12:33:45,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:45,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_12-33-45.log]
[testng] 12:33:45,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@335f7b5f - End of configuration.
[testng] [2024-10-17 12:33:49,756] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif:
[testng] 12:33:49,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 12:33:49,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:49,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_12-33-49.log]
[testng] 12:33:49,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6361fd67 - End of configuration.
[testng] [2024-10-17 12:33:54,688] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff:
[testng] 12:33:54,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 12:33:54,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:54,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_12-33-54.log]
[testng] 12:33:54,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25bb9f8a - End of configuration.
[testng] [2024-10-17 12:33:59,574] [pool-1-thread-3] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif:
[testng] 12:33:59,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 12:33:59,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:59,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_12-33-59.log]
[testng] 12:33:59,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6358d1a8 - End of configuration.
[testng] [2024-10-17 12:34:04,261] [pool-1-thread-2] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif:
[testng] 12:34:04,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 12:34:04,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:34:04,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_12-34-04.log]
[testng] 12:34:04,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40655c91 - End of configuration.
[testng] [2024-10-17 12:34:39,603] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif:
[testng] [2024-10-17 12:34:44,382] [pool-1-thread-5] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 742, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 4 minutes 5 seconds
Finished: SUCCESS