search

cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
GNU Affero General Public License v3.0
636 stars 487 forks source link

mvn compile fails with error about `${PORTAL_HOME}` #11

Closed serverhorror closed 9 years ago

serverhorror commented 9 years ago

Hi,

I'm trying to evaluate cbioportal for an on premise installation. I cloned the repository and tried a simple mvn compile. It fails with some error about ${PORTAL_HOME}.

Unfortunately there aren't any installation instructions or I am unable to find them. Let me know if you need any details about this.

$ lsb_release -a
LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: Scientific
Description:    Scientific Linux release 6.6 (Carbon)
Release:        6.6
Codename:       Carbon
$ java -version
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)
$ mvn --version
Apache Maven 3.3.3 (7994120775791599e205a5524ec3e0dfe41d4a06; 2015-04-22T13:57:37+02:00)
Maven home: /net/home/marcherm/easybuildinstall/software/Maven/3.3.3
Java version: 1.8.0_45, vendor: Oracle Corporation
Java home: /apps/prod/easybuild/software/Java/1.8.0_45/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.32-431.11.2.el6.x86_64", arch: "amd64", family: "unix"
$ mvn -X compile
Apache Maven 3.3.3 (7994120775791599e205a5524ec3e0dfe41d4a06; 2015-04-22T13:57:37+02:00)
Maven home: /net/home/marcherm/easybuildinstall/software/Maven/3.3.3
Java version: 1.8.0_45, vendor: Oracle Corporation
Java home: /apps/prod/easybuild/software/Java/1.8.0_45/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.32-431.11.2.el6.x86_64", arch: "amd64", family: "unix"
[DEBUG] Created new class realm maven.api
[DEBUG] Importing foreign packages into class realm maven.api
[DEBUG]   Imported: javax.enterprise.inject.* < plexus.core
[DEBUG]   Imported: javax.enterprise.util.* < plexus.core
[DEBUG]   Imported: javax.inject.* < plexus.core
[DEBUG]   Imported: org.apache.maven.* < plexus.core
[DEBUG]   Imported: org.apache.maven.artifact < plexus.core
[DEBUG]   Imported: org.apache.maven.classrealm < plexus.core
[DEBUG]   Imported: org.apache.maven.cli < plexus.core
[DEBUG]   Imported: org.apache.maven.configuration < plexus.core
[DEBUG]   Imported: org.apache.maven.exception < plexus.core
[DEBUG]   Imported: org.apache.maven.execution < plexus.core
[DEBUG]   Imported: org.apache.maven.execution.scope < plexus.core
[DEBUG]   Imported: org.apache.maven.lifecycle < plexus.core
[DEBUG]   Imported: org.apache.maven.model < plexus.core
[DEBUG]   Imported: org.apache.maven.monitor < plexus.core
[DEBUG]   Imported: org.apache.maven.plugin < plexus.core
[DEBUG]   Imported: org.apache.maven.profiles < plexus.core
[DEBUG]   Imported: org.apache.maven.project < plexus.core
[DEBUG]   Imported: org.apache.maven.reporting < plexus.core
[DEBUG]   Imported: org.apache.maven.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.rtinfo < plexus.core
[DEBUG]   Imported: org.apache.maven.settings < plexus.core
[DEBUG]   Imported: org.apache.maven.toolchain < plexus.core
[DEBUG]   Imported: org.apache.maven.usability < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.* < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.authentication < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.authorization < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.events < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.observers < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.proxy < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.resource < plexus.core
[DEBUG]   Imported: org.codehaus.classworlds < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.* < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.classworlds < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.component < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.configuration < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.container < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.context < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.lifecycle < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.logging < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.personality < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.Xpp3Dom < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlPullParser < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlPullParserException < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlSerializer < plexus.core
