Your message dated Sat, 04 Feb 2023 23:52:33 +0000
with message-id <e1poskf-008ams...@fasolo.debian.org>
and subject line Bug#1030414: fixed in jalview 2.11.2.5+dfsg-3
has caused the Debian Bug report #1030414,
regarding jalview: FTBFS: JLoggerLog4j.java:23: error: package 
org.apache.logging.log4j does not exist
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1030414: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1030414
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.

--- End Message ---
--- Begin Message ---
Source: jalview
Source-Version: 2.11.2.5+dfsg-3
Done: tony mancill <tmanc...@debian.org>

We believe that the bug you reported is fixed in the latest version of
jalview, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1030...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
tony mancill <tmanc...@debian.org> (supplier of updated jalview package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sat, 04 Feb 2023 15:21:07 -0800
Source: jalview
Architecture: source
Version: 2.11.2.5+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Java Maintainers 
<pkg-java-maintain...@lists.alioth.debian.org>
Changed-By: tony mancill <tmanc...@debian.org>
Closes: 1030414
Changes:
 jalview (2.11.2.5+dfsg-3) unstable; urgency=medium
 .
   * Team upload
   * Update log4j dependency to use log4j2 (Closes: #1030414)
Checksums-Sha1:
 0580d63f7440fb02b00ebc03af599b1e01765963 2680 jalview_2.11.2.5+dfsg-3.dsc
 3142b5ac0ab6b3e5d703173c692dd105512253e2 46144 
jalview_2.11.2.5+dfsg-3.debian.tar.xz
 576313ac7fe4c83bbc21cd422afdd2d61bbce11e 19002 
jalview_2.11.2.5+dfsg-3_amd64.buildinfo
Checksums-Sha256:
 c4820c1f8e7c8547ce589d6576b590c36cdbe31fa5083b1571f17ff126800586 2680 
jalview_2.11.2.5+dfsg-3.dsc
 aa2b58e1c316cedb42e0cf81a9c3e37ba121c1b7a5331ea08efcc8e0529f8dbe 46144 
jalview_2.11.2.5+dfsg-3.debian.tar.xz
 37215870d28aadb81f84466e7de787f6bffc845955ea4514f5db4662fbcb0fcd 19002 
jalview_2.11.2.5+dfsg-3_amd64.buildinfo
Files:
 66ee40c9080a5fa12413e2047bd7a38f 2680 science optional 
jalview_2.11.2.5+dfsg-3.dsc
 7934be3d4761cf2614a7d0e94db38981 46144 science optional 
jalview_2.11.2.5+dfsg-3.debian.tar.xz
 5763e7e3c43b33790445ff0104c14cf1 19002 science optional 
jalview_2.11.2.5+dfsg-3_amd64.buildinfo

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--- End Message ---

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