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alter-sequence-alignment switched build system to maven - some final hints are needed


the new version of alter-sequence-alignment[1] has switched build system
to maven.  The Debian package is only providing the desktop app and I've
got the build creating at least this.  However, upstream provides a web
interface in addition (which is not target of the actual packaging and I
so no reason to provide this in the near future).  The current build
fails with:

        /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/alter-sequence-alignment-1.3.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/alter-sequence-alignment-1.3.4/debian -Dmaven.repo.local=/build/alter-sequence-alignment-1.3.4/debian/maven-repo package -DskipTests -Dnotimestamp=true -Dlocale=en_US
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/usr/share/maven/lib/guice.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] The ALTER Project                                                  [pom]
[INFO] ALTER Core Library and Desktop app                                 [jar]
[INFO] ALTER Web app                                                      [war]
[INFO] -------------------< es.uvigo.ei.sing:alter-project >-------------------
[INFO] Building The ALTER Project 1.3.4                                   [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] ---------------------< es.uvigo.ei.sing:alter-lib >---------------------
[INFO] Building ALTER Core Library and Desktop app 1.3.4                  [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] --- javacc-maven-plugin:2.6:javacc (javacc) @ alter-lib ---
[INFO] Skipping - all parsers are up to date
[INFO] --- maven-resources-plugin:3.0.2:resources (default-resources) @ alter-lib ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] --- maven-compiler-plugin:3.6.2:compile (default-compile) @ alter-lib ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 130 source files to /build/alter-sequence-alignment-1.3.4/alter-lib/target/classes
[INFO] /build/alter-sequence-alignment-1.3.4/alter-lib/src/main/java/es/uvigo/ei/sing/alter/gui/MainFrame.java: /build/alter-sequence-alignment-1.3.4/alter-lib/src/main/java/es/uvigo/ei/sing/alter/gui/MainFrame.java uses or overrides a deprecated API.
[INFO] /build/alter-sequence-alignment-1.3.4/alter-lib/src/main/java/es/uvigo/ei/sing/alter/gui/MainFrame.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/alter-sequence-alignment-1.3.4/alter-lib/src/main/java/es/uvigo/ei/sing/alter/types/MSA.java: Some input files use unchecked or unsafe operations.
[INFO] /build/alter-sequence-alignment-1.3.4/alter-lib/src/main/java/es/uvigo/ei/sing/alter/types/MSA.java: Recompile with -Xlint:unchecked for details.
[INFO] --- maven-resources-plugin:3.0.2:testResources (default-testResources) @ alter-lib ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /build/alter-sequence-alignment-1.3.4/alter-lib/src/test/resources
[INFO] --- maven-compiler-plugin:3.6.2:testCompile (default-testCompile) @ alter-lib ---
[INFO] No sources to compile
[INFO] --- maven-surefire-plugin:2.21.0:test (default-test) @ alter-lib ---
[INFO] Tests are skipped.
[INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ alter-lib ---
[INFO] Building jar: /build/alter-sequence-alignment-1.3.4/alter-lib/target/alter-lib-1.3.4.jar
[INFO] --- maven-assembly-plugin:3.1.0:single (make-assembly) @ alter-lib ---
[INFO] Building jar: /build/alter-sequence-alignment-1.3.4/alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar
[INFO] ---------------------< es.uvigo.ei.sing:alter-web >---------------------
[INFO] Building ALTER Web app 1.3.4                                       [3/3]
[INFO] --------------------------------[ war ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-war-plugin:jar:2.2 is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] The ALTER Project 1.3.4 ............................ SUCCESS [  0.003 s]
[INFO] ALTER Core Library and Desktop app ................. SUCCESS [  5.377 s]
[INFO] ALTER Web app 1.3.4 ................................ FAILURE [  0.038 s]
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5.594 s
[INFO] Finished at: 2018-07-04T11:20:27Z
[INFO] ------------------------------------------------------------------------
[ERROR] Plugin org.apache.maven.plugins:maven-war-plugin:2.2 or one of its dependencies could not be resolved: Cannot access zkmaven (http://mavensync.zkoss.org/maven2/) in offline mode and the artifact org.apache.maven.plugins:maven-war-plugin:jar:2.2 has not been downloaded from it before. -> [Help 1]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginResolutionException
dh_auto_build: /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/alter-sequence-alignment-

For the sake of some maven training I'd get some hint how to get also
the Web app build succeed.  I have no idea why maven-war-plugin should
be missing since libmaven-war-plugin-java is in Build-Depends.  Anyway
if this might turn out too complex is there any hint how to restrict the
build just to "ALTER Core Library and Desktop app" and ignore the Web

Kind regards


[1] https://salsa.debian.org/med-team/alter-sequence-alignment


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