[DEBUG]   Imported: org.eclipse.aether.* < plexus.core
[DEBUG]   Imported: org.eclipse.aether.artifact < plexus.core
[DEBUG]   Imported: org.eclipse.aether.collection < plexus.core
[DEBUG]   Imported: org.eclipse.aether.deployment < plexus.core
[DEBUG]   Imported: org.eclipse.aether.graph < plexus.core
[DEBUG]   Imported: org.eclipse.aether.impl < plexus.core
[DEBUG]   Imported: org.eclipse.aether.installation < plexus.core
[DEBUG]   Imported: org.eclipse.aether.internal.impl < plexus.core
[DEBUG]   Imported: org.eclipse.aether.metadata < plexus.core
[DEBUG]   Imported: org.eclipse.aether.repository < plexus.core
[DEBUG]   Imported: org.eclipse.aether.resolution < plexus.core
[DEBUG]   Imported: org.eclipse.aether.spi < plexus.core
[DEBUG]   Imported: org.eclipse.aether.transfer < plexus.core
[DEBUG]   Imported: org.eclipse.aether.version < plexus.core
[DEBUG]   Imported: org.slf4j.* < plexus.core
[DEBUG]   Imported: org.slf4j.spi.* < plexus.core
[DEBUG] Populating class realm maven.api
[INFO] Error stacktraces are turned on.
[DEBUG] Reading global settings from /net/home/marcherm/easybuildinstall/software/Maven/3.3.3/conf/settings.xml
[DEBUG] Reading user settings from /net/home/marcherm/.m2/settings.xml
[DEBUG] Reading global toolchains from /net/home/marcherm/easybuildinstall/software/Maven/3.3.3/conf/toolchains.xml
[DEBUG] Reading user toolchains from /net/home/marcherm/.m2/toolchains.xml
[DEBUG] Using local repository at /net/home/marcherm/.m2/repository
[DEBUG] Using manager EnhancedLocalRepositoryManager with priority 10.0 for /net/home/marcherm/.m2/repository
[INFO] Scanning for projects...
[DEBUG] Extension realms for project org.mskcc.cbio:master:pom:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging pom from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:cbioportal:war:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging war from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:core:jar:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:business:jar:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:web:jar:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] Portal Master
[INFO] Portal Business Layer
[INFO] Portal Core
[INFO] Portal Web Layer
[INFO] cBio Cancer Genomics Portal
[DEBUG] === REACTOR BUILD PLAN ================================================
[DEBUG] Project: org.mskcc.cbio:master:pom:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:business:jar:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:core:jar:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:web:jar:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:cbioportal:war:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] =======================================================================
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Portal Master 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] === PROJECT BUILD PLAN ================================================
[DEBUG] Project:       org.mskcc.cbio:master:1.0-SNAPSHOT
[DEBUG] Dependencies (collect): []
[DEBUG] Dependencies (resolve): []
[DEBUG] Repositories (dependencies): [spring-milestones (http://repo.spring.io/milestone, default, releases), central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] Repositories (plugins)     : [central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] =======================================================================
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Portal Business Layer 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] === PROJECT BUILD PLAN ================================================
[DEBUG] Project:       org.mskcc.cbio:business:1.0-SNAPSHOT
[DEBUG] Dependencies (collect): []
[DEBUG] Dependencies (resolve): [compile]
[DEBUG] Repositories (dependencies): [spring-milestones (http://repo.spring.io/milestone, default, releases), central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] Repositories (plugins)     : [central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources (copy-parent-resources)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <buildFilters default-value="${project.build.filters}"/>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${maven.resources.escapeString}</escapeString>
  <escapeWindowsPaths default-value="true">${maven.resources.escapeWindowsPaths}</escapeWindowsPaths>
  <includeEmptyDirs default-value="false">${maven.resources.includeEmptyDirs}</includeEmptyDirs>
