Started by upstream project "BIOFORMATS-test-repo" build number 234
originally caused by:
Started by upstream project "Trigger" build number 259
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins15148761529197452550.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_36722_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] 01:36:03,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:36:03,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 01:36:03,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:36:03,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:36:03,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:36:03,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:36:03,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:36:03,767 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:36:03,768 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:36:03,768 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:36:03,768 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:36:03,768 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 01:36:03,769 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 01:36:03,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 252 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-25 01:36:03,779] [main] java.version = 1.8.0_342
[testng] 01:36:03,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:36:03,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:03,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_01-36-03.log]
[testng] 01:36:03,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-10-25 01:36:03,829] [main] testng.directory = /data
[testng] [2024-10-25 01:36:03,829] [main] testng.configDirectory = /config
[testng] [2024-10-25 01:36:03,841] [main] testng.multiplier = 1.0
[testng] [2024-10-25 01:36:03,841] [main] testng.in-memory = false
[testng] [2024-10-25 01:36:03,841] [main] testng.allow-missing = false
[testng] [2024-10-25 01:36:03,841] [main] user.language = en
[testng] [2024-10-25 01:36:03,841] [main] user.country = ${user.country}
[testng] [2024-10-25 01:36:03,841] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-10-25 01:36:36,947] [main] ----------------------------------------
[testng] [2024-10-25 01:36:36,947] [main] Total files: 164
[testng] [2024-10-25 01:36:36,947] [main] Scan time: 33.106 s (201 ms/file)
[testng] [2024-10-25 01:36:36,948] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-25 01:37:11,311] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 01:37:11,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:37:11,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:11,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_01-37-11.log]
[testng] 01:37:11,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67f08917 - End of configuration.
[testng] [2024-10-25 01:37:11,617] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] 01:37:11,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:37:11,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:11,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_01-37-11.log]
[testng] 01:37:11,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e91729c - End of configuration.
[testng] [2024-10-25 01:37:11,724] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] 01:37:11,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:37:11,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:11,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_01-37-11.log]
[testng] 01:37:11,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@334f8613 - End of configuration.
[testng] [2024-10-25 01:37:12,126] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm:
[testng] 01:37:12,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:37:12,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:12,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_01-37-12.log]
[testng] 01:37:12,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7c78b0 - End of configuration.
[testng] [2024-10-25 01:37:12,520] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk:
[testng] 01:37:12,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:37:12,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:12,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_01-37-12.log]
[testng] 01:37:12,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a053e3c - End of configuration.
[testng] [2024-10-25 01:37:13,357] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] 01:37:13,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:37:13,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_01-37-13.log]
[testng] 01:37:13,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1952b94f - End of configuration.
[testng] [2024-10-25 01:37:13,404] [pool-1-thread-7] Initializing /data/ome/embryo.lsm:
[testng] 01:37:13,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:37:13,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_01-37-13.log]
[testng] 01:37:13,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4149fd68 - End of configuration.
[testng] [2024-10-25 01:37:13,607] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] 01:37:13,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:37:13,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_01-37-13.log]
[testng] 01:37:13,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eaa15ca - End of configuration.
[testng] [2024-10-25 01:37:13,643] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] 01:37:13,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:37:13,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_01-37-13.log]
[testng] 01:37:13,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fb6cba0 - End of configuration.
[testng] [2024-10-25 01:37:13,882] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] 01:37:13,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:37:13,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_01-37-13.log]
[testng] 01:37:13,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@343b3632 - End of configuration.
[testng] [2024-10-25 01:37:13,929] [pool-1-thread-3] Initializing /data/ome/worm.tiff:
[testng] 01:37:13,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:37:13,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_01-37-13.log]
[testng] 01:37:13,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3678757c - End of configuration.
[testng] [2024-10-25 01:37:14,390] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 01:37:14,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:37:14,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:14,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_01-37-14.log]
[testng] 01:37:14,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73304895 - End of configuration.
[testng] [2024-10-25 01:37:16,278] [pool-1-thread-6] Initializing /data/ome/C1.lsm:
[testng] [2024-10-25 01:37:16,924] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-10-25 01:37:16,979] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-10-25 01:37:17,012] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-10-25 01:37:17,136] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-10-25 01:37:17,161] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-10-25 01:37:17,307] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern:
[testng] [2024-10-25 01:37:20,213] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-10-25 01:37:20,661] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-10-25 01:37:21,178] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-10-25 01:37:21,522] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2024-10-25 01:37:22,508] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-10-25 01:37:22,544] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-10-25 01:37:22,607] [pool-1-thread-6] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-10-25 01:37:23,051] [pool-1-thread-9] Initializing /data/ome/cb_1.r3d:
[testng] [2024-10-25 01:37:23,178] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-10-25 01:37:23,345] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-10-25 01:37:23,658] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] [2024-10-25 01:37:23,987] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-10-25 01:37:24,320] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-10-25 01:37:24,604] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-10-25 01:37:24,690] [pool-1-thread-11] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-10-25 01:37:25,221] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-10-25 01:37:25,513] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-10-25 01:37:25,978] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-10-25 01:37:26,135] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-10-25 01:37:26,542] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-10-25 01:37:27,422] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-10-25 01:37:27,567] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-10-25 01:37:27,984] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-10-25 01:37:28,091] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-10-25 01:37:28,498] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-10-25 01:37:29,500] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-10-25 01:37:29,616] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-10-25 01:37:29,851] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-10-25 01:37:30,480] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-10-25 01:37:30,672] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-10-25 01:37:31,431] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-10-25 01:37:40,585] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-10-25 01:37:40,800] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-10-25 01:37:41,019] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-10-25 01:37:41,182] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-10-25 01:37:41,754] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-10-25 01:37:42,448] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-10-25 01:37:42,564] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-10-25 01:37:43,291] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-10-25 01:37:43,678] [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: 3 minutes 1 second
Finished: SUCCESS