Started by upstream project "BIOFORMATS-test-repo" build number 99
originally caused by:
Started by upstream project "Trigger" build number 110
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/jenkins1219645920331681199.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_15255_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/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] 01:26:49,222 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:26:49,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:26:49,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:26:49,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:26:49,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:26:49,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:26:49,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:26:49,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:26:49,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:26:49,227 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:26:49,227 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:26:49,227 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:26:49,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:26:49,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:26:49,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:26:49,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:26:49,564 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:26:49,564 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:26:49,565 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:26:49,565 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:26:49,565 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:26:49,566 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:26:49,566 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 340 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-21 01:26:49,578] [main] java.version = 1.8.0_342
[testng] 01:26:49,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:26:49,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:49,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-21_01-26-49.log]
[testng] 01:26:49,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-06-21 01:26:49,637] [main] testng.directory = /data
[testng] [2024-06-21 01:26:49,637] [main] testng.configDirectory = /config
[testng] [2024-06-21 01:26:49,651] [main] testng.multiplier = 1.0
[testng] [2024-06-21 01:26:49,651] [main] testng.in-memory = false
[testng] [2024-06-21 01:26:49,651] [main] testng.allow-missing = false
[testng] [2024-06-21 01:26:49,651] [main] user.language = en
[testng] [2024-06-21 01:26:49,651] [main] user.country = ${user.country}
[testng] [2024-06-21 01:26:49,652] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-06-21 01:27:14,687] [main] ----------------------------------------
[testng] [2024-06-21 01:27:14,688] [main] Total files: 164
[testng] [2024-06-21 01:27:14,688] [main] Scan time: 25.035 s (152 ms/file)
[testng] [2024-06-21 01:27:14,688] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-21 01:27:25,359] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 01:27:25,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:27:25,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-21_01-27-25.log]
[testng] 01:27:25,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3857c62f - End of configuration.
[testng] [2024-06-21 01:27:25,411] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] 01:27:25,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:27:25,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-21_01-27-25.log]
[testng] 01:27:25,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a053e3c - End of configuration.
[testng] [2024-06-21 01:27:25,460] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] 01:27:25,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:27:25,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,462 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-21_01-27-25.log]
[testng] 01:27:25,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@343b3632 - End of configuration.
[testng] [2024-06-21 01:27:25,539] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm:
[testng] 01:27:25,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:27:25,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-21_01-27-25.log]
[testng] 01:27:25,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@690d26c4 - End of configuration.
[testng] [2024-06-21 01:27:25,635] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2:
[testng] 01:27:25,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:27:25,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-21_01-27-25.log]
[testng] 01:27:25,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b1dc4b2 - End of configuration.
[testng] [2024-06-21 01:27:25,662] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] 01:27:25,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:27:25,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-21_01-27-25.log]
[testng] 01:27:25,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a20edf2 - End of configuration.
[testng] [2024-06-21 01:27:25,714] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] 01:27:25,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:27:25,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-21_01-27-25.log]
[testng] 01:27:25,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68f14b4b - End of configuration.
[testng] [2024-06-21 01:27:25,783] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] 01:27:25,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:27:25,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-21_01-27-25.log]
[testng] 01:27:25,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34d3a533 - End of configuration.
[testng] [2024-06-21 01:27:25,794] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] 01:27:25,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:27:25,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-21_01-27-25.log]
[testng] 01:27:25,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51f029e6 - End of configuration.
[testng] [2024-06-21 01:27:25,810] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] 01:27:25,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:27:25,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-21_01-27-25.log]
[testng] 01:27:25,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d947e00 - End of configuration.
[testng] [2024-06-21 01:27:25,865] [pool-1-thread-3] Initializing /data/ome/C1.lsm:
[testng] 01:27:25,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:27:25,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-21_01-27-25.log]
[testng] 01:27:25,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30cedecb - End of configuration.
[testng] [2024-06-21 01:27:25,928] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] 01:27:25,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:27:25,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:25,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-21_01-27-25.log]
[testng] 01:27:25,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@623bb5e0 - End of configuration.
[testng] [2024-06-21 01:27:28,191] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-06-21 01:27:28,206] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-06-21 01:27:28,285] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk:
[testng] [2024-06-21 01:27:28,471] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-06-21 01:27:28,483] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-06-21 01:27:28,498] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d:
[testng] [2024-06-21 01:27:29,178] [pool-1-thread-2] Initializing /data/ome/embryo.lsm:
[testng] [2024-06-21 01:27:29,241] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-06-21 01:27:29,258] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-06-21 01:27:29,268] [pool-1-thread-5] Initializing /data/ome/Adultmidsection.lsm:
[testng] [2024-06-21 01:27:29,318] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-06-21 01:27:29,617] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-06-21 01:27:29,735] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern:
[testng] [2024-06-21 01:27:30,187] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] [2024-06-21 01:27:30,350] [pool-1-thread-12] Initializing /data/ome/worm.tiff:
[testng] [2024-06-21 01:27:30,412] [pool-1-thread-11] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-06-21 01:27:30,463] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-06-21 01:27:30,562] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-06-21 01:27:30,842] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-06-21 01:27:30,849] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-06-21 01:27:30,854] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-06-21 01:27:30,973] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-06-21 01:27:31,219] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-06-21 01:27:31,323] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-06-21 01:27:31,411] [pool-1-thread-6] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] [2024-06-21 01:27:31,502] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-06-21 01:27:32,125] [pool-1-thread-2] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-06-21 01:27:32,404] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-06-21 01:27:32,463] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-06-21 01:27:32,557] [pool-1-thread-8] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-06-21 01:27:32,697] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-06-21 01:27:32,785] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-06-21 01:27:32,894] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-06-21 01:27:32,927] [pool-1-thread-4] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-06-21 01:27:34,184] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-06-21 01:27:34,224] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-06-21 01:27:34,737] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-06-21 01:27:34,773] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-06-21 01:27:34,777] [pool-1-thread-7] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] [2024-06-21 01:27:34,877] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-06-21 01:27:35,000] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2024-06-21 01:27:35,087] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-06-21 01:27:35,175] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] [2024-06-21 01:27:35,217] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-06-21 01:27:35,527] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-06-21 01:27:35,988] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-06-21 01:27:36,054] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 3127, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 2 minutes 35 seconds
Finished: SUCCESS