  <outputDirectory>/net/home/marcherm/git/cbioportal/business/target/classes</outputDirectory>
  <overwrite default-value="false">${maven.resources.overwrite}</overwrite>
  <project default-value="${project}"/>
  <resources>
    <resource>
      <directory>${PORTAL_HOME}/src/main/resources</directory>
      <includes>
        <include>**/*.properties</include>
      </includes>
      <excludes>
        <exclude>**/portal.properties.*</exclude>
        <exclude>**/log4j.properties.*</exclude>
        <exclude>**/*.EXAMPLE</exclude>
      </excludes>
    </resource>
  </resources>
  <session default-value="${session}"/>
  <supportMultiLineFiltering default-value="false">${maven.resources.supportMultiLineFiltering}</supportMultiLineFiltering>
  <useBuildFilters default-value="true"/>
  <useDefaultDelimiters default-value="true"/>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-resources-plugin:2.6:resources (default-resources)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <buildFilters default-value="${project.build.filters}"/>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${maven.resources.escapeString}</escapeString>
  <escapeWindowsPaths default-value="true">${maven.resources.escapeWindowsPaths}</escapeWindowsPaths>
  <includeEmptyDirs default-value="false">${maven.resources.includeEmptyDirs}</includeEmptyDirs>
  <outputDirectory default-value="${project.build.outputDirectory}"/>
  <overwrite default-value="false">${maven.resources.overwrite}</overwrite>
  <project default-value="${project}"/>
  <resources default-value="${project.resources}"/>
  <session default-value="${session}"/>
  <supportMultiLineFiltering default-value="false">${maven.resources.supportMultiLineFiltering}</supportMultiLineFiltering>
  <useBuildFilters default-value="true"/>
  <useDefaultDelimiters default-value="true"/>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <basedir>${basedir}</basedir>
  <buildDirectory>${project.build.directory}</buildDirectory>
  <classpathElements>${project.compileClasspathElements}</classpathElements>
  <compileSourceRoots>${project.compileSourceRoots}</compileSourceRoots>
  <compilerId default-value="javac">${maven.compiler.compilerId}</compilerId>
  <compilerVersion>${maven.compiler.compilerVersion}</compilerVersion>
  <debug default-value="true">${maven.compiler.debug}</debug>
  <encoding>${maven.compiler.encoding}</encoding>
  <executable>${maven.compiler.executable}</executable>
  <failOnError default-value="true">${maven.compiler.failOnError}</failOnError>
  <fork default-value="false"/>
  <maxmem>${maven.compiler.maxmem}</maxmem>
  <meminitial>${maven.compiler.meminitial}</meminitial>
  <optimize default-value="false">${maven.compiler.optimize}</optimize>
  <outputDirectory>${project.build.outputDirectory}</outputDirectory>
  <outputFileName>${project.build.finalName}</outputFileName>
  <projectArtifact>${project.artifact}</projectArtifact>
  <showDeprecation default-value="false">${maven.compiler.showDeprecation}</showDeprecation>
  <showWarnings default-value="false">${maven.compiler.showWarnings}</showWarnings>
  <source>1.7</source>
  <staleMillis default-value="0">${lastModGranularityMs}</staleMillis>
  <target>1.7</target>
  <verbose default-value="false">${maven.compiler.verbose}</verbose>
</configuration>
[DEBUG] =======================================================================
[DEBUG] Dependency collection stats: {ConflictMarker.analyzeTime=4, ConflictMarker.markTime=2, ConflictMarker.nodeCount=349, ConflictIdSorter.graphTime=2, ConflictIdSorter.topsortTime=1, ConflictIdSorter.conflictIdCount=80, ConflictIdSorter.conflictIdCycleCount=0, ConflictResolver.totalTime=19, ConflictResolver.conflictItemCount=219, DefaultDependencyCollector.collectTime=1515, DefaultDependencyCollector.transformTime=38}
[DEBUG] org.mskcc.cbio:business:jar:1.0-SNAPSHOT
[DEBUG]    commons-collections:commons-collections:jar:3.2.1:compile
[DEBUG]    log4j:apache-log4j-extras:jar:1.1:compile
[DEBUG]    commons-dbcp:commons-dbcp:jar:1.4:compile
[DEBUG]       commons-pool:commons-pool:jar:1.5.4:compile
[DEBUG]    commons-beanutils:commons-beanutils:jar:1.9.1:compile
[DEBUG]       commons-logging:commons-logging:jar:1.1.1:compile
[DEBUG]    org.apache.httpcomponents:httpclient:jar:4.3.4:compile
[DEBUG]       commons-codec:commons-codec:jar:1.6:compile
[DEBUG]    org.apache.httpcomponents:httpcore:jar:4.3.2:compile
[DEBUG]    junit:junit:jar:4.8.2:compile
[DEBUG]    log4j:log4j:jar:1.2.16:compile
[DEBUG]    mysql:mysql-connector-java:jar:5.1.16:provided
[DEBUG]    org.slf4j:slf4j-log4j12:jar:1.6.6:compile
[DEBUG]    org.slf4j:slf4j-api:jar:1.6.6:compile
[DEBUG]    org.springframework:spring-core:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-expression:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-beans:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-aop:jar:4.0.4.RELEASE:compile
[DEBUG]       aopalliance:aopalliance:jar:1.0:compile
[DEBUG]    org.springframework:spring-context:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-context-support:jar:4.1.2.RELEASE:compile
[DEBUG]    org.springframework.integration:spring-integration-core:jar:4.1.0.RELEASE:compile
[DEBUG]       org.projectreactor:reactor-core:jar:1.1.4.RELEASE:compile
[DEBUG]          com.goldmansachs:gs-collections:jar:5.1.0:compile
[DEBUG]             com.goldmansachs:gs-collections-api:jar:5.1.0:compile
[DEBUG]          com.lmax:disruptor:jar:3.2.1:compile
[DEBUG]          io.gatling:jsr166e:jar:1.0:compile
[DEBUG]       org.springframework:spring-messaging:jar:4.1.2.RELEASE:compile
[DEBUG]       org.springframework.retry:spring-retry:jar:1.1.1.RELEASE:compile
[DEBUG]    org.springframework.integration:spring-integration-sftp:jar:4.1.0.RELEASE:compile
[DEBUG]       org.springframework.integration:spring-integration-stream:jar:4.1.0.RELEASE:compile
[DEBUG]       com.jcraft:jsch:jar:0.1.51:compile
[DEBUG]       org.springframework.integration:spring-integration-file:jar:4.1.0.RELEASE:compile
[DEBUG]          commons-io:commons-io:jar:2.4:compile
[DEBUG]    org.springframework:spring-tx:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-orm:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-jdbc:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-webmvc:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-web:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-acl:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-config:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-core:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-ldap:jar:3.2.5.RELEASE:compile
[DEBUG]       org.springframework.ldap:spring-ldap-core:jar:1.3.2.RELEASE:compile
[DEBUG]          commons-lang:commons-lang:jar:2.4:compile
[DEBUG]    org.springframework.security:spring-security-openid:jar:3.2.5.RELEASE:compile
[DEBUG]       com.google.inject:guice:jar:2.0:compile
[DEBUG]       org.openid4java:openid4java-nodeps:jar:0.9.6:compile
[DEBUG]          net.jcip:jcip-annotations:jar:1.0:compile
[DEBUG]       net.sourceforge.nekohtml:nekohtml:jar:1.9.20:runtime
[DEBUG]          xerces:xercesImpl:jar:2.10.0:runtime
[DEBUG]    org.springframework.security.extensions:spring-security-saml2-core:jar:1.0.0.RELEASE:compile
[DEBUG]       org.opensaml:opensaml:jar:2.6.1:compile
[DEBUG]          org.opensaml:openws:jar:1.5.1:compile
[DEBUG]             org.opensaml:xmltooling:jar:1.4.1:compile
[DEBUG]                org.bouncycastle:bcprov-jdk15:jar:1.46:compile
[DEBUG]                ca.juliusdavies:not-yet-commons-ssl:jar:0.3.9:compile
[DEBUG]             commons-httpclient:commons-httpclient:jar:3.1:compile
[DEBUG]             org.apache.santuario:xmlsec:jar:1.5.6:compile
[DEBUG]          org.apache.velocity:velocity:jar:1.7:compile
[DEBUG]          org.owasp.esapi:esapi:jar:2.0.1:compile
[DEBUG]          joda-time:joda-time:jar:2.2:compile
[DEBUG]          xalan:serializer:jar:2.7.1:runtime
[DEBUG]          xml-resolver:xml-resolver:jar:1.2:runtime
[DEBUG]          xalan:xalan:jar:2.7.1:runtime
[DEBUG]       xml-apis:xml-apis:jar:1.4.01:runtime
[DEBUG]    org.springframework.security:spring-security-taglibs:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-web:jar:3.2.5.RELEASE:compile
[DEBUG]    org.mybatis:mybatis-spring:jar:1.2.2:compile
[DEBUG]    org.mybatis:mybatis:jar:3.2.7:compile
[DEBUG]    org.springframework.social:spring-social-config:jar:1.1.0.RELEASE:compile
[DEBUG]    org.springframework.social:spring-social-core:jar:1.1.0.RELEASE:compile
[DEBUG]    org.springframework.social:spring-social-security:jar:1.1.0.RELEASE:compile
[DEBUG]    org.springframework.social:spring-social-web:jar:1.1.0.RELEASE:compile
[DEBUG]       javax.inject:javax.inject:jar:1:compile
[DEBUG]    org.springframework.social:spring-social-google:jar:1.0.0.RELEASE:compile
[DEBUG]       com.fasterxml.jackson.core:jackson-annotations:jar:2.3.3:compile
