Docker: NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil #271

KonradHoeffner · 2022-02-02T10:53:20Z

After docker build . -t limes and cd-ing to a directory with a link specification, I get the following error:

$docker run -it --rm \
  -v $(pwd):/data \
  limes \       
    /data/citation-classified.xml
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil
	at org.apache.logging.slf4j.Log4jLoggerFactory.getContext(Log4jLoggerFactory.java:42)
	at org.apache.logging.log4j.spi.AbstractLoggerAdapter.getLogger(AbstractLoggerAdapter.java:47)
	at org.apache.logging.slf4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:29)
	at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:358)
	at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:383)
	at org.aksw.limes.core.controller.Controller.main(Controller.java:75)
Caused by: java.lang.ClassNotFoundException: org.apache.logging.log4j.util.ReflectionUtil
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(Unknown Source)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(Unknown Source)
	at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
	... 6 more

The error does not occur when using the prebuilt dicegroup/limes image.

The text was updated successfully, but these errors were encountered:

KonradHoeffner · 2022-02-07T12:34:19Z

According to https://stackoverflow.com/questions/52700803/im-getting-noclassdeffounderror-org-apache-logging-log4j-util-reflectionutil, this can happen if there are mixed versions of log4j on the classpath.

KonradHoeffner · 2022-02-07T12:35:02Z

$ mvn dependency:tree
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] LIMES                                                              [pom]
[INFO] LIMES Core Library                                                 [jar]
[INFO] limes-debian-cli                                                   [jar]
[INFO] 
[INFO] ---------------------< org.aksw.limes:limes-full >----------------------
[INFO] Building LIMES 1.7.7-SNAPSHOT                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:3.0.2:tree (default-cli) @ limes-full ---
[INFO] org.aksw.limes:limes-full:pom:1.7.7-SNAPSHOT
[INFO] 
[INFO] ---------------------< org.aksw.limes:limes-core >----------------------
[INFO] Building LIMES Core Library 1.7.7-SNAPSHOT                         [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact xstream:xstream:jar:1.2.2 has been relocated to com.thoughtworks.xstream:xstream:jar:1.2.2
[INFO] 
[INFO] --- maven-dependency-plugin:3.0.2:tree (default-cli) @ limes-core ---
[INFO] org.aksw.limes:limes-core:jar:1.7.7-SNAPSHOT
[INFO] +- org.slf4j:slf4j-api:jar:1.7.21:compile
[INFO] +- de.vandermeer:asciitable:jar:0.3.2:compile
[INFO] |  +- de.vandermeer:ascii-utf-themes:jar:0.0.1:compile
[INFO] |  |  \- de.vandermeer:skb-interfaces:jar:0.0.1:compile
[INFO] |  |     +- org.antlr:ST4:jar:4.0.8:compile
[INFO] |  |     |  \- org.antlr:antlr-runtime:jar:3.5.2:compile
[INFO] |  |     \- org.antlr:antlr4:jar:4.5.1:compile
[INFO] |  \- de.vandermeer:char-translation:jar:0.0.2:compile
[INFO] +- org.apache.commons:commons-math3:jar:3.3:compile
[INFO] +- org.apache.logging.log4j:log4j-slf4j-impl:jar:2.6.1:compile
[INFO] +- org.slf4j:log4j-over-slf4j:jar:1.7.21:compile
[INFO] +- org.slf4j:jcl-over-slf4j:jar:1.7.21:compile
