Source: jalview Version: 2.11.2.5+dfsg-2 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230203 ftbfs-bookworm
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > # Placing pom.xml at root, with a hack to put the package version number > # inside the pom. > sed 's/\(VERSION_PACKAGE\)/\12.11.2.5+dfsg/; > s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/pom.xml > pom.xml > # Putting the jars needed for the build in cpJars to avoid exposing the whole > # /usr/share/java contents in the build classpath. > mkdir cpJars > for F in /usr/share/java/apache-mime4j-core.jar /usr/share/java/axis.jar > /usr/share/java/axis-jaxrpc.jar /usr/share/java/biojava6-ontology.jar > /usr/share/java/commons-discovery.jar /usr/share/java/groovy-all.jar > /usr/share/java/htsjdk.jar /usr/share/java/httpclient.jar > /usr/share/java/httpcore.jar /usr/share/java/httpmime.jar > /usr/share/java/intervalstorej.jar /usr/share/java/jaxb-api.jar > /usr/share/java/jaxrs-api.jar /usr/share/java/jersey1-client.jar > /usr/share/java/jersey1-core.jar /usr/share/java/jetty9-util.jar > /usr/share/java/jetty9-server.jar /usr/share/java/jh.jar > /usr/share/java/Jmol.jar /usr/share/java/jsearch-indexer.jar > /usr/share/java/json.jar /usr/share/java/json-simple.jar > /usr/share/java/jsoup.jar /usr/share/java/jswingreader.jar > /usr/share/java/log4j-1.2.jar /usr/share/java/log4j-api.jar > /usr/share/java/log4j-core.jar /usr/share/java/miglayout.jar > /usr/share/java/min-jaba-client.jar /usr/share/java/org.jfree.svg.jar > /usr/share/java/slf4j-api.jar /usr/share/java/vamsas-client.jar > /usr/share/java/varna.jar; do \ > cp $F cpJars; \ > done > cp: cannot stat '/usr/share/java/log4j-api.jar': No such file or directory > cp: cannot stat '/usr/share/java/log4j-core.jar': No such file or directory > dh_auto_configure > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > jh_linkjars > dh_auto_build > mkdir -p .gradle/init.d > cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ > gradle --info --console plain --offline --stacktrace --no-daemon > --refresh-dependencies --gradle-user-home .gradle -Duser.home=. > -Duser.name=debian -Ddebian.package=jalview -Dfile.encoding=UTF-8 --parallel > --max-workers=8 jar > openjdk version "17.0.6" 2023-01-17 > OpenJDK Runtime Environment (build 17.0.6+10-Debian-1) > OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing) > Initialized native services in: /<<PKGBUILDDIR>>/.gradle/native > To honour the JVM settings for this build a new JVM will be forked. Please > consider using the daemon: > https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. > Starting process 'Gradle build daemon'. Working directory: > /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1 Command: > /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens > java.base/java.lang=ALL-UNNAMED > -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar > -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp > /usr/share/gradle/lib/gradle-launcher-4.4.1.jar > org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 > Successfully started process 'Gradle build daemon' > An attempt to start the daemon took 0.66 secs. > The client will now receive all logging from the daemon (pid: 1852595). The > daemon log file: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1/daemon-1852595.out.log > Daemon will be stopped at the end of the build stopping after processing > Closing daemon's stdin at end of input. > The daemon will no longer process any standard input. > Using 8 worker leases. > Creating new cache for fileHashes, path > /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access > org.gradle.cache.internal.DefaultCacheAccess@25134dd1 > Creating new cache for resourceHashesCache, path > /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, > access org.gradle.cache.internal.DefaultCacheAccess@25134dd1 > Creating new cache for fileHashes, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access > org.gradle.cache.internal.DefaultCacheAccess@2e01a468 > Starting Build > Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle' > using SubsetScriptTransformer. > Creating new cache for metadata-1.1/results, path > /<<PKGBUILDDIR>>/.gradle/caches/transforms-1/metadata-1.1/results.bin, access > org.gradle.cache.internal.DefaultCacheAccess@7ece68ce > Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle' > using BuildScriptTransformer. > Compiling settings file '/<<PKGBUILDDIR>>/settings.gradle' using > SubsetScriptTransformer. > Compiling settings file '/<<PKGBUILDDIR>>/settings.gradle' using > BuildScriptTransformer. > Settings evaluated using settings file '/<<PKGBUILDDIR>>/settings.gradle'. > Projects loaded. Root project using build file > '/<<PKGBUILDDIR>>/build.gradle'. > Included projects: [root project 'jalview'] > Keep-alive timer started > Adding Debian repository to project 'jalview' > Parallel execution is an incubating feature. > Evaluating root project 'jalview' using build file > '/<<PKGBUILDDIR>>/build.gradle'. > Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using > SubsetScriptTransformer. > Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using > BuildScriptTransformer. > Using properties from file > './utils/channels/default/channel_gradle.properties' > JALVIEW_VERSION is set to '2.11.2.5' > J2S ENABLED > file or directory '/<<PKGBUILDDIR>>/build/resources/doc_build', not found > file or directory '/<<PKGBUILDDIR>>/classes', not found > file or directory '/<<PKGBUILDDIR>>/utils/jalviewjs/classlists', not found > Adding Maven pom generation to project 'jalview' > Linking the generated