Started by upstream project "BIOFORMATS-test-repo" build number 365
originally caused by:
Started by upstream project "Trigger" build number 391
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/jenkins8603526046904388453.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58158_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] 00:32:45,493 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 00:32:45,494 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service.
[testng] 00:32:45,494 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:32:45,495 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:32:45,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:32:45,497 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:32:45,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:32:45,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:32:45,498 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:32:45,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:32:45,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:32:45,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:32:45,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:32:45,690 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:32:45,690 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:32:45,690 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:32:45,691 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:32:45,691 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration.
[testng] 00:32:45,692 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point
[testng] 00:32:45,692 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-05 00:32:45,701] [main] java.version = 17.0.2
[testng] 00:32:45,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:32:45,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:32:45,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_00-32-45.log]
[testng] 00:32:45,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration.
[testng] [2025-03-05 00:32:45,748] [main] testng.directory = /data
[testng] [2025-03-05 00:32:45,748] [main] testng.configDirectory = /config
[testng] [2025-03-05 00:32:45,757] [main] testng.multiplier = 1.0
[testng] [2025-03-05 00:32:45,757] [main] testng.in-memory = false
[testng] [2025-03-05 00:32:45,758] [main] testng.allow-missing = false
[testng] [2025-03-05 00:32:45,758] [main] user.language = en
[testng] [2025-03-05 00:32:45,758] [main] user.country = ${user.country}
[testng] [2025-03-05 00:32:45,758] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-05 00:33:28,578] [main] ----------------------------------------
[testng] [2025-03-05 00:33:28,578] [main] Total files: 164
[testng] [2025-03-05 00:33:28,579] [main] Scan time: 42.82 s (261 ms/file)
[testng] [2025-03-05 00:33:28,579] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-05 00:34:13,261] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD:
[testng] 00:34:13,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:34:13,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:13,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_00-34-13.log]
[testng] 00:34:13,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460b4533 - End of configuration.
[testng] [2025-03-05 00:34:14,054] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] 00:34:14,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:34:14,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:14,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_00-34-14.log]
[testng] 00:34:14,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a5b45 - End of configuration.
[testng] [2025-03-05 00:34:14,101] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv:
[testng] 00:34:14,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:34:14,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:14,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_00-34-14.log]
[testng] 00:34:14,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c1bf6dd - End of configuration.
[testng] [2025-03-05 00:34:14,199] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern:
[testng] 00:34:14,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:34:14,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:14,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_00-34-14.log]
[testng] 00:34:14,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f4cc7aa - End of configuration.
[testng] [2025-03-05 00:34:17,625] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm:
[testng] 00:34:17,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:34:17,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:17,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_00-34-17.log]
[testng] 00:34:17,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1c8076 - End of configuration.
[testng] [2025-03-05 00:34:17,694] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv:
[testng] 00:34:17,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:34:17,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:17,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_00-34-17.log]
[testng] 00:34:17,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e10020f - End of configuration.
[testng] [2025-03-05 00:34:17,841] [pool-1-thread-7] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] 00:34:17,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:34:17,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:17,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_00-34-17.log]
[testng] 00:34:17,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39b57268 - End of configuration.
[testng] [2025-03-05 00:34:18,924] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] 00:34:18,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:34:18,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:18,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_00-34-18.log]
[testng] 00:34:18,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60240f0b - End of configuration.
[testng] [2025-03-05 00:34:19,392] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] 00:34:19,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:34:19,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:19,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_00-34-19.log]
[testng] 00:34:19,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6703580a - End of configuration.
[testng] [2025-03-05 00:34:19,473] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 00:34:19,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:34:19,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:19,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_00-34-19.log]
[testng] 00:34:19,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55b7c62c - End of configuration.
[testng] [2025-03-05 00:34:20,263] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] 00:34:20,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:34:20,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:20,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_00-34-20.log]
[testng] 00:34:20,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166a90ed - End of configuration.
[testng] [2025-03-05 00:34:21,315] [pool-1-thread-2] Initializing /data/ome/worm.tiff:
[testng] 00:34:21,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:34:21,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:21,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_00-34-21.log]
[testng] 00:34:21,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration.
[testng] [2025-03-05 00:34:24,325] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2025-03-05 00:34:24,879] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2025-03-05 00:34:24,969] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp:
[testng] [2025-03-05 00:34:25,042] [pool-1-thread-11] Initializing /data/ome/tiffany.color.tiff:
[testng] [2025-03-05 00:34:26,420] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2025-03-05 00:34:27,603] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2025-03-05 00:34:27,773] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2025-03-05 00:34:28,827] [pool-1-thread-12] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2025-03-05 00:34:29,731] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2025-03-05 00:34:30,127] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2025-03-05 00:34:31,301] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2025-03-05 00:34:31,579] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2:
[testng] [2025-03-05 00:34:32,069] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] [2025-03-05 00:34:32,173] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2025-03-05 00:34:32,734] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] [2025-03-05 00:34:33,855] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2025-03-05 00:34:33,996] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] [2025-03-05 00:34:34,481] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2025-03-05 00:34:34,593] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2025-03-05 00:34:35,428] [pool-1-thread-4] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2025-03-05 00:34:35,899] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2025-03-05 00:34:36,864] [pool-1-thread-5] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2025-03-05 00:34:37,192] [pool-1-thread-11] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2025-03-05 00:34:38,068] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2025-03-05 00:34:38,665] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern:
[testng] [2025-03-05 00:34:57,691] [pool-1-thread-7] Initializing /data/ome/Adultmidsection.lsm:
[testng] [2025-03-05 00:34:58,033] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2025-03-05 00:34:58,320] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] [2025-03-05 00:34:58,480] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] [2025-03-05 00:34:58,967] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2025-03-05 00:34:59,576] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2025-03-05 00:35:00,602] [pool-1-thread-3] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2025-03-05 00:35:01,013] [pool-1-thread-9] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] [2025-03-05 00:35:01,547] [pool-1-thread-7] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2025-03-05 00:35:01,877] [pool-1-thread-5] Initializing /data/ome/embryo.lsm:
[testng] [2025-03-05 00:35:02,435] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2025-03-05 00:35:03,587] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2025-03-05 00:35:04,240] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2025-03-05 00:35:04,572] [pool-1-thread-4] Initializing /data/ome/C1.lsm:
[testng] [2025-03-05 00:35:05,650] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2025-03-05 00:35:06,180] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2025-03-05 00:35:06,999] [pool-1-thread-7] Initializing /data/ome/654Atemp.stk:
[testng] [2025-03-05 00:35:08,169] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d:
[testng] [2025-03-05 00:35:08,397] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2025-03-05 00:35:08,597] [pool-1-thread-9] Initializing /data/openjpeg/Facade.pnm:
[testng] [2025-03-05 00:35:09,199] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2025-03-05 00:35:10,538] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 3127, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 3 minutes 54 seconds
Finished: SUCCESS