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Started by upstream project "BIOFORMATS-test-repo" build number 97 originally caused by: Started by upstream project "Trigger" build number 108 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/jenkins6466383859130293777.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14959_merge_ci -v /uod/idr/repos/curated/simplepci:/data -v /uod/idr-scratch/merge-ci/curated/simplepci:/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] 01:40:58,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:40:58,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:40:59,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:40:59,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:40:59,029 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:40:59,030 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:40:59,030 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:40:59,031 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:40:59,031 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 01:40:59,032 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 01:40:59,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 657 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-19 01:40:59,043] [main] java.version = 17.0.2 [testng] 01:40:59,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:40:59,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:59,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-19_01-40-59.log] [testng] 01:40:59,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-19 01:40:59,288] [main] testng.directory = /data [testng] [2024-06-19 01:40:59,289] [main] testng.configDirectory = /config [testng] [2024-06-19 01:40:59,356] [main] testng.multiplier = 1.0 [testng] [2024-06-19 01:40:59,358] [main] testng.in-memory = false [testng] [2024-06-19 01:40:59,359] [main] testng.allow-missing = false [testng] [2024-06-19 01:40:59,359] [main] user.language = en [testng] [2024-06-19 01:40:59,359] [main] user.country = ${user.country} [testng] [2024-06-19 01:40:59,359] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-19 01:41:01,607] [main] ---------------------------------------- [testng] [2024-06-19 01:41:01,608] [main] Total files: 76 [testng] [2024-06-19 01:41:01,608] [main] Scan time: 2.248 s (29 ms/file) [testng] [2024-06-19 01:41:01,608] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-19 01:42:55,458] [pool-1-thread-1] Initializing /data/hopi/#2 phase.tif: [testng] 01:42:55,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:42:55,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:55,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-19_01-42-55.log] [testng] 01:42:55,461 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b74536d - End of configuration. [testng] [2024-06-19 01:42:55,545] [pool-1-thread-12] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] 01:42:55,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:42:55,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:55,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-19_01-42-55.log] [testng] 01:42:55,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dd6ce2c - End of configuration. [testng] [2024-06-19 01:42:56,004] [pool-1-thread-11] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] 01:42:56,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:42:56,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-19_01-42-56.log] [testng] 01:42:56,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@612c0260 - End of configuration. [testng] [2024-06-19 01:42:56,050] [pool-1-thread-10] Initializing /data/arvonn/gfpras_623.cxd: [testng] 01:42:56,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:42:56,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-19_01-42-56.log] [testng] 01:42:56,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@940f2a4 - End of configuration. [testng] [2024-06-19 01:42:56,089] [pool-1-thread-9] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] 01:42:56,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:42:56,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-19_01-42-56.log] [testng] 01:42:56,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c74be94 - End of configuration. [testng] [2024-06-19 01:42:56,133] [pool-1-thread-8] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] 01:42:56,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:42:56,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-19_01-42-56.log] [testng] 01:42:56,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a9b6d6 - End of configuration. [testng] [2024-06-19 01:42:56,275] [pool-1-thread-7] Initializing /data/ben/Data1.cxd: [testng] 01:42:56,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:42:56,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-19_01-42-56.log] [testng] 01:42:56,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14008e9e - End of configuration. [testng] [2024-06-19 01:42:56,376] [pool-1-thread-6] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] 01:42:56,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:42:56,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-19_01-42-56.log] [testng] 01:42:56,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14eaf69 - End of configuration. [testng] [2024-06-19 01:42:56,401] [pool-1-thread-5] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] 01:42:56,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:42:56,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-19_01-42-56.log] [testng] 01:42:56,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@247e09bd - End of configuration. [testng] [2024-06-19 01:42:56,444] [pool-1-thread-4] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] 01:42:56,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:42:56,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-19_01-42-56.log] [testng] 01:42:56,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53182484 - End of configuration. [testng] [2024-06-19 01:42:56,470] [pool-1-thread-3] Initializing /data/arvonn/good pollen 2z.cxd: [testng] 01:42:56,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:42:56,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-19_01-42-56.log] [testng] 