Started by upstream project "BIOFORMATS-test-repo" build number 55
originally caused by:
Started by upstream project "Trigger" build number 62
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins17468334610788977606.sh
+ '[' micromanager = slidebook ']'
++ date +%u
+ '[' 1 -le 1 ']'
+ DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR'
+ sudo docker run --rm --name BIOFORMATS-test-folder_8097_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 -Duser.language=fr -Duser.country=FR
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] 02:11:30,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:11:31,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:11:31,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:11:31,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:11:31,127 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:11:31,127 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:11:31,127 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:11:31,128 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:11:31,128 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration.
[testng] 02:11:31,129 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point
[testng] 02:11:31,129 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 452 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-06 02:11:31,140] [main] java.version = 1.8.0_342
[testng] 02:11:31,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:11:31,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:11:31,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-06_02-11-31.log]
[testng] 02:11:31,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-05-06 02:11:31,208] [main] testng.directory = /data
[testng] [2024-05-06 02:11:31,208] [main] testng.configDirectory = /config
[testng] [2024-05-06 02:11:31,226] [main] testng.multiplier = 1.0
[testng] [2024-05-06 02:11:31,226] [main] testng.in-memory = false
[testng] [2024-05-06 02:11:31,226] [main] testng.allow-missing = false
[testng] [2024-05-06 02:11:31,226] [main] user.language = fr
[testng] [2024-05-06 02:11:31,226] [main] user.country = FR
[testng] [2024-05-06 02:11:31,227] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-05-06 02:11:41,886] [main] ----------------------------------------
[testng] [2024-05-06 02:11:41,886] [main] Total files: 1686
[testng] [2024-05-06 02:11:41,887] [main] Scan time: 10.659 s (6 ms/file)
[testng] [2024-05-06 02:11:41,887] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 49 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-06 02:19:00,208] [pool-1-thread-1] Initializing /data/david/res test/res test.tif:
[testng] 02:19:00,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:19:00,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:00,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-06_02-19-00.log]
[testng] 02:19:00,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@366bb064 - End of configuration.
[testng] [2024-05-06 02:19:00,321] [pool-1-thread-12] Initializing /data/nico/Untitled_4_multi_file/img_000000000_gfpFast_000.tif:
[testng] 02:19:00,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:19:00,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:00,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-06_02-19-00.log]
[testng] 02:19:00,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@180be0be - End of configuration.
[testng] [2024-05-06 02:19:01,884] [pool-1-thread-11] Initializing /data/public/1.4.16/serge/Pos4/img_000000000_00-BF0_000.tif:
[testng] 02:19:01,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:19:01,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:01,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-06_02-19-01.log]
[testng] 02:19:01,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a3f4966 - End of configuration.
[testng] [2024-05-06 02:19:02,223] [pool-1-thread-10] Initializing /data/nico/S2-GFP-Histone-Cherry-tub_9_Great2/metadata.txt:
[testng] 02:19:02,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:19:02,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:02,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-06_02-19-02.log]
[testng] 02:19:02,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@134b34d5 - End of configuration.
[testng] [2024-05-06 02:19:37,079] [pool-1-thread-9] Initializing /data/nico/test2/img_000000000_Cy5_000.tif:
[testng] 02:19:37,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:19:37,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:37,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-06_02-19-37.log]
[testng] 02:19:37,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12a66399 - End of configuration.
[testng] [2024-05-06 02:19:37,120] [pool-1-thread-8] Initializing /data/scott/EMonchanfurst2Time_0/img_000000000_491_000.tif:
[testng] 02:19:37,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:19:37,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:37,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-06_02-19-37.log]
[testng] 02:19:37,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43aacd7d - End of configuration.
[testng] [2024-05-06 02:19:37,165] [pool-1-thread-7] Initializing /data/nico/test_1/Acqusition.xml:
[testng] 02:19:37,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:19:37,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:37,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-06_02-19-37.log]
[testng] 02:19:37,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69154e46 - End of configuration.