[INFO] +- org.apache.logging.log4j:log4j-api:jar:2.17.1:compile
[INFO] +- org.apache.logging.log4j:log4j-core:jar:2.17.1:compile
[INFO] +- commons-codec:commons-codec:jar:1.11:compile
[INFO] +- org.apache.jena:apache-jena-libs:pom:4.2.0:compile
[INFO] |  +- org.apache.jena:jena-shacl:jar:4.2.0:compile
[INFO] |  +- org.apache.jena:jena-shex:jar:4.2.0:compile
[INFO] |  |  \- org.apache.jena:jena-arq:jar:tests:4.2.0:compile
[INFO] |  |     +- com.apicatalog:titanium-json-ld:jar:1.1.0:compile
[INFO] |  |     \- org.glassfish:jakarta.json:jar:2.0.1:compile
[INFO] |  +- org.apache.jena:jena-tdb:jar:4.2.0:compile
[INFO] |  +- org.apache.jena:jena-tdb2:jar:4.2.0:compile
[INFO] |  |  \- org.apache.jena:jena-dboe-storage:jar:4.2.0:compile
[INFO] |  |     \- org.apache.jena:jena-dboe-trans-data:jar:4.2.0:compile
[INFO] |  |        +- org.apache.jena:jena-dboe-transaction:jar:4.2.0:compile
[INFO] |  |        |  \- org.apache.jena:jena-dboe-base:jar:4.2.0:compile
[INFO] |  |        \- org.apache.jena:jena-dboe-index:jar:4.2.0:compile
[INFO] |  \- org.apache.jena:jena-rdfconnection:jar:4.2.0:compile
[INFO] +- org.aksw.jena-sparql-api:jena-sparql-api-cache-h2:jar:3.9.0-1:compile
[INFO] |  +- org.aksw.jena-sparql-api:jena-sparql-api-resources:jar:3.9.0-1:compile
[INFO] |  \- com.h2database:h2:jar:1.4.196:compile
[INFO] +- org.apache.logging.log4j:log4j-web:jar:2.6.2:test
[INFO] +- org.aksw.jena-sparql-api:jena-sparql-api-core:jar:3.9.0-1:compile
[INFO] |  +- org.aksw.jena-sparql-api:jena-sparql-api-mapper-annotations:jar:3.9.0-1:compile
[INFO] |  +- org.aksw.jena-sparql-api:jena-sparql-api-utils:jar:3.9.0-1:compile
[INFO] |  |  +- org.apache.jena:jena-sdb:jar:3.9.0:compile
[INFO] |  |  |  \- org.apache.jena:jena-cmds:jar:3.9.0:compile
[INFO] |  |  +- org.aksw.commons:aksw-commons-util:jar:0.8.10:compile
[INFO] |  |  |  \- net.sourceforge.collections:collections-generic:jar:4.01:compile
[INFO] |  |  \- com.google.code.gson:gson:jar:2.8.2:compile
[INFO] |  +- org.aksw.jena-sparql-api:jena-sparql-api-vocabs:jar:3.9.0-1:compile
[INFO] |  +- org.aksw.jena-sparql-api:jena-sparql-api-sparql-ext:jar:3.9.0-1:compile
[INFO] |  |  +- net.sf.jopt-simple:jopt-simple:jar:5.0.4:compile
[INFO] |  |  +- com.jayway.jsonpath:json-path:jar:2.4.0:compile
[INFO] |  |  |  \- net.minidev:json-smart:jar:2.3:compile
[INFO] |  |  |     \- net.minidev:accessors-smart:jar:1.2:compile
[INFO] |  |  |        \- org.ow2.asm:asm:jar:5.0.4:compile
[INFO] |  |  +- commons-validator:commons-validator:jar:1.6:compile
[INFO] |  |  |  +- commons-beanutils:commons-beanutils:jar:1.9.2:compile
[INFO] |  |  |  \- commons-digester:commons-digester:jar:1.8.1:compile
[INFO] |  |  +- com.vividsolutions:jts-core:jar:1.14.0:compile
[INFO] |  |  +- com.vividsolutions:jts-io:jar:1.14.0:compile
[INFO] |  |  |  \- com.googlecode.json-simple:json-simple:jar:1.1:compile
[INFO] |  |  \- org.codehaus.plexus:plexus-utils:jar:3.1.0:compile
[INFO] |  +- io.reactivex.rxjava2:rxjava:jar:2.1.14:compile
[INFO] |  |  \- org.reactivestreams:reactive-streams:jar:1.0.2:compile
[INFO] |  +- com.github.davidmoten:rxjava2-extras:jar:0.1.28:compile
[INFO] |  |  \- com.github.davidmoten:guava-mini:jar:0.1.1:compile
[INFO] |  +- org.apache.jena:jena-iri:jar:3.9.0:compile
[INFO] |  +- org.aksw.commons:aksw-commons-collections:jar:0.8.10:compile
[INFO] |  |  \- com.codepoetics:protonpack:jar:1.11:compile
