Started by upstream project "BIOFORMATS-test-repo" build number 287
originally caused by:
Started by upstream project "Trigger" build number 306
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13699802501918802415.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_45331_merge_ci -v /uod/idr/repos/curated/tillvision:/data -v /uod/idr-scratch/merge-ci/curated/tillvision:/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] 02:12:40,989 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:12:40,990 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 02:12:40,990 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:12:40,991 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:12:40,992 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:12:40,992 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:12:40,992 |-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] 02:12:40,992 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:12:40,993 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:12:40,993 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:12:40,993 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:12:40,994 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:12:41,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:12:41,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:12:41,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:12:41,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:12:41,184 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:12:41,184 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:12:41,184 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:12:41,184 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:12:41,184 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 02:12:41,185 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 02:12:41,185 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-11 02:12:41,194] [main] java.version = 17.0.2
[testng] 02:12:41,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:12:41,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:12:41,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_02-12-41.log]
[testng] 02:12:41,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-11 02:12:41,241] [main] testng.directory = /data
[testng] [2024-12-11 02:12:41,241] [main] testng.configDirectory = /config
[testng] [2024-12-11 02:12:41,250] [main] testng.multiplier = 1.0
[testng] [2024-12-11 02:12:41,251] [main] testng.in-memory = false
[testng] [2024-12-11 02:12:41,251] [main] testng.allow-missing = false
[testng] [2024-12-11 02:12:41,251] [main] user.language = en
[testng] [2024-12-11 02:12:41,251] [main] user.country = ${user.country}
[testng] [2024-12-11 02:12:41,251] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-11 02:13:04,709] [main] ----------------------------------------
[testng] [2024-12-11 02:13:04,709] [main] Total files: 46
[testng] [2024-12-11 02:13:04,709] [main] Scan time: 23.458 s (509 ms/file)
[testng] [2024-12-11 02:13:04,709] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-11 02:14:12,115] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] 02:14:12,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:14:12,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:12,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-11_02-14-12.log]
[testng] 02:14:12,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70b36351 - End of configuration.
[testng] [2024-12-11 02:14:12,886] [pool-1-thread-12] Initializing /data/gerhard/test.vws:
[testng] 02:14:12,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:14:12,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:12,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-11_02-14-12.log]
[testng] 02:14:12,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41d2ea91 - End of configuration.
[testng] [2024-12-11 02:14:14,132] [pool-1-thread-11] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] 02:14:14,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:14:14,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:14,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-11_02-14-14.log]
[testng] 02:14:14,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53ba5213 - End of configuration.
[testng] [2024-12-11 02:14:16,640] [pool-1-thread-10] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] 02:14:16,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:14:16,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:16,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-11_02-14-16.log]
[testng] 02:14:16,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1be1814c - End of configuration.
[testng] [2024-12-11 02:14:21,189] [pool-1-thread-9] Initializing /data/samples/fibre.vws:
[testng] 02:14:21,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:14:21,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:21,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-11_02-14-21.log]
[testng] 02:14:21,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4576c0 - End of configuration.
[testng] [2024-12-11 02:14:21,958] [pool-1-thread-8] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] 02:14:21,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:14:21,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:21,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-11_02-14-21.log]
[testng] 02:14:21,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39a51e9f - End of configuration.
[testng] [2024-12-11 02:14:23,668] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] 02:14:23,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:14:23,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:23,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-11_02-14-23.log]
[testng] 02:14:23,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb989b - End of configuration.
[testng] [2024-12-11 02:14:24,722] [pool-1-thread-6] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] 02:14:24,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:14:24,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:24,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-11_02-14-24.log]
[testng] 02:14:24,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1298b0d1 - End of configuration.
[testng] [2024-12-11 02:14:25,594] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] 02:14:25,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:14:25,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:25,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-11_02-14-25.log]
[testng] 02:14:25,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49bcfe18 - End of configuration.
[testng] [2024-12-11 02:14:27,870] [pool-1-thread-4] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] 02:14:27,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:14:27,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:27,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-11_02-14-27.log]
[testng] 02:14:27,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18c500a3 - End of configuration.
[testng] [2024-12-11 02:14:28,803] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] 02:14:28,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:14:28,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:28,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-11_02-14-28.log]
[testng] 02:14:28,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2750c33 - End of configuration.
[testng] [2024-12-11 02:14:29,730] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] 02:14:29,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:14:29,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:29,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-11_02-14-29.log]
[testng] 02:14:29,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5503af77 - End of configuration.
[testng] [2024-12-11 02:14:42,887] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2024-12-11 02:14:44,433] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws:
[testng] [2024-12-11 02:14:47,127] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws:
[testng] [2024-12-11 02:15:08,357] [pool-1-thread-6] Initializing /data/imagesc-84715/working.vws:
[testng] [2024-12-11 02:15:09,862] [pool-1-thread-4] Initializing /data/stephan/two sequences.vws:
[testng] [2024-12-11 02:15:21,245] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] [2024-12-11 02:15:22,832] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2024-12-11 02:15:26,127] [pool-1-thread-1] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] [2024-12-11 02:15:39,148] [pool-1-thread-12] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] [2024-12-11 02:15:56,762] [pool-1-thread-9] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] [2024-12-11 02:15:58,373] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2024-12-11 02:16:03,072] [pool-1-thread-1] Initializing /data/andreas/090812E4.vws:
[testng] [2024-12-11 02:16:26,615] [pool-1-thread-5] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 27 minutes 54 seconds
Finished: SUCCESS