[DEBUG]       com.fasterxml.jackson.core:jackson-core:jar:2.3.3:compile
[DEBUG]       com.fasterxml.jackson.core:jackson-databind:jar:2.3.3:compile
[INFO]
[INFO] --- maven-resources-plugin:2.6:copy-resources (copy-parent-resources) @ business ---
[DEBUG] Dependency collection stats: {ConflictMarker.analyzeTime=1, ConflictMarker.markTime=1, ConflictMarker.nodeCount=77, ConflictIdSorter.graphTime=0, ConflictIdSorter.topsortTime=0, ConflictIdSorter.conflictIdCount=26, ConflictIdSorter.conflictIdCycleCount=0, ConflictResolver.totalTime=5, ConflictResolver.conflictItemCount=74, DefaultDependencyCollector.collectTime=760, DefaultDependencyCollector.transformTime=7}
[DEBUG] org.apache.maven.plugins:maven-resources-plugin:jar:2.6:
[DEBUG]    org.apache.maven:maven-plugin-api:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-project:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-profile:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-artifact-manager:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-plugin-registry:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-core:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-plugin-parameter-documenter:jar:2.0.6:compile
[DEBUG]       org.apache.maven.reporting:maven-reporting-api:jar:2.0.6:compile
[DEBUG]          org.apache.maven.doxia:doxia-sink-api:jar:1.0-alpha-7:compile
[DEBUG]       org.apache.maven:maven-repository-metadata:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-error-diagnostics:jar:2.0.6:compile
[DEBUG]       commons-cli:commons-cli:jar:1.0:compile
[DEBUG]       org.apache.maven:maven-plugin-descriptor:jar:2.0.6:compile
[DEBUG]       org.codehaus.plexus:plexus-interactivity-api:jar:1.0-alpha-4:compile
[DEBUG]       classworlds:classworlds:jar:1.1:compile
[DEBUG]    org.apache.maven:maven-artifact:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-settings:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-model:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-monitor:jar:2.0.6:compile
[DEBUG]    org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-9-stable-1:compile
[DEBUG]       junit:junit:jar:3.8.1:compile
[DEBUG]    org.codehaus.plexus:plexus-utils:jar:2.0.5:compile
[DEBUG]    org.apache.maven.shared:maven-filtering:jar:1.1:compile
[DEBUG]       org.sonatype.plexus:plexus-build-api:jar:0.0.4:compile
[DEBUG]    org.codehaus.plexus:plexus-interpolation:jar:1.13:compile
[DEBUG] Created new class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.6
[DEBUG] Importing foreign packages into class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.6
[DEBUG]   Imported:  < maven.api
[DEBUG] Populating class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.6
[DEBUG]   Included: org.apache.maven.plugins:maven-resources-plugin:jar:2.6
[DEBUG]   Included: org.apache.maven.reporting:maven-reporting-api:jar:2.0.6
[DEBUG]   Included: org.apache.maven.doxia:doxia-sink-api:jar:1.0-alpha-7
[DEBUG]   Included: commons-cli:commons-cli:jar:1.0
[DEBUG]   Included: org.codehaus.plexus:plexus-interactivity-api:jar:1.0-alpha-4
[DEBUG]   Included: junit:junit:jar:3.8.1
[DEBUG]   Included: org.codehaus.plexus:plexus-utils:jar:2.0.5
[DEBUG]   Included: org.apache.maven.shared:maven-filtering:jar:1.1
[DEBUG]   Included: org.sonatype.plexus:plexus-build-api:jar:0.0.4
[DEBUG]   Included: org.codehaus.plexus:plexus-interpolation:jar:1.13
[DEBUG] Configuring mojo org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources from plugin realm ClassRealm[plugin>org.apache.maven.plugins:maven-resources-plugin:2.6, parent: sun.misc.Launcher$AppClassLoader@4e25154f]
[DEBUG] Configuring mojo 'org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources' with basic configurator -->
[DEBUG]   (f) buildFilters = [/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties]
[DEBUG]   (f) encoding = UTF-8
[DEBUG]   (f) escapeWindowsPaths = true
[DEBUG]   (s) includeEmptyDirs = false
[DEBUG]   (s) outputDirectory = /net/home/marcherm/git/cbioportal/business/target/classes
[DEBUG]   (s) overwrite = false
[DEBUG]   (f) project = MavenProject: org.mskcc.cbio:business:1.0-SNAPSHOT @ /net/home/marcherm/git/cbioportal/business/pom.xml
[DEBUG]   (s) directory = ${PORTAL_HOME}/src/main/resources
[DEBUG]   (s) includes = [**/*.properties]
[DEBUG]   (s) excludes = [**/portal.properties.*, **/log4j.properties.*, **/*.EXAMPLE]