[INFO] |  +- com.google.guava:guava:jar:24.0-jre:compile
[INFO] |  |  +- com.google.code.findbugs:jsr305:jar:1.3.9:compile
[INFO] |  |  +- org.checkerframework:checker-compat-qual:jar:2.0.0:compile
[INFO] |  |  +- com.google.errorprone:error_prone_annotations:jar:2.1.3:compile
[INFO] |  |  +- com.google.j2objc:j2objc-annotations:jar:1.1:compile
[INFO] |  |  \- org.codehaus.mojo:animal-sniffer-annotations:jar:1.14:compile
[INFO] |  +- org.apache.commons:commons-compress:jar:1.15:compile
[INFO] |  |  \- org.objenesis:objenesis:jar:2.6:compile
[INFO] |  +- org.aksw.jena-sparql-api:jena-sparql-api-resources-test-config:jar:3.9.0-1:compile
[INFO] |  \- com.nurkiewicz.asyncretry:asyncretry-jdk7:jar:0.0.6:compile
[INFO] +- org.apache.jena:jena-core:jar:3.9.0:compile
[INFO] |  +- commons-cli:commons-cli:jar:1.4:compile
[INFO] |  \- org.apache.jena:jena-base:jar:3.9.0:compile
[INFO] |     +- org.apache.commons:commons-csv:jar:1.5:compile
[INFO] |     +- commons-io:commons-io:jar:2.6:compile
[INFO] |     \- com.github.andrewoma.dexx:collection:jar:0.7:compile
[INFO] +- org.apache.jena:jena-arq:jar:3.9.0:compile
[INFO] |  +- org.apache.jena:jena-shaded-guava:jar:3.9.0:compile
[INFO] |  +- org.apache.httpcomponents:httpclient:jar:4.5.5:compile
[INFO] |  |  \- org.apache.httpcomponents:httpcore:jar:4.4.9:compile
[INFO] |  +- com.github.jsonld-java:jsonld-java:jar:0.12.1:compile
[INFO] |  |  +- com.fasterxml.jackson.core:jackson-core:jar:2.9.6:compile
[INFO] |  |  \- com.fasterxml.jackson.core:jackson-databind:jar:2.9.6:compile
[INFO] |  |     \- com.fasterxml.jackson.core:jackson-annotations:jar:2.9.0:compile
[INFO] |  +- org.apache.httpcomponents:httpclient-cache:jar:4.5.5:compile
[INFO] |  +- org.apache.thrift:libthrift:jar:0.10.0:compile
[INFO] |  \- org.apache.commons:commons-lang3:jar:3.4:compile
[INFO] +- org.apache.jena:jena-jdbc-driver-mem:jar:3.6.0:compile
[INFO] |  \- org.apache.jena:jena-jdbc-core:jar:3.6.0:compile
[INFO] +- org.apache.jena:jena-jdbc-driver-remote:jar:3.6.0:compile
[INFO] +- org.apache.jena:jena-jdbc-driver-tdb:jar:3.6.0:compile
[INFO] +- org.locationtech.jts:jts:pom:1.16.0:compile
[INFO] +- org.locationtech.jts:jts-core:jar:1.16.0:compile
[INFO] +- algorithms.edjoin:edjoin-plus:jar:2011:compile
[INFO] +- uk.ac.shef.wit:simmetrics:jar:1.6.2:compile
[INFO] +- com.opencsv:opencsv:jar:3.7:compile
[INFO] +- commons-lang:commons-lang:jar:2.5:compile
[INFO] +- edu.mit:jwi:jar:2.4.0:compile
[INFO] +- jgraphx:jgraphx:jar:1.0:compile
[INFO] +- commons-collections:commons-collections:jar:3.2.2:compile
[INFO] +- ssjoin:ssjoin:jar:1.0:compile
[INFO] +- junit:junit:jar:4.12:compile
[INFO] |  \- org.hamcrest:hamcrest-core:jar:1.3:compile
[INFO] +- fr.ign.cogit:geoxygene-api:jar:1.6:compile
[INFO] +- fr.ign.cogit:geoxygene-spatial:jar:1.6:compile
[INFO] +- net.sf.jgap:jgap:jar:3.4.4:compile
[INFO] |  +- net.sf.trove4j:trove4j:jar:2.0.2:compile
[INFO] |  +- com.thoughtworks.xstream:xstream:jar:1.2.2:compile
[INFO] |  |  \- xpp3:xpp3_min:jar:1.1.3.4.O:compile
[INFO] |  +- xpp3:xpp3:jar:1.1.3.4.O:compile
[INFO] |  +- tablelayout:TableLayout:jar:20050920:compile
[INFO] |  +- net.sf.jcgrid:jcgrid:jar:0.05:compile
[INFO] |  \- junit-addons:junit-addons:jar:1.4:compile
[INFO] |     +- xerces:xercesImpl:jar:2.6.2:compile
[INFO] |     \- xerces:xmlParserAPIs:jar:2.6.2:compile
[INFