Started by upstream project "BIOFORMATS-test-repo" build number 294
originally caused by:
Started by upstream project "Trigger" build number 313
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins16873872036787039248.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_46437_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] 00:54:02,918 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:54:02,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 00:54:02,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:54:02,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:54:02,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:54:02,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:54:02,921 |-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] 00:54:02,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:54:02,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:54:02,922 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:54:02,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:54:02,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:54:03,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:54:03,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:54:03,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:54:03,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:54:03,115 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:54:03,116 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:54:03,116 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:54:03,116 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:54:03,116 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 00:54:03,117 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 00:54:03,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-18 00:54:03,126] [main] java.version = 17.0.2
[testng] 00:54:03,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:54:03,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:03,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_00-54-03.log]
[testng] 00:54:03,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-18 00:54:03,176] [main] testng.directory = /data
[testng] [2024-12-18 00:54:03,176] [main] testng.configDirectory = /config
[testng] [2024-12-18 00:54:03,185] [main] testng.multiplier = 1.0
[testng] [2024-12-18 00:54:03,186] [main] testng.in-memory = false
[testng] [2024-12-18 00:54:03,186] [main] testng.allow-missing = false
[testng] [2024-12-18 00:54:03,186] [main] user.language = en
[testng] [2024-12-18 00:54:03,186] [main] user.country = ${user.country}
[testng] [2024-12-18 00:54:03,186] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-18 00:55:47,766] [main] ----------------------------------------
[testng] [2024-12-18 00:55:47,766] [main] Total files: 164
[testng] [2024-12-18 00:55:47,767] [main] Scan time: 104.58 s (637 ms/file)
[testng] [2024-12-18 00:55:47,767] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-18 00:58:55,944] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm:
[testng] 00:58:55,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:58:55,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:55,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_00-58-55.log]
[testng] 00:58:55,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28d720b6 - End of configuration.
[testng] [2024-12-18 00:58:56,879] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm:
[testng] 00:58:56,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:58:56,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:56,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_00-58-56.log]
[testng] 00:58:56,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e6c1b29 - End of configuration.
[testng] [2024-12-18 00:58:57,636] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm:
[testng] 00:58:57,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:58:57,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:57,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_00-58-57.log]
[testng] 00:58:57,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54249d81 - End of configuration.
[testng] [2024-12-18 00:58:58,729] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] 00:58:58,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:58:58,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:58,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_00-58-58.log]
[testng] 00:58:58,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7940257c - End of configuration.
[testng] [2024-12-18 00:58:58,938] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] 00:58:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:58:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:58,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_00-58-58.log]
[testng] 00:58:58,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40dfd862 - End of configuration.
[testng] [2024-12-18 00:58:59,058] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] 00:58:59,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:58:59,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:59,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_00-58-59.log]
[testng] 00:58:59,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1970e753 - End of configuration.
[testng] [2024-12-18 00:58:59,165] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] 00:58:59,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:58:59,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:58:59,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_00-58-59.log]
[testng] 00:58:59,169 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45014310 - End of configuration.
[testng] [2024-12-18 00:59:01,511] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] 00:59:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:59:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:59:01,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_00-59-01.log]
[testng] 00:59:01,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68dcba6d - End of configuration.
[testng] [2024-12-18 00:59:02,302] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] 00:59:02,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:59:02,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:59:02,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_00-59-02.log]
[testng] 00:59:02,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4744ae1b - End of configuration.
[testng] [2024-12-18 00:59:04,033] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern:
[testng] 00:59:04,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:59:04,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:59:04,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_00-59-04.log]
[testng] 00:59:04,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4df0432c - End of configuration.
[testng] [2024-12-18 00:59:14,745] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] 00:59:14,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:59:14,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:59:14,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_00-59-14.log]
[testng] 00:59:14,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ac1715e - End of configuration.
[testng] [2024-12-18 00:59:16,031] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] 00:59:16,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:59:16,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:59:16,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_00-59-16.log]
[testng] 00:59:16,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f24812e - End of configuration.
[testng] [2024-12-18 00:59:21,373] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-12-18 00:59:22,057] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-12-18 00:59:22,778] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-12-18 00:59:25,039] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2024-12-18 00:59:26,771] [pool-1-thread-2] Initializing /data/ome/embryo.lsm:
[testng] [2024-12-18 00:59:27,969] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-12-18 00:59:28,366] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-12-18 00:59:29,274] [pool-1-thread-12] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-12-18 00:59:32,340] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] [2024-12-18 00:59:32,965] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-12-18 00:59:34,576] [pool-1-thread-3] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-12-18 00:59:34,835] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-12-18 00:59:37,257] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] [2024-12-18 00:59:39,825] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-12-18 00:59:43,580] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-12-18 00:59:44,450] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-12-18 00:59:44,712] [pool-1-thread-5] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-12-18 00:59:44,878] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-12-18 00:59:46,963] [pool-1-thread-2] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-12-18 00:59:47,518] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-12-18 00:59:48,979] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-12-18 00:59:51,912] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-12-18 00:59:54,087] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] [2024-12-18 00:59:54,545] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-12-18 00:59:55,046] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-12-18 00:59:55,930] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d:
[testng] [2024-12-18 00:59:56,473] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-12-18 00:59:58,974] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-12-18 01:00:01,041] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] [2024-12-18 01:00:01,587] [pool-1-thread-11] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-12-18 01:00:01,784] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-12-18 01:00:02,630] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-12-18 01:00:50,612] [pool-1-thread-1] Initializing /data/ome/C1.lsm:
[testng] [2024-12-18 01:00:54,935] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-12-18 01:00:59,133] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-12-18 01:00:59,504] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] [2024-12-18 01:01:01,217] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2024-12-18 01:01:01,427] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-12-18 01:01:06,757] [pool-1-thread-12] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-12-18 01:01:09,006] [pool-1-thread-6] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-12-18 01:01:11,276] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-12-18 01:01:12,571] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk:
[testng] [2024-12-18 01:01:16,138] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-12-18 01:01:17,395] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-12-18 01:01:17,667] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-12-18 01:01:19,665] [pool-1-thread-7] Initializing /data/ome/worm.tiff:
[testng] [2024-12-18 01:01:22,856] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 3127, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 11 minutes 31 seconds
Finished: SUCCESS