javadoc to the system JDK API documentation > All projects evaluated. > Selected primary task 'jar' from project : > Creating new cache for annotation-processors, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/fileContent/annotation-processors.bin, access > org.gradle.cache.internal.DefaultCacheAccess@710c18d2 > Tasks to be executed: [task ':copyHelp', task ':buildIndices', task > ':copyResources', task ':copyChannelResources', task > ':createBuildProperties', task ':buildResources', task ':copyDocs', task > ':convertMdFiles', task ':releasesTemplates', task ':prepare', task > ':compileJava', task ':processResources', task ':classes', task > ':debianMavenPom', task ':jar'] > Creating new cache for resourceHashesCache, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access > org.gradle.cache.internal.DefaultCacheAccess@2e01a468 > Creating new cache for taskHistory, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access > org.gradle.cache.internal.DefaultCacheAccess@74a226fd > Creating new cache for outputFiles, path > /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access > org.gradle.cache.internal.DefaultCacheAccess@7c1a3349 > :copyHelp (Thread[Task worker for ':',5,main]) started. > :copyHelp > Putting task artifact state for task ':copyHelp' into context took 0.0 secs. > Up-to-date check for task ':copyHelp' took 0.098 secs. It is not up-to-date > because: > No history is available. > :copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.544 secs. > :buildIndices (Thread[Task worker for ':',5,main]) started. > :buildIndices > Putting task artifact state for task ':buildIndices' into context took 0.0 > secs. > Up-to-date check for task ':buildIndices' took 0.09 secs. It is not > up-to-date because: > No history is available. > Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java''. > Working directory: /<<PKGBUILDDIR>>/build/resources/help_build/help Command: > /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 > -Duser.country -Duser.language=en -Duser.variant -cp > /<<PKGBUILDDIR>>/classes:/<<PKGBUILDDIR>>/cpJars/jetty9-util.jar:/<<PKGBUILDDIR>>/cpJars/httpmime.jar:/<<PKGBUILDDIR>>/cpJars/org.jfree.svg.jar:/<<PKGBUILDDIR>>/cpJars/jswingreader.jar:/<<PKGBUILDDIR>>/cpJars/log4j-1.2.jar:/<<PKGBUILDDIR>>/cpJars/json.jar:/<<PKGBUILDDIR>>/cpJars/intervalstorej.jar:/<<PKGBUILDDIR>>/cpJars/jetty9-server.jar:/<<PKGBUILDDIR>>/cpJars/httpclient.jar:/<<PKGBUILDDIR>>/cpJars/biojava6-ontology.jar:/<<PKGBUILDDIR>>/cpJars/jaxb-api.jar:/<<PKGBUILDDIR>>/cpJars/vamsas-client.jar:/<<PKGBUILDDIR>>/cpJars/jaxrs-api.jar:/<<PKGBUILDDIR>>/cpJars/varna.jar:/<<PKGBUILDDIR>>/cpJars/axis.jar:/<<PKGBUILDDIR>>/cpJars/jersey1-client.jar:/<<PKGBUILDDIR>>/cpJars/jersey1-core.jar:/<<PKGBUILDDIR>>/cpJars/slf4j-api.jar:/<<PKGBUILDDIR>>/cpJars/json-simple.jar:/<<PKGBUILDDIR>>/cpJars/groovy-all.jar:/<<PKGBUILDDIR>>/cpJars/commons-discovery.jar:/<<PKGBUILDDIR>>/cpJars/miglayout.jar:/<<PKGBUILDDIR>>/cpJars/Jmol.jar:/<<PKGBUILDDIR>>/cpJars/apache-mime4j-core.jar:/<<PKGBUILDDIR>>/cpJars/jsoup.jar:/<<PKGBUILDDIR>>/cpJars/axis-jaxrpc.jar:/<<PKGBUILDDIR>>/cpJars/min-jaba-client.jar:/<<PKGBUILDDIR>>/cpJars/jh.jar:/<<PKGBUILDDIR>>/cpJars/jsearch-indexer.jar:/<<PKGBUILDDIR>>/cpJars/htsjdk.jar:/<<PKGBUILDDIR>>/cpJars/httpcore.jar > com.sun.java.help.search.Indexer html > Successfully started process 'command > '/usr/lib/jvm/java-17-openjdk-amd64/bin/java'' > :buildIndices (Thread[Task worker for ':',5,main]) completed. Took 0.781 secs. > :copyResources (Thread[Task worker for ':',5,main]) started. > :copyResources > Putting task artifact state for task ':copyResources' into context took 0.0 > secs. > Up-to-date check for task ':copyResources' took 0.02 secs. It is not > up-to-date because: > No history is available. > :copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.061 > secs. > :copyChannelResources (Thread[Task worker for ':' Thread 7,5,main]) started. > :copyChannelResources > Putting task artifact state for task ':copyChannelResources' into context > took 0.0 secs. > Up-to-date check for task ':copyChannelResources' took 0.004 secs. It is not > up-to-date because: > No history is available. > :copyChannelResources (Thread[Task worker for ':' Thread 7,5,main]) > completed. Took 0.019 secs. > :createBuildProperties (Thread[Task worker for ':' Thread 2,5,main]) started. > :createBuildProperties > Putting task artifact state for task ':createBuildProperties' into context > took 0.0 secs. > Up-to-date check for task ':createBuildProperties' took 0.0 secs. It is not > up-to-date because: > Task has not declared any outputs. > Starting process 'command 'sh''. Working directory: /<<PKGBUILDDIR>> Command: > sh debian/write_build_properties_file.sh > Successfully started process 'command 'sh'' > :createBuildProperties (Thread[Task worker for ':' Thread 2,5,main]) > completed. Took 0.118 secs. > :buildResources (Thread[Task worker for ':' Thread 2,5,main]) started. > :buildResources > Skipping task ':buildResources' as it has no actions. > :buildResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took > 0.0 secs. > :copyDocs (Thread[Task worker for ':' Thread 2,5,main]) started. > :copyDocs > Putting task artifact state for task ':copyDocs' into context took 0.0 secs. > Up-to-date check for task ':copyDocs' took 0.009 secs. It is not up-to-date > because: > No history is available. > :copyDocs (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.053 > secs. > :convertMdFiles (Thread[Daemon worker,5,main]) started. > :convertMdFiles > Putting task artifact state for task ':convertMdFiles' into context took 0.0 > secs. > Up-to-date check for task ':convertMdFiles' took 0.001 secs. It is not > up-to-date because: > No history is available. > :convertMdFiles (Thread[Daemon worker,5,main]) completed. Took 0.002 secs. > :releasesTemplates (Thread[Daemon worker,5,main]) started. > :releasesTemplates > Skipping task ':releasesTemplates' as it has no actions. > :releasesTemplates (Thread[Daemon worker,5,main]) completed. Took 0.0 secs. > :prepare (Thread[Daemon worker,5,main]) started. > :prepare > Skipping task ':prepare' as it has no actions. > :prepare (Thread[Daemon worker,5,main]) completed. Took 0.0 secs. > :compileJava (Thread[Daemon worker,5,main]) started. > :compileJava > Putting task artifact state for task ':compileJava' into context took 0.0 > secs. > file or directory '/<<PKGBUILDDIR>>/src/main/java', not found > file or directory '/<<PKGBUILDDIR>>/src/main/java', not found > Up-to-date check for task ':compileJava' took 0.521 secs. It is not > up-to-date because: > No history is available. > Setting target compatibility to 11 > All input files are considered out-of-date for incremental task > ':compileJava'. > file or directory '/<<PKGBUILDDIR>>/src/main/java', not found > Compiling with JDK Java compiler API. > /<<PKGBUILDDIR>>/src/jalview/log/JLoggerLog4j.java:23: error: package > org.apache.logging.log4j does not exist > import org.apache.logging.log4j.Logger; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JLoggerLog4j.java:24: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.Appender; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JLoggerLog4j.java:31: error: cannot find > symbol > private Logger logger = null; > ^ > symbol: class Logger > location: class JLoggerLog4j > /<<PKGBUILDDIR>>/src/jalview/log/JLoggerLog4j.java:147: error: cannot find > symbol > private Logger getLoggerObject() > ^ > symbol: class Logger > location: class JLoggerLog4j > /<<PKGBUILDDIR>>/src/jalview/log/JLoggerLog4j.java:153: error: cannot find > symbol > Appender appender) > ^ > symbol: class Appender > location: class JLoggerLog4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:25: error: package > org.apache.logging.log4j does not exist > import org.apache.logging.log4j.Level; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:26: error: package > org.apache.logging.log4j does not exist > import org.apache.logging.log4j.LogManager; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:27: error: package > org.apache.logging.log4j does not exist > import org.apache.logging.log4j.Logger; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:28: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.Appender; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:29: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.Filter; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:30: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.Layout; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:31: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.LoggerContext; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:32: error: package > org.apache.logging.log4j.core.appender does not exist > import org.apache.logging.log4j.core.appender.ConsoleAppender; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:33: error: package > org.apache.logging.log4j.core.config does not exist > import org.apache.logging.log4j.core.config.Configuration; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:34: error: package > org.apache.logging.log4j.core.config does not exist > import org.apache.logging.log4j.core.config.ConfigurationFactory; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:35: error: package > org.apache.logging.log4j.core.config does not exist > import org.apache.logging.log4j.core.config.Configurator; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:36: error: package > org.apache.logging.log4j.core.config does not exist > import org.apache.logging.log4j.core.config.LoggerConfig; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:37: error: package > org.apache.logging.log4j.core.config.builder.api does not exist > import > org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:38: error: package > org.apache.logging.log4j.core.config.builder.api does not exist > import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:39: error: package > org.apache.logging.log4j.core.config.builder.api does not exist > import > org.apache.logging.log4j.core.config.builder.api.FilterComponentBuilder; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:40: error: package > org.apache.logging.log4j.core.config.builder.api does not exist > import > org.apache.logging.log4j.core.config.builder.api.LayoutComponentBuilder; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:41: error: package > org.apache.logging.log4j.core.config.builder.impl does not exist > import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:42: error: package > org.apache.logging.log4j.core.filter does not exist > import org.apache.logging.log4j.core.filter.ThresholdFilter; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:43: error: package > org.apache.logging.log4j.core.layout does not exist > import org.apache.logging.log4j.core.layout.PatternLayout; > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:60: error: cannot find symbol > public static Level log4jLevel(JLogger.LogLevel loglevel) > ^ > symbol: class Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:70: error: cannot find symbol > public static void init(Level myLevel) > ^ > symbol: class Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:104: