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Started by upstream project "BIOFORMATS-test-repo" build number 234 originally caused by: Started by upstream project "Trigger" build number 259 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins8418083152795277025.sh + '[' micromanager = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36780_merge_ci -v /uod/idr/repos/curated/micromanager:/data -v /uod/idr-scratch/merge-ci/curated/micromanager:/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] 02:44:57,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:44:57,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:44:57,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:44:57,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:44:57,550 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:44:57,551 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:44:57,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:44:57,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:44:57,551 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1139b2f3 - End of configuration. [testng] 02:44:57,552 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3f197a46 - Registering current configuration as safe fallback point [testng] 02:44:57,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@636be97c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 438 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-25 02:44:57,564] [main] java.version = 1.8.0_342 [testng] 02:44:57,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:44:57,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:57,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_02-44-57.log] [testng] 02:44:57,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-25 02:44:57,623] [main] testng.directory = /data [testng] [2024-10-25 02:44:57,623] [main] testng.configDirectory = /config [testng] [2024-10-25 02:44:57,638] [main] testng.multiplier = 1.0 [testng] [2024-10-25 02:44:57,638] [main] testng.in-memory = false [testng] [2024-10-25 02:44:57,638] [main] testng.allow-missing = false [testng] [2024-10-25 02:44:57,638] [main] user.language = en [testng] [2024-10-25 02:44:57,638] [main] user.country = ${user.country} [testng] [2024-10-25 02:44:57,638] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-25 02:45:53,247] [main] ---------------------------------------- [testng] [2024-10-25 02:45:53,248] [main] Total files: 1686 [testng] [2024-10-25 02:45:53,248] [main] Scan time: 55.609 s (32 ms/file) [testng] [2024-10-25 02:45:53,248] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 49 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-25 02:52:45,829] [pool-1-thread-1] Initializing /data/eric/GFP-Aladin mCh-Tub_0/Acqusition.xml: [testng] 02:52:45,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:52:45,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:45,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_02-52-45.log] [testng] 02:52:45,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1115524f - End of configuration. [testng] [2024-10-25 02:52:47,303] [pool-1-thread-12] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_008.tif: [testng] 02:52:47,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:52:47,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:47,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_02-52-47.log] [testng] 02:52:47,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b67e1d - End of configuration. [testng] [2024-10-25 02:52:50,348] [pool-1-thread-12] Used files list does not include base file [testng] [2024-10-25 02:52:50,351] [pool-1-thread-11] Initializing /data/public/1.4.22/thomas/test/test2_sep/Pos0/metadata.txt: [testng] 02:52:50,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:52:50,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:50,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_02-52-50.log] [testng] 02:52:50,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3719ae20 - End of configuration. [testng] [2024-10-25 02:52:51,396] [pool-1-thread-10] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_007.tif: [testng] 02:52:51,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:52:51,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:51,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_02-52-51.log] [testng] 02:52:51,397 |-INFO in ch.qos.logback.core.sift.SiftProcessor@757cf911 - End of configuration. [testng] [2024-10-25 02:52:54,659] [pool-1-thread-10] Used files list does not include base file [testng] [2024-10-25 02:52:54,662] [pool-1-thread-9] Initializing /data/pr-3253/img_000000000__000.tif: [testng] 02:52:54,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:52:54,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:54,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_02-52-54.log] [testng] 02:52:54,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a6e93fd - End of configuration. [testng] [2024-10-25 02:52:55,703] [pool-1-thread-8] Initializing /data/public/1.4.16/serge/Pos0/img_000000000_00-BF0_000.tif: [testng] 02:52:55,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:52:55,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:55,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_02-52-55.log] [testng] 02:52:55,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44da85cc - End of configuration. [testng] [2024-10-25 02:52:57,567] [pool-1-thread-7] Initializing /data/public/1.4.22/sebastien/Test_Dataset_MultiPosition_Stack_1_MMStack_Pos0_metadata.txt: [testng] 02:52:57,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:52:57,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:57,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_02-52-57.log] [testng] 02:52:57,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd8ec95 - End of configuration. [testng] [2024-10-25 02:53:23,350] [pool-1-thread-6] Initializing /data/public/1.4.16/serge/Pos1/img_000000000_00-BF0_000.tif: [testng] 02:53:23,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:53:23,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:23,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_02-53-23.log] [testng] 02:53:23,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53c626f8 - End of configuration. [testng] [2024-10-25 02:53:25,091] [pool-1-thread-5] Initializing /data/colin/20121205_H_rel_3c_0nm_1/img_000000000_Cy5_000.tif: [testng] 02:53:25,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:53:25,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:25,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_02-53-25.log] [testng] 02:53:25,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54720046 - End of configuration. [testng] [2024-10-25 02:53:29,889] [pool-1-thread-4] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_001_000_metadata.txt: [testng] 02:53:29,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:53:29,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:29,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_02-53-29.log] [testng] 02:53:29,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dde365f - End of configuration. [testng] [2024-10-25 02:53:30,949] [pool-1-thread-3] Initializing /data/public/1.4.16/serge/Pos2/img_000000000_00-BF0_000.tif: [testng] 02:53:30,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:53:30,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:30,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_02-53-30.log] [testng] 02:53:30,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eff5f57 - End of configuration. [testng] [2024-10-25 02:53:32,900] [pool-1-thread-2] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_006.tif: [testng] 02:53:32,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:53:32,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:32,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_02-53-32.log] [testng] 02:53:32,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b9425ee - End of configuration. [testng] [2024-10-25 02:53:35,978] [pool-1-thread-2] Used files list does not include base file [testng] [2024-10-25 02:53:49,404] [pool-1-thread-4] Initializing /data/stanislav/s105-GFP-_0/img_000000000_GFP_000.tif: [testng] [2024-10-25 02:53:53,728] [pool-1-thread-9] Initializing /data/public/1.4.16/serge/Pos3/img_000000000_00-BF0_000.tif: [testng] [2024-10-25 02:54:01,002] [pool-1-thread-11] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_009.tif: [testng] [2024-10-25 02:54:04,825] [pool-1-thread-11] Used files list does not include base file [testng] [2024-10-25 02:55:42,113] [pool-1-thread-4] Initializing /data/public/1.4.22/thomas/test/test_sep/Pos0/img_000000000_FITC_000.tif: [testng] [2024-10-25 02:55:43,572] [pool-1-thread-8] Initializing /data/david/res test/res test.tif: [testng] [2024-10-25 02:55:45,045] [pool-1-thread-6] Initializing /data/david/img_000000000_white_000.tif: [testng] [2024-10-25 02:55:48,087] [pool-1-thread-3] Initializing /data/eric/GFP-Aladin mCh-Tub_4/Acqusition.xml: [testng] [2024-10-25 02:56:05,483] [pool-1-thread-8] Initializing /data/qa-4984/img_000000000__000.tif: [testng] [2024-10-25 02:56:06,535] [pool-1-thread-9] Initializing /data/public/1.4.22/thomas/test/test_stack/test_stack_MMStack_Pos0_metadata.txt: [testng] [2024-10-25 02:56:18,453] [pool-1-thread-9] Initializing /data/scott/EMoffslicefurst2Time_0/img_000000000_491_000.tif: [testng] [2024-10-25 02:56:22,520] [pool-1-thread-6] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_000_000_metadata.txt: [testng] [2024-10-25 02:56:23,524] [pool-1-thread-8] Initializing /data/david/trial 2 part 3 40x_0/Acqusition.xml: [testng] [2024-10-25 02:56:27,523] [pool-1-thread-7] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_008.tif: [testng] [2024-10-25 02:56:30,891] [pool-1-thread-7] Used files list does not include base file [testng] [2024-10-25 02:56:34,092] [pool-1-thread-4] Initializing /data/public/1.4.23/jens/fucci_GFP-geminin_RFP-cdt1_2_MMStack_Pos0_metadata.txt: [testng] [2024-10-25 02:56:39,727] [pool-1-thread-6] Initializing /data/public/1.4.22/thomas/test/test2_stack/MMStack_Pos0_metadata.txt: [testng] [2024-10-25 02:56:49,923] [pool-1-thread-4] Initializing /data/scott/EMonslicefurst2Time_0/img_000000000_491_000.tif: [testng] [2024-10-25 02:56:51,435] [pool-1-thread-6] Initializing /data/eik/1-Pos_000_000/img_000000000_Blue_002.tif: [testng] [2024-10-25 02:57:07,114] [pool-1-thread-8] Initializing /data/kally/img_000000000_Brightfield_000.tif: [testng] [2024-10-25 02:57:28,166] [pool-1-thread-9] Initializing /data/scott/EMoffchanfurst2Time_0/img_000000000_491_000.tif: [testng] [2024-10-25 02:57:50,567] [pool-1-thread-1] Initializing /data/eric/GFP-Aladin mCh-Tub_2/Acqusition.xml: [testng] [2024-10-25 02:57:59,002] [pool-1-thread-4] Initializing /data/eric/GFP-Aladin mCh-Tub_5/Acqusition.xml: [testng] [2024-10-25 02:58:16,956] [pool-1-thread-6] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_006.tif: [testng] [2024-10-25 02:58:19,814] [pool-1-thread-6] Used files list does not include base file [testng] [2024-10-25 02:58:45,478] [pool-1-thread-9] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_001_001_metadata.txt: [testng] [2024-10-25 02:58:58,714] [pool-1-thread-9] Initializing /data/eric/GFP-Aladin mCh-Tub_1/Acqusition.xml: [testng] [2024-10-25 02:59:42,541] [pool-1-thread-1] Initializing /data/public/1.4.16/serge/Pos4/img_000000000_00-BF0_000.tif: [testng] [2024-10-25 03:00:50,368] [pool-1-thread-9] Initializing /data/nico/S2-GFP-Histone-Cherry-tub_9_Great2/metadata.txt: [testng] [2024-10-25 03:01:37,343] [pool-1-thread-2] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_009.tif: [testng] [2024-10-25 03:01:41,547] [pool-1-thread-2] Used files list does not include base file [testng] [2024-10-25 03:01:41,548] [pool-1-thread-12] Initializing /data/scott/EMonchanfurst2Time_0/img_000000000_491_000.tif: [testng] [2024-10-25 03:01:43,523] [pool-1-thread-10] Initializing /data/nico/test_1/Acqusition.xml: [testng] [2024-10-25 03:01:46,040] [pool-1-thread-1] Initializing /data/nico/Untitled_4_multi_file/img_000000000_gfpFast_000.tif: [testng] [2024-10-25 03:02:04,319] [pool-1-thread-8] Initializing /data/pr-3229/1.4-large-acq-take-2_1_MMStack_Pos0_metadata.txt: [testng] [2024-10-25 03:04:57,355] [pool-1-thread-11] Initializing /data/nico/MM_test_0/img_0_Cy5_0.tif: [testng] [2024-10-25 03:05:10,409] [pool-1-thread-7] Initializing /data/public/1.4.16/serge/Pos5/img_000000000_00-BF0_000.tif: [testng] [2024-10-25 03:05:34,269] [pool-1-thread-12] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_000_001_metadata.txt: [testng] [2024-10-25 03:05:44,348] [pool-1-thread-10] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_007.tif: [testng] [2024-10-25 03:05:48,971] [pool-1-thread-10] Used files list does not include base file [testng] [2024-10-25 03:05:49,440] [pool-1-thread-5] Initializing /data/eric/GFP-Aladin mCh-Tub_3/Acqusition.xml: [testng] [2024-10-25 03:05:56,174] [pool-1-thread-12] Initializing /data/nico/test2/img_000000000_Cy5_000.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2597, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 57 minutes 27 seconds Finished: SUCCESS