Re: alter-sequence-alignment switched build system to maven - some final hints are needed
Hi again,
I went on with patching pom.xml to skip the web app (like I did before
by patching build.xml). This finally works - so there is no real need
to spent time on this question.
Thanks for your attention anyway
Andreas.
On Wed, Jul 04, 2018 at 01:40:06PM +0200, Andreas Tille wrote:
> Hi,
>
> 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:
>
>
> 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-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]
> [INFO] The ALTER Project [pom]
> [INFO] ALTER Core Library and Desktop app [jar]
> [INFO] ALTER Web app [war]
> [INFO]
> [INFO] -------------------< es.uvigo.ei.sing:alter-project >-------------------
> [INFO] Building The ALTER Project 1.3.4 [1/3]
> [INFO] --------------------------------[ pom ]---------------------------------
> [INFO]
> [INFO] ---------------------< es.uvigo.ei.sing:alter-lib >---------------------
> [INFO] Building ALTER Core Library and Desktop app 1.3.4 [2/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- javacc-maven-plugin:2.6:javacc (javacc) @ alter-lib ---
> [INFO] Skipping - all parsers are up to date
> [INFO]
> [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]
> [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]
> [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]
> [INFO] --- maven-compiler-plugin:3.6.2:testCompile (default-testCompile) @ alter-lib ---
> [INFO] No sources to compile
> [INFO]
> [INFO] --- maven-surefire-plugin:2.21.0:test (default-test) @ alter-lib ---
> [INFO] Tests are skipped.
> [INFO]
> [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]
> [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]
> [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]
> [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] BUILD FAILURE
> [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]
> [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]
> [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
> app?
>
> Kind regards
>
> Andreas.
>
>
> [1] https://salsa.debian.org/med-team/alter-sequence-alignment
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
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