Started by upstream project "BIOFORMATS-test-repo" build number 23
originally caused by:
Started by upstream project "Trigger" build number 26
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/jenkins6818081096056280147.sh
+ '[' bmp = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_2785_merge_ci -v /uod/idr/repos/curated/bmp:/data -v /uod/idr-scratch/merge-ci/curated/bmp:/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] 01:23:49,565 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:23:49,567 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:23:49,567 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:23:49,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:23:49,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:23:49,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:23:49,570 |-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] 01:23:49,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:23:49,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:23:49,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:23:49,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:23:49,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:23:49,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:23:49,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:23:49,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:23:49,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:23:49,933 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:23:49,933 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:23:49,933 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:23:49,934 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:23:49,934 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:23:49,935 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:23:49,935 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 364 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-05 01:23:49,946] [main] java.version = 1.8.0_342
[testng] 01:23:49,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:23:49,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:50,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-05_01-23-49.log]
[testng] 01:23:50,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-04-05 01:23:50,031] [main] testng.directory = /data
[testng] [2024-04-05 01:23:50,031] [main] testng.configDirectory = /config
[testng] [2024-04-05 01:23:50,051] [main] testng.multiplier = 1.0
[testng] [2024-04-05 01:23:50,051] [main] testng.in-memory = false
[testng] [2024-04-05 01:23:50,051] [main] testng.allow-missing = false
[testng] [2024-04-05 01:23:50,051] [main] user.language = en
[testng] [2024-04-05 01:23:50,051] [main] user.country = ${user.country}
[testng] [2024-04-05 01:23:50,051] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-04-05 01:23:50,733] [main] ----------------------------------------
[testng] [2024-04-05 01:23:50,733] [main] Total files: 31
[testng] [2024-04-05 01:23:50,733] [main] Scan time: 0.682 s (22 ms/file)
[testng] [2024-04-05 01:23:50,733] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 31 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-05 01:23:52,548] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp:
[testng] 01:23:52,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:23:52,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-05_01-23-52.log]
[testng] 01:23:52,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c6260fa - End of configuration.
[testng] [2024-04-05 01:23:52,569] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Five.bmp:
[testng] 01:23:52,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:23:52,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-05_01-23-52.log]
[testng] 01:23:52,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d593f88 - End of configuration.
[testng] [2024-04-05 01:23:52,578] [pool-1-thread-11] Initializing /data/ticket-12971/foo.bmp:
[testng] 01:23:52,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:23:52,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-05_01-23-52.log]
[testng] 01:23:52,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e7d7029 - End of configuration.
[testng] [2024-04-05 01:23:52,585] [pool-1-thread-10] Initializing /data/brian/images/raw_a.bmp:
[testng] 01:23:52,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:23:52,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,587 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-05_01-23-52.log]
[testng] 01:23:52,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6866cf8 - End of configuration.
[testng] [2024-04-05 01:23:52,594] [pool-1-thread-9] Initializing /data/big-images/6kx6k.bmp:
[testng] 01:23:52,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:23:52,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-05_01-23-52.log]
[testng] 01:23:52,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14ec3f25 - End of configuration.
[testng] [2024-04-05 01:23:52,608] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp:
[testng] 01:23:52,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:23:52,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-05_01-23-52.log]
[testng] 01:23:52,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a06445c - End of configuration.
[testng] [2024-04-05 01:23:52,617] [pool-1-thread-7] Initializing /data/brian/images/23srp5dksub.bmp:
[testng] 01:23:52,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:23:52,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-05_01-23-52.log]
[testng] 01:23:52,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e2da187 - End of configuration.
[testng] [2024-04-05 01:23:52,630] [pool-1-thread-6] Initializing /data/curtis/image3.bmp:
[testng] 01:23:52,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:23:52,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-05_01-23-52.log]
[testng] 01:23:52,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4863c78e - End of configuration.
[testng] [2024-04-05 01:23:52,638] [pool-1-thread-5] Initializing /data/big-images/6kx6k-grey.bmp:
[testng] 01:23:52,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:23:52,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-05_01-23-52.log]
[testng] 01:23:52,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ad204f - End of configuration.
[testng] [2024-04-05 01:23:52,650] [pool-1-thread-4] Initializing /data/big-images/8kx8k.bmp:
[testng] 01:23:52,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:23:52,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-05_01-23-52.log]
[testng] 01:23:52,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178fa80e - End of configuration.
[testng] [2024-04-05 01:23:52,664] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_One.bmp:
[testng] 01:23:52,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:23:52,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-05_01-23-52.log]
[testng] 01:23:52,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79a1f79f - End of configuration.
[testng] [2024-04-05 01:23:52,674] [pool-1-thread-2] Initializing /data/curtis/image5.bmp:
[testng] 01:23:52,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:23:52,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:52,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-05_01-23-52.log]
[testng] 01:23:52,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18fd912e - End of configuration.
[testng] [2024-04-05 01:23:54,736] [pool-1-thread-2] Initializing /data/curtis/image1.bmp:
[testng] [2024-04-05 01:23:54,743] [pool-1-thread-8] Initializing /data/stephane/holo0908.bmp:
[testng] [2024-04-05 01:23:54,753] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Eight.bmp:
[testng] [2024-04-05 01:23:54,761] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Seven.bmp:
[testng] [2024-04-05 01:23:54,768] [pool-1-thread-10] Initializing /data/curtis/image2.bmp:
[testng] [2024-04-05 01:23:54,774] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Six.bmp:
[testng] [2024-04-05 01:23:54,781] [pool-1-thread-11] Initializing /data/big-images/8kx8k-grey.bmp:
[testng] [2024-04-05 01:23:54,794] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Three.bmp:
[testng] [2024-04-05 01:23:54,802] [pool-1-thread-1] Initializing /data/frank/cell_mask_error.bmp:
[testng] [2024-04-05 01:23:55,429] [pool-1-thread-2] Initializing /data/brian/images/raw_a_rg.tiff:
[testng] [2024-04-05 01:23:55,467] [pool-1-thread-10] Initializing /data/brian/images/DMSOHigh_001.bmp:
[testng] [2024-04-05 01:23:55,709] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Two.bmp:
[testng] [2024-04-05 01:23:55,773] [pool-1-thread-6] Initializing /data/brian/images/raw_a_rg.bmp:
[testng] [2024-04-05 01:23:55,779] [pool-1-thread-1] Initializing /data/curtis/image4.bmp:
[testng] [2024-04-05 01:23:55,787] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Four.bmp:
[testng] [2024-04-05 01:23:55,844] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Nine.bmp:
[testng] [2024-04-05 01:23:56,061] [pool-1-thread-1] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp:
[testng] [2024-04-05 01:23:56,183] [pool-1-thread-12] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp:
[testng] [2024-04-05 01:23:56,203] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1.bmp:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1643, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 30 seconds
Finished: SUCCESS