error: cannot find symbol > public static Logger getLogger(String name) > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:109: error: cannot find symbol > public static Logger getLogger(String name, JLogger.LogLevel loglevel) > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:114: error: cannot find symbol > public static Logger getLogger(String name, Level level) > ^ > symbol: class Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:114: error: cannot find symbol > public static Logger getLogger(String name, Level level) > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:121: error: cannot find symbol > public static ConfigurationBuilder<BuiltConfiguration> > getConfigurationBuilder() > ^ > symbol: class ConfigurationBuilder > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:121: error: cannot find symbol > public static ConfigurationBuilder<BuiltConfiguration> > getConfigurationBuilder() > ^ > symbol: class BuiltConfiguration > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:126: error: cannot find symbol > public static Layout getSimpleLayout() > ^ > symbol: class Layout > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:131: error: cannot find symbol > public static LayoutComponentBuilder getSimpleLayoutBuilder() > ^ > symbol: class LayoutComponentBuilder > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:137: error: cannot find symbol > public static Filter getThresholdFilter(Level level) > ^ > symbol: class Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:137: error: cannot find symbol > public static Filter getThresholdFilter(Level level) > ^ > symbol: class Filter > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:143: error: cannot find symbol > public static FilterComponentBuilder getThresholdFilterBuilder() > ^ > symbol: class FilterComponentBuilder > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:149: error: cannot find symbol > public static void setLevel(Logger logger, JLogger.LogLevel loglevel) > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:154: error: cannot find symbol > public static void setLevel(Logger logger, Level level) > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:154: error: cannot find symbol > public static void setLevel(Logger logger, Level level) > ^ > symbol: class Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:176: error: cannot find symbol > public static void setRootLevel(Level level) > ^ > symbol: class Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:181: error: cannot find symbol > public static Appender getAppender(String name) > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:189: error: cannot find symbol > public static void addAppender(Logger logger, Logger logger2, > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:189: error: cannot find symbol > public static void addAppender(Logger logger, Logger logger2, > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:202: error: cannot find symbol > public static void addAppender(Logger logger, Appender appender) > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:202: error: cannot find symbol > public static void addAppender(Logger logger, Appender appender) > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:220: error: cannot find symbol > public static void addAppenderToRootLogger(Appender appender) > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:29: error: package > org.apache.logging.log4j does not exist > import org.apache.logging.log4j.Level; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:30: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.Filter; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:31: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.Layout; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:32: error: package > org.apache.logging.log4j.core does not exist > import org.apache.logging.log4j.core.LogEvent; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:33: error: package > org.apache.logging.log4j.core.appender does not exist > import org.apache.logging.log4j.core.appender.AbstractAppender; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:34: error: package > org.apache.logging.log4j.core.config does not exist > import org.apache.logging.log4j.core.config.Property; > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:43: error: cannot find > symbol > public class JalviewAppender extends AbstractAppender > ^ > symbol: class AbstractAppender > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:60: error: cannot find > symbol > protected JalviewAppender(String name, Filter filter, > ^ > symbol: class Filter > location: class JalviewAppender > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:61: error: cannot find > symbol > Layout<? extends Serializable> layout, boolean ignoreExceptions, > ^ > symbol: class Layout > location: class JalviewAppender > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:62: error: cannot find > symbol > Property[] properties) > ^ > symbol: class Property > location: class JalviewAppender > /<<PKGBUILDDIR>>/src/jalview/log/JalviewAppender.java:79: error: cannot find > symbol > public void append(LogEvent logEvent) > ^ > symbol: class LogEvent > location: class JalviewAppender > /<<PKGBUILDDIR>>/src/mc_view/Atom.java:86: warning: [removal] Float(String) > in Float has been deprecated and marked for removal > this.x = (new Float(str.substring(30, 38).trim()).floatValue()); > ^ > /<<PKGBUILDDIR>>/src/mc_view/Atom.java:87: warning: [removal] Float(String) > in Float has been deprecated and marked for removal > this.y = (new