Started by upstream project "BIOFORMATS-test-repo" build number 219
originally caused by:
Started by upstream project "Trigger" build number 246
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins6355438709390327060.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_34726_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
[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] 01:36:28,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:36:28,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 01:36:28,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:28,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:28,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:28,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:28,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:36:28,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:36:28,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:36:28,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:36:28,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:36:28,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:36:28,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:36:28,398 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:36:28,398 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:36:28,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:36:28,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:36:28,399 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 01:36:28,400 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 01:36:28,400 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-13 01:36:28,408] [main] java.version = 17.0.2
[testng] 01:36:28,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:36:28,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:28,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_01-36-28.log]
[testng] 01:36:28,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-13 01:36:28,453] [main] testng.directory = /data
[testng] [2024-10-13 01:36:28,453] [main] testng.configDirectory = /config
[testng] [2024-10-13 01:36:28,461] [main] testng.multiplier = 1.0
[testng] [2024-10-13 01:36:28,462] [main] testng.in-memory = false
[testng] [2024-10-13 01:36:28,462] [main] testng.allow-missing = false
[testng] [2024-10-13 01:36:28,462] [main] user.language = en
[testng] [2024-10-13 01:36:28,463] [main] user.country = ${user.country}
[testng] [2024-10-13 01:36:28,463] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-13 01:37:33,535] [main] ----------------------------------------
[testng] [2024-10-13 01:37:33,535] [main] Total files: 164
[testng] [2024-10-13 01:37:33,535] [main] Scan time: 65.072 s (396 ms/file)
[testng] [2024-10-13 01:37:33,535] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-13 01:38:59,178] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] 01:38:59,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:38:59,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:59,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-13_01-38-59.log]
[testng] 01:38:59,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@128e22ca - End of configuration.
[testng] [2024-10-13 01:39:00,093] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] 01:39:00,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:39:00,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:00,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-13_01-39-00.log]
[testng] 01:39:00,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5952fd83 - End of configuration.
[testng] [2024-10-13 01:39:00,519] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 01:39:00,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:39:00,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:00,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-13_01-39-00.log]
[testng] 01:39:00,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c88ec - End of configuration.
[testng] [2024-10-13 01:39:01,162] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] 01:39:01,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:39:01,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:01,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-13_01-39-01.log]
[testng] 01:39:01,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f33c897 - End of configuration.
[testng] [2024-10-13 01:39:01,367] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] 01:39:01,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:39:01,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:01,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-13_01-39-01.log]
[testng] 01:39:01,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2eaf4 - End of configuration.
[testng] [2024-10-13 01:39:01,455] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] 01:39:01,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:39:01,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:01,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-13_01-39-01.log]
[testng] 01:39:01,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4922ba - End of configuration.
[testng] [2024-10-13 01:39:01,539] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] 01:39:01,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:39:01,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:01,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-13_01-39-01.log]
[testng] 01:39:01,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration.
[testng] [2024-10-13 01:39:01,853] [pool-1-thread-6] Initializing /data/ome/embryo.lsm:
[testng] 01:39:01,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:39:01,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:01,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-13_01-39-01.log]
[testng] 01:39:01,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1a1e58 - End of configuration.
[testng] [2024-10-13 01:39:02,230] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 01:39:02,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:39:02,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:02,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-13_01-39-02.log]
[testng] 01:39:02,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5e1c72 - End of configuration.
[testng] [2024-10-13 01:39:02,838] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] 01:39:02,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:39:02,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:02,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-13_01-39-02.log]
[testng] 01:39:02,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8a5b823 - End of configuration.
[testng] [2024-10-13 01:39:02,951] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff:
[testng] 01:39:02,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:39:02,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:02,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-13_01-39-02.log]
[testng] 01:39:02,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25904576 - End of configuration.
[testng] [2024-10-13 01:39:03,809] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm:
[testng] 01:39:03,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:39:03,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:03,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-13_01-39-03.log]
[testng] 01:39:03,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6732c8bc - End of configuration.
[testng] [2024-10-13 01:39:07,531] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] [2024-10-13 01:39:07,628] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-10-13 01:39:07,860] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-10-13 01:39:08,364] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2024-10-13 01:39:08,869] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-10-13 01:39:09,421] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm:
[testng] [2024-10-13 01:39:10,068] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-10-13 01:39:10,142] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] [2024-10-13 01:39:11,000] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-10-13 01:39:11,132] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-10-13 01:39:11,897] [pool-1-thread-1] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-10-13 01:39:12,337] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-10-13 01:39:12,907] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d:
[testng] [2024-10-13 01:39:13,618] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-10-13 01:39:14,293] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-10-13 01:39:15,807] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-10-13 01:39:15,929] [pool-1-thread-8] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-10-13 01:39:16,428] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-10-13 01:39:16,555] [pool-1-thread-9] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-10-13 01:39:17,028] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-10-13 01:39:17,571] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-10-13 01:39:17,700] [pool-1-thread-6] Initializing /data/ome/C1.lsm:
[testng] [2024-10-13 01:39:18,276] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-10-13 01:39:20,146] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-10-13 01:39:21,001] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-10-13 01:39:21,356] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-10-13 01:39:21,520] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-10-13 01:39:21,780] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-10-13 01:39:21,916] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-10-13 01:39:23,482] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk:
[testng] [2024-10-13 01:39:24,589] [pool-1-thread-12] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-10-13 01:39:25,040] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-10-13 01:39:41,646] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-10-13 01:39:42,292] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-10-13 01:39:42,562] [pool-1-thread-10] Initializing /data/ome/worm.tiff:
[testng] [2024-10-13 01:39:45,928] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-10-13 01:39:46,114] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-10-13 01:39:47,562] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-10-13 01:39:50,423] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-10-13 01:39:51,893] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-10-13 01:39:52,430] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern:
[testng] [2024-10-13 01:40:04,447] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-10-13 01:40:05,463] [pool-1-thread-1] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-10-13 01:40:07,437] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-10-13 01:40:07,579] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] [2024-10-13 01:40:07,829] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-10-13 01:40:08,735] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 3127, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 5 minutes 17 seconds
Finished: SUCCESS