Bug#1030414: jalview: FTBFS: JLoggerLog4j.java:23: error: package org.apache.logging.log4j does not exist
Lucas Nussbaum
lucas at debian.org
Sat Feb 4 07:20:03 GMT 2023
Source: jalview
Version: 2.11.2.5+dfsg-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at 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 at 25134dd1
> Creating new cache for resourceHashesCache, path /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at 25134dd1
> Creating new cache for fileHashes, path /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 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 at 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 at 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 at 2e01a468
> Creating new cache for taskHistory, path /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess at 74a226fd
> Creating new cache for outputFiles, path /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230203&fusertaguser=lucas@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.
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