Float(str.substring(38, 46).trim()).floatValue()); > ^ > /<<PKGBUILDDIR>>/src/mc_view/Atom.java:88: warning: [removal] Float(String) > in Float has been deprecated and marked for removal > this.z = (new Float(str.substring(47, 55).trim()).floatValue()); > ^ > /<<PKGBUILDDIR>>/src/mc_view/Atom.java:93: warning: [removal] Float(String) > in Float has been deprecated and marked for removal > occupancy = (new Float(tm)).floatValue(); > ^ > /<<PKGBUILDDIR>>/src/mc_view/Atom.java:103: warning: [removal] Float(String) > in Float has been deprecated and marked for removal > tfactor = (new Float(tm).floatValue()); > ^ > /<<PKGBUILDDIR>>/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: > warning: [synchronization] attempt to synchronize on an instance of a > value-based class > synchronized (firing) > ^ > /<<PKGBUILDDIR>>/src/jalview/gui/Console.java:513: error: cannot find symbol > jappender.start(); > ^ > symbol: method start() > location: variable jappender of type JalviewAppender > /<<PKGBUILDDIR>>/src/jalview/gui/FeatureEditor.java:313: warning: [removal] > Integer(int) in Integer has been deprecated and marked for removal > start.setValue(new Integer(sf.getBegin())); > ^ > /<<PKGBUILDDIR>>/src/jalview/gui/FeatureEditor.java:314: warning: [removal] > Integer(int) in Integer has been deprecated and marked for removal > end.setValue(new Integer(sf.getEnd())); > ^ > /<<PKGBUILDDIR>>/src/jalview/gui/FeatureEditor.java:402: warning: [removal] > Integer(int) in Integer has been deprecated and marked for removal > start.setValue(new Integer(firstFeature.getBegin())); > ^ > /<<PKGBUILDDIR>>/src/jalview/gui/FeatureEditor.java:403: warning: [removal] > Integer(int) in Integer has been deprecated and marked for removal > end.setValue(new Integer(firstFeature.getEnd())); > ^ > /<<PKGBUILDDIR>>/src/jalview/log/JLoggerLog4j.java:66: error: reference to > getLogger is ambiguous > this.logger = Log4j.isInit() ? Log4j.getLogger(this.name, this.level) > ^ > both method getLogger(String,LogLevel) in Log4j and method > getLogger(String,Level) in Log4j match > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:62: error: cannot find symbol > return Level.toLevel(loglevel.toString()); > ^ > symbol: variable Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:77: error: cannot find symbol > ConfigurationBuilder<BuiltConfiguration> configBuilder = Log4j > ^ > symbol: class ConfigurationBuilder > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:77: error: cannot find symbol > ConfigurationBuilder<BuiltConfiguration> configBuilder = Log4j > ^ > symbol: class BuiltConfiguration > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:80: error: cannot find symbol > configBuilder.setStatusLevel(Level.WARN); > ^ > symbol: variable Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:83: error: cannot find symbol > AppenderComponentBuilder appenderBuilder = configBuilder > ^ > symbol: class AppenderComponentBuilder > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:86: error: package > ConsoleAppender does not exist > ConsoleAppender.Target.SYSTEM_ERR); > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:94: error: cannot find symbol > Configurator.initialize(configBuilder.build()); > ^ > symbol: variable Configurator > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:106: error: cannot find symbol > return getLogger(name, Level.INFO); > ^ > symbol: variable Level > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:116: error: cannot find symbol > Logger logger = LogManager.getLogger(name); > ^ > symbol: class Logger > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:116: error: cannot find symbol > Logger logger = LogManager.getLogger(name); > ^ > symbol: variable LogManager > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:123: error: cannot find symbol > return ConfigurationFactory.newConfigurationBuilder(); > ^ > symbol: variable ConfigurationFactory > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:128: error: cannot find symbol > return PatternLayout.newBuilder().withPattern(SIMPLE_PATTERN).build(); > ^ > symbol: variable PatternLayout > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:139: error: package Filter does > not exist > return ThresholdFilter.createFilter(level, Filter.Result.ACCEPT, > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:140: error: package Filter does > not exist > Filter.Result.NEUTRAL); > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:139: error: cannot find symbol > return ThresholdFilter.createFilter(level, Filter.Result.ACCEPT, > ^ > symbol: variable ThresholdFilter > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:146: error: package Filter does > not exist > Filter.Result.ACCEPT, Filter.Result.NEUTRAL); > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:146: error: package Filter does > not exist > Filter.Result.ACCEPT, Filter.Result.NEUTRAL); > ^ > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:158: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:158: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:158: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: variable LogManager > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:159: error: cannot find symbol > Configuration config = context.getConfiguration(); > ^ > symbol: class Configuration > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:160: error: cannot find symbol > LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName()); > ^ > symbol: class LoggerConfig > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:163: error: cannot find symbol > Map<String, Appender> appenders = config.getAppenders(); > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:165: error: cannot find symbol > Appender jappender = config.getAppender(JalviewAppender.NAME); > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:178: error: cannot find symbol > setLevel(LogManager.getRootLogger(), level); > ^ > symbol: variable LogManager > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:183: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:183: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:183: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: variable LogManager > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:184: error: cannot find symbol > Configuration config = context.getConfiguration(); > ^ > symbol: class Configuration > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:185: error: cannot find symbol > Map<String, Appender> appenders = config.getAppenders(); > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:192: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:192: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:192: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: variable LogManager > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:193: error: cannot find symbol > Configuration config = context.getConfiguration(); > ^ > symbol: class Configuration > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:194: error: cannot find symbol > LoggerConfig logger2Config = config.getLoggerConfig(logger2.getName()); > ^ > symbol: class LoggerConfig > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:195: error: cannot find symbol > Map<String, Appender> logger2AppendersMap = logger2Config > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:197: error: cannot find symbol > Appender appender = logger2AppendersMap.get(name2); > ^ > symbol: class Appender > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:206: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:206: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: class LoggerContext > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/util/Log4j.java:206: error: cannot find symbol > LoggerContext context = (LoggerContext) LogManager.getContext(false); > ^ > symbol: variable LogManager > location: class Log4j > /<<PKGBUILDDIR>>/src/jalview/bin/Jalview.java:129: warning: [removal] Policy > in java.security has been deprecated and marked for removal > Policy.setPolicy(new Policy() > ^ > /<<PKGBUILDDIR>>/src/jalview/bin/Jalview.java:129: warning: [removal] Policy > in java.security has been deprecated and marked for removal > Policy.setPolicy(new Policy() > ^ > /<<PKGBUILDDIR>>/src/jalview/bin/Jalview.java:272: warning: [removal] > setSecurityManager(SecurityManager) in System has been deprecated and marked > for removal > System.setSecurityManager(null); > ^ > /<<PKGBUILDDIR>>/src/jalview/io/AppletFormatAdapter.java:564: warning: > [removal] getSecurityManager() in System has been deprecated and marked for > removal > InputStream is = System.getSecurityManager().getClass() > ^ > Note: Some input files use or override a deprecated API. > Note: Recompile with -Xlint:deprecation for details. > Note: Some input files use unchecked or unsafe operations. > Note: Recompile with -Xlint:unchecked for details. > 100 errors > 14 warnings > only showing the first 100 errors, of 107 total; use -Xmaxerrs if you would > like to see more > :compileJava FAILED > :compileJava (Thread[Daemon worker,5,main]) completed. Took 8.256 secs. > > FAILURE: Build failed with an exception. > > * What went wrong: > Execution failed for task ':compileJava'. > > Compilation failed; see the compiler error output for details. > > * Try: > Run with --debug option to get more log output. Run with --scan to get full > insights. > > * Exception is: > org.gradle.api.tasks.TaskExecutionException: Execution failed for task > ':compileJava'. > at > org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100) > at > org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70) > at > org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51) > at > org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:62) > at > org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54) > at > org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60) > at > org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97) > at > org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87) > at > org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52) > at > org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52) > at > org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54) > at > org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) > at > org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34) > at > org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) > at > org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241) > at > org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230) > at > org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123) > at > org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79) > at > org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104) > at > org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98) > at > org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626) > at > org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581) > at > org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98) > at > org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) > at > org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) > at > org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) > at > org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) > at > org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) > at > org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) > at > org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) > at > org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) > at > org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) > at > org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) > at > org.gradle.