[DEBUG]   (s) resources = [Resource {targetPath: null, filtering: false, FileSet {directory: ${PORTAL_HOME}/src/main/resources, PatternSet [includes: {**/*.properties}, excludes: {**/portal.properties.*, **/log4j.properties.*, **/*.EXAMPLE}]}}]
[DEBUG]   (f) session = org.apache.maven.execution.MavenSession@26b894bd
[DEBUG]   (f) supportMultiLineFiltering = false
[DEBUG]   (f) useBuildFilters = true
[DEBUG]   (s) useDefaultDelimiters = true
[DEBUG] -- end configuration --
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Portal Master ...................................... SUCCESS [  0.004 s]
[INFO] Portal Business Layer .............................. FAILURE [  3.481 s]
[INFO] Portal Core ........................................ SKIPPED
[INFO] Portal Web Layer ................................... SKIPPED
[INFO] cBio Cancer Genomics Portal ........................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.738 s
[INFO] Finished at: 2015-05-06T14:04:05+02:00
[INFO] Final Memory: 26M/1963M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources (copy-parent-resources) on project business: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties' -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources (copy-parent-resources) on project business: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties'
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:216)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
        at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
        at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
        at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
        at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
        at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
        at org.apache.maven.cli.MavenCli.execute(MavenCli.java:862)
        at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:286)
        at org.apache.maven.cli.MavenCli.main(MavenCli.java:197)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
        at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
        at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
        at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties'
        at org.apache.maven.plugin.resources.ResourcesMojo.execute(ResourcesMojo.java:307)
        at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
        ... 20 more
Caused by: org.apache.maven.shared.filtering.MavenFilteringException: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties'
        at org.apache.maven.shared.filtering.DefaultMavenFileFilter.loadProperties(DefaultMavenFileFilter.java:290)
        at org.apache.maven.shared.filtering.DefaultMavenFileFilter.getDefaultFilterWrappers(DefaultMavenFileFilter.java:205)
        at org.apache.maven.shared.filtering.DefaultMavenResourcesFiltering.filterResources(DefaultMavenResourcesFiltering.java:161)
        at org.apache.maven.plugin.resources.ResourcesMojo.execute(ResourcesMojo.java:301)
        ... 22 more
Caused by: java.io.FileNotFoundException: /net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties
        at org.apache.maven.shared.filtering.PropertyUtils.loadPropertyFile(PropertyUtils.java:65)
        at org.apache.maven.shared.filtering.DefaultMavenFileFilter.loadProperties(DefaultMavenFileFilter.java:284)
        ... 25 more
[ERROR]
[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/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :business
aedion99 commented 9 years ago

Did you setup PORTAL_HOME in your env as described in the doc? https://github.com/cBioPortal/cbioportal/wiki/Pre-Build-Steps#set-the-portal_home-variable

ecerami commented 9 years ago

This is good timing, as we have actually just released new instructions on building from source.

The complete instructions are here: https://github.com/cBioPortal/cbioportal/wiki

There are currently many steps (which we would like to fix sometime in the future). But, these steps should now all make sense.

If you notice any issues as you go through the steps, please log a new issue, and we will update the wiki pages.

serverhorror commented 9 years ago

I'll scan thru the wiki and report back. Thanks for the information.

How about a file like typically found in other projects: "INSTALLATION" that at least points to the wiki?

serverhorror commented 9 years ago

Hi,

Thanks the docs work for me (for the most part) I opened #14 since that seems to be a different topic.