01:42:56,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d88f36 - End of configuration. [testng] [2024-06-19 01:42:56,537] [pool-1-thread-2] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] 01:42:56,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:42:56,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:56,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-19_01-42-56.log] [testng] 01:42:56,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f0a70a - End of configuration. [testng] [2024-06-19 01:42:58,853] [pool-1-thread-6] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-06-19 01:42:58,892] [pool-1-thread-4] Initializing /data/martin/Data1.cxd: [testng] [2024-06-19 01:42:58,914] [pool-1-thread-10] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-06-19 01:42:58,950] [pool-1-thread-3] Initializing /data/nico/b00/Image4.tif: [testng] [2024-06-19 01:42:58,971] [pool-1-thread-11] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-06-19 01:42:59,226] [pool-1-thread-5] Initializing /data/nico/b00/Image6.tif: [testng] [2024-06-19 01:42:59,245] [pool-1-thread-9] Initializing /data/nico/b00/Image8.tif: [testng] [2024-06-19 01:42:59,264] [pool-1-thread-7] Initializing /data/nico/b00/Image1.tif: [testng] [2024-06-19 01:42:59,396] [pool-1-thread-1] Initializing /data/arvonn/shark.cxd: [testng] [2024-06-19 01:42:59,769] [pool-1-thread-8] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-06-19 01:42:59,826] [pool-1-thread-3] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd: [testng] [2024-06-19 01:42:59,953] [pool-1-thread-4] Initializing /data/martin/XY-03.tif: [testng] [2024-06-19 01:43:00,040] [pool-1-thread-9] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-06-19 01:43:00,219] [pool-1-thread-7] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-06-19 01:43:00,277] [pool-1-thread-10] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-06-19 01:43:01,894] [pool-1-thread-5] Initializing /data/martin/XYT-01.tif: [testng] [2024-06-19 01:43:01,923] [pool-1-thread-12] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-06-19 01:43:01,973] [pool-1-thread-2] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-06-19 01:43:02,309] [pool-1-thread-11] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-06-19 01:43:02,808] [pool-1-thread-5] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-06-19 01:43:02,852] [pool-1-thread-1] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-06-19 01:43:02,949] [pool-1-thread-6] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-06-19 01:43:04,321] [pool-1-thread-2] Initializing /data/nico/b00/Image5.tif: [testng] [2024-06-19 01:43:04,392] [pool-1-thread-4] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-06-19 01:43:04,517] [pool-1-thread-7] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-06-19 01:43:04,547] [pool-1-thread-8] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-06-19 01:43:05,173] [pool-1-thread-2] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-06-19 01:43:05,247] [pool-1-thread-5] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-06-19 01:43:05,497] [pool-1-thread-9] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-06-19 01:43:05,863] [pool-1-thread-11] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-06-19 01:43:06,210] [pool-1-thread-7] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-06-19 01:43:06,266] [pool-1-thread-8] Initializing /data/hopi/#21 phase.tif: [testng] [2024-06-19 01:43:06,438] [pool-1-thread-12] Initializing /data/martin/XYT-01.cxd: [testng] [2024-06-19 01:43:06,465] [pool-1-thread-1] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-06-19 01:43:06,524] [pool-1-thread-3] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-06-19 01:43:06,609] [pool-1-thread-11] Initializing /data/jesper/1q35.cxd: [testng] [2024-06-19 01:43:06,702] [pool-1-thread-2] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-06-19 01:43:06,770] [pool-1-thread-9] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-06-19 01:43:06,902] [pool-1-thread-4] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-06-19 01:43:07,351] [pool-1-thread-12] Initializing /data/nico/b00.cxd: [testng] [2024-06-19 01:43:07,409] [pool-1-thread-3] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-06-19 01:43:07,493] [pool-1-thread-5] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-06-19 01:43:07,658] [pool-1-thread-11] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-06-19 01:43:07,859] [pool-1-thread-7] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-06-19 01:43:08,041] [pool-1-thread-9] Initializing /data/martin/XY-02.tif: [testng] [2024-06-19 01:43:08,093] [pool-1-thread-12] Initializing /data/nico/b00/Image2.tif: [testng] [2024-06-19 01:43:08,143] [pool-1-thread-4] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-06-19 01:43:08,184] [pool-1-thread-1] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] [2024-06-19 01:43:08,475] [pool-1-thread-12] Initializing /data/nico/b00/Image3.tif: [testng] [2024-06-19 01:43:08,496] [pool-1-thread-8] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-06-19 01:43:10,417] [pool-1-thread-3] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-06-19 01:43:10,476] [pool-1-thread-4] Initializing /data/martin/XY-01.tif: [testng] [2024-06-19 01:43:10,529] [pool-1-thread-11] Initializing /data/arvonn/fura.cxd: [testng] [2024-06-19 01:43:10,661] [pool-1-thread-12] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-06-19 01:43:10,947] [pool-1-thread-9] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-06-19 01:43:11,169] [pool-1-thread-5] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-06-19 01:43:11,514] [pool-1-thread-2] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-06-19 01:43:12,172] [pool-1-thread-11] Initializing /data/nico/b00/Image7.tif: [testng] [2024-06-19 01:43:12,300] [pool-1-thread-7] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-06-19 01:43:12,447] [pool-1-thread-2] Initializing /data/hopi/3 colors YFP(green)2.99s gain4 CFP(red) 0.48s gain4 and Hoechst(blue)0.96gain4.tif: [testng] [2024-06-19 01:43:12,644] [pool-1-thread-11] Initializing /data/imagesc-72023/Data727.cxd: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3869, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 30 seconds Finished: SUCCESS