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) > at > org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) > at > org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) > at > org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) > at > org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) > at > org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) > at > org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) > at > org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) > at > org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) > at > org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) > at > org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) > at > org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) > at > org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) > at > org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) > at > org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) > at > org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) > at > org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) > at > org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) > at > org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) > at > org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) > at > org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) > at > org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) > at > org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) > at > org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) > at > org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) > at > org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) > at > org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) > at > org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) > at > org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) > at > org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) > at > org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) > at > org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) > at > org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) > at > org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) > at > org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) > at org.gradle.util.Swapper.swap(Swapper.java:38) > at > org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) > at > org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) > at > org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) > at > org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) > at > org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) > at > org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) > at > org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) > at > org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) > at > org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) > Caused by: org.gradle.api.internal.tasks.compile.CompilationFailedException: > Compilation failed; see the compiler error output for details. > at > org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:50) > at > org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:35) > at > org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:98) > at > org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:51) > at > org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37) > at > org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35) > at > org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25) > at > org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:207) > at > org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:192) > at > org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:124) > at > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) > at > java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73) > at > org.gradle.api.internal.project.taskfactory.IncrementalTaskAction.doExecute(IncrementalTaskAction.java:46) > at > org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39) > at > org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26) > at > org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) > at > org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) > at > org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110) > at > org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92) > ... 103 more > > > * Get more help at https://help.gradle.org > > BUILD FAILED in 15s > 8 actionable tasks: 8 executed > dh_auto_build: error: gradle --info --console plain --offline --stacktrace > --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. > -Duser.name=debian -Ddebian.package=jalview -Dfile.encoding=UTF-8 --parallel > --max-workers=8 jar returned exit code 1 > make: *** [debian/rules:48: binary] Error 25 The full build log is available from: http://qa-logs.debian.net/2023/02/03/jalview_2.11.2.5+dfsg-2_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230203;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230203&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
