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Started by upstream project "BIOFORMATS-test-repo" build number 66 originally caused by: Started by upstream project "Trigger" build number 74 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins17439169371266023936.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9930_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 08:52:04,585 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:52:04,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 08:52:04,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:52:04,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:52:04,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:52:04,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:52:04,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:52:04,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:52:04,590 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:52:04,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:52:04,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:52:04,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:52:04,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:52:04,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:52:04,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:52:04,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:52:04,883 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:52:04,883 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:52:04,884 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:52:04,884 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:52:04,884 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 08:52:04,885 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 08:52:04,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 295 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-17 08:52:04,896] [main] java.version = 1.8.0_342 [testng] 08:52:04,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:52:04,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:04,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-17_08-52-04.log] [testng] 08:52:04,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-17 08:52:04,952] [main] testng.directory = /data [testng] [2024-05-17 08:52:04,952] [main] testng.configDirectory = /config [testng] [2024-05-17 08:52:04,966] [main] testng.multiplier = 1.0 [testng] [2024-05-17 08:52:04,966] [main] testng.in-memory = false [testng] [2024-05-17 08:52:04,966] [main] testng.allow-missing = false [testng] [2024-05-17 08:52:04,966] [main] user.language = en [testng] [2024-05-17 08:52:04,966] [main] user.country = ${user.country} [testng] [2024-05-17 08:52:04,966] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-17 08:52:12,419] [main] ---------------------------------------- [testng] [2024-05-17 08:52:12,419] [main] Total files: 67 [testng] [2024-05-17 08:52:12,420] [main] Scan time: 7.453 s (111 ms/file) [testng] [2024-05-17 08:52:12,420] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-17 08:52:35,261] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved_IMS3.ims: [testng] 08:52:35,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:52:35,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-17_08-52-35.log] [testng] 08:52:35,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17676384 - End of configuration. [testng] [2024-05-17 08:52:35,325] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0000.ims: [testng] 08:52:35,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:52:35,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,326 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-17_08-52-35.log] [testng] 08:52:35,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36beff60 - End of configuration. [testng] [2024-05-17 08:52:35,346] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0005.ims: [testng] 08:52:35,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:52:35,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-17_08-52-35.log] [testng] 08:52:35,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2768b6a2 - End of configuration. [testng] [2024-05-17 08:52:35,360] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0003.ims: [testng] 08:52:35,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:52:35,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-17_08-52-35.log] [testng] 08:52:35,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c0dbec2 - End of configuration. [testng] [2024-05-17 08:52:35,375] [pool-1-thread-9] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 08:52:35,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:52:35,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-17_08-52-35.log] [testng] 08:52:35,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b4ce3b0 - End of configuration. [testng] [2024-05-17 08:52:35,413] [pool-1-thread-8] Initializing /data/generated/mri-stack-original.ims: [testng] 08:52:35,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:52:35,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-17_08-52-35.log] [testng] 08:52:35,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28fc1fc6 - End of configuration. [testng] [2024-05-17 08:52:35,453] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0015.ims: [testng] 08:52:35,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:52:35,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-17_08-52-35.log] [testng] 08:52:35,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@469b1056 - End of configuration. [testng] [2024-05-17 08:52:35,469] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0009.ims: [testng] 08:52:35,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:52:35,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-17_08-52-35.log] [testng] 08:52:35,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@737c12e3 - End of configuration. [testng] [2024-05-17 08:52:35,486] [pool-1-thread-5] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] 08:52:35,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:52:35,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-17_08-52-35.log] [testng] 08:52:35,488 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ff2d2b7 - End of configuration. [testng] [2024-05-17 08:52:35,550] [pool-1-thread-4] Initializing /data/kay/Imaris503_test_Kay.ims: [testng] 08:52:35,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:52:35,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-17_08-52-35.log] [testng] 08:52:35,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c5ee04a - End of configuration. [testng] [2024-05-17 08:52:35,576] [pool-1-thread-3] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] 08:52:35,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:52:35,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-17_08-52-35.log] [testng] 08:52:35,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11f1a1b2 - End of configuration. [testng] [2024-05-17 08:52:35,612] [pool-1-thread-2] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] 08:52:35,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:52:35,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:35,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-17_08-52-35.log] [testng] 08:52:35,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@669bfb12 - End of configuration. [testng] [2024-05-17 08:52:37,576] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0012.ims: [testng] [2024-05-17 08:52:37,594] [pool-1-thread-8] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: [testng] [2024-05-17 08:52:37,712] [pool-1-thread-11] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] [2024-05-17 08:52:37,750] [pool-1-thread-7] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] [2024-05-17 08:52:37,826] [pool-1-thread-4] Initializing /data/public/davemason/TransFactors_2C_SRRF.ims: [testng] [2024-05-17 08:52:37,853] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0010.ims: [testng] [2024-05-17 08:52:37,866] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0006.ims: [testng] [2024-05-17 08:52:39,322] [pool-1-thread-3] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [2024-05-17 08:52:39,408] [pool-1-thread-6] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] [2024-05-17 08:52:39,505] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0014.ims: [testng] [2024-05-17 08:52:39,522] [pool-1-thread-10] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] [2024-05-17 08:52:40,400] [pool-1-thread-1] Initializing /data/public/eliana/retina_large.ims: [testng] [2024-05-17 08:52:40,433] [pool-1-thread-12] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] [2024-05-17 08:52:41,242] [pool-1-thread-2] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-05-17 08:52:41,294] [pool-1-thread-3] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF.ims: [testng] [2024-05-17 08:52:41,528] [pool-1-thread-6] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal_IMS3.ims: [testng] [2024-05-17 08:52:42,190] [pool-1-thread-12] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] [2024-05-17 08:52:54,196] [pool-1-thread-2] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] [2024-05-17 08:52:54,296] [pool-1-thread-5] Initializing /data/generated/MF-2CH-Z-T.ims: [testng] [2024-05-17 08:52:54,555] [pool-1-thread-5] Initializing /data/qa-17515/Organoid=1.ims: [testng] [2024-05-17 08:52:55,991] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: BUILD SUCCESSFUL Total time: 1 minute 39 seconds Finished: SUCCESS