[testng] [2024-05-06 02:19:37,658] [pool-1-thread-6] Initializing /data/public/1.4.16/serge/Pos3/img_000000000_00-BF0_000.tif:
[testng] 02:19:37,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:19:37,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:37,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-06_02-19-37.log]
[testng] 02:19:37,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19114cc0 - End of configuration.
[testng] [2024-05-06 02:19:37,793] [pool-1-thread-5] Initializing /data/pr-3229/1.4-large-acq-take-2_1_MMStack_Pos0_metadata.txt:
[testng] 02:19:37,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:19:37,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:19:37,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-06_02-19-37.log]
[testng] 02:19:37,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@242ebae5 - End of configuration.
[testng] [2024-05-06 02:23:18,915] [pool-1-thread-4] Initializing /data/public/1.4.23/jens/fucci_GFP-geminin_RFP-cdt1_2_MMStack_Pos0_metadata.txt:
[testng] 02:23:18,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:23:18,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:18,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-06_02-23-18.log]
[testng] 02:23:18,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42871fb5 - End of configuration.
[testng] [2024-05-06 02:23:19,463] [pool-1-thread-3] Initializing /data/pr-3253/img_000000000__000.tif:
[testng] 02:23:19,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:23:19,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:19,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-06_02-23-19.log]
[testng] 02:23:19,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f11c15b - End of configuration.
[testng] [2024-05-06 02:23:19,555] [pool-1-thread-2] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_007.tif:
[testng] 02:23:19,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:23:19,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:19,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-06_02-23-19.log]
[testng] 02:23:19,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a124365 - End of configuration.
[testng] [2024-05-06 02:23:22,210] [pool-1-thread-2] Used files list does not include base file
[testng] [2024-05-06 02:23:24,326] [pool-1-thread-1] Initializing /data/scott/EMoffslicefurst2Time_0/img_000000000_491_000.tif:
[testng] [2024-05-06 02:23:24,410] [pool-1-thread-9] Initializing /data/public/1.4.16/serge/Pos0/img_000000000_00-BF0_000.tif:
[testng] [2024-05-06 02:23:25,726] [pool-1-thread-3] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_006.tif:
[testng] [2024-05-06 02:23:25,922] [pool-1-thread-3] Used files list does not include base file
[testng] [2024-05-06 02:23:27,559] [pool-1-thread-7] Initializing /data/public/1.4.22/sebastien/Test_Dataset_MultiPosition_Stack_1_MMStack_Pos0_metadata.txt:
[testng] [2024-05-06 02:23:47,424] [pool-1-thread-8] Initializing /data/eric/GFP-Aladin mCh-Tub_1/Acqusition.xml:
[testng] [2024-05-06 02:23:48,138] [pool-1-thread-1] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_000_001_metadata.txt:
[testng] [2024-05-06 02:23:48,761] [pool-1-thread-12] Initializing /data/public/1.4.22/thomas/test/test2_sep/Pos0/metadata.txt:
[testng] [2024-05-06 02:23:49,242] [pool-1-thread-1] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_001_001_metadata.txt:
[testng] [2024-05-06 02:23:49,640] [pool-1-thread-6] Initializing /data/public/1.4.22/thomas/test/test_sep/Pos0/img_000000000_FITC_000.tif:
[testng] [2024-05-06 02:23:49,747] [pool-1-thread-11] Initializing /data/colin/20121205_H_rel_3c_0nm_1/img_000000000_Cy5_000.tif:
[testng] [2024-05-06 02:23:53,015] [pool-1-thread-4] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_009.tif:
[testng] [2024-05-06 02:23:53,119] [pool-1-thread-4] Used files list does not include base file
[testng] [2024-05-06 02:23:53,120] [pool-1-thread-12] Initializing /data/public/1.4.22/thomas/test/test2_stack/MMStack_Pos0_metadata.txt:
[testng] [2024-05-06 02:23:53,305] [pool-1-thread-8] Initializing /data/public/1.4.16/serge/Pos5/img_000000000_00-BF0_000.tif:
[testng] [2024-05-06 02:23:54,617] [pool-1-thread-1] Initializing /data/scott/EMoffchanfurst2Time_0/img_000000000_491_000.tif:
[testng] [2024-05-06 02:23:54,773] [pool-1-thread-6] Initializing /data/david/img_000000000_white_000.tif:
[testng] [2024-05-06 02:23:58,865] [pool-1-thread-12] Initializing /data/eric/GFP-Aladin mCh-Tub_3/Acqusition.xml:
[testng] [2024-05-06 02:24:01,038] [pool-1-thread-3] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_001_000_metadata.txt:
[testng] [2024-05-06 02:24:01,159] [pool-1-thread-2] Initializing /data/eik/1-Pos_000_000/img_000000000_Blue_002.tif:
[testng] [2024-05-06 02:24:01,811] [pool-1-thread-9] Initializing /data/eric/GFP-Aladin mCh-Tub_2/Acqusition.xml:
[testng] [2024-05-06 02:24:02,260] [pool-1-thread-1] Initializing /data/nico/MM_test_0/img_0_Cy5_0.tif:
[testng] [2024-05-06 02:24:02,460] [pool-1-thread-3] Initializing /data/qa-17040/hyper2.0_1_MMStack_1-Pos_000_000_metadata.txt:
[testng] [2024-05-06 02:24:03,316] [pool-1-thread-3] Initializing /data/stanislav/s105-GFP-_0/img_000000000_GFP_000.tif:
[testng] [2024-05-06 02:24:04,174] [pool-1-thread-1] Initializing /data/david/trial 2 part 3 40x_0/Acqusition.xml:
[testng] [2024-05-06 02:24:05,741] [pool-1-thread-9] Initializing /data/public/1.4.16/serge/Pos1/img_000000000_00-BF0_000.tif:
[testng] [2024-05-06 02:24:07,165] [pool-1-thread-1] Initializing /data/eric/GFP-Aladin mCh-Tub_5/Acqusition.xml:
[testng] [2024-05-06 02:24:08,498] [pool-1-thread-3] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_006.tif:
[testng] [2024-05-06 02:24:08,624] [pool-1-thread-3] Used files list does not include base file
[testng] [2024-05-06 02:24:08,636] [pool-1-thread-12] Initializing /data/qa-4984/img_000000000__000.tif:
[testng] [2024-05-06 02:24:08,887] [pool-1-thread-2] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_008.tif:
[testng] [2024-05-06 02:24:09,106] [pool-1-thread-2] Used files list does not include base file
[testng] [2024-05-06 02:24:10,119] [pool-1-thread-8] Initializing /data/kally/img_000000000_Brightfield_000.tif:
[testng] [2024-05-06 02:24:13,345] [pool-1-thread-12] Initializing /data/scott/EMonslicefurst2Time_0/img_000000000_491_000.tif:
[testng] [2024-05-06 02:24:14,572] [pool-1-thread-4] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_009.tif:
[testng] [2024-05-06 02:24:14,830] [pool-1-thread-4] Used files list does not include base file
[testng] [2024-05-06 02:24:17,640] [pool-1-thread-12] Initializing /data/eric/GFP-Aladin mCh-Tub_4/Acqusition.xml:
[testng] [2024-05-06 02:24:27,739] [pool-1-thread-2] Initializing /data/public/1.4.16/serge/Pos2/img_000000000_00-BF0_000.tif:
[testng] [2024-05-06 02:24:28,948] [pool-1-thread-3] Initializing /data/public/1.4.22/thomas/test/test_stack/test_stack_MMStack_Pos0_metadata.txt:
[testng] [2024-05-06 02:24:29,598] [pool-1-thread-3] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_008.tif:
[testng] [2024-05-06 02:24:29,738] [pool-1-thread-3] Used files list does not include base file
[testng] [2024-05-06 02:24:29,789] [pool-1-thread-6] Initializing /data/eric/GFP-Aladin mCh-Tub_0/Acqusition.xml:
[testng] [2024-05-06 02:24:32,311] [pool-1-thread-9] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_007.tif:
[testng] [2024-05-06 02:24:32,412] [pool-1-thread-9] Used files list does not include base file
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2597, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 43 minutes 39 seconds
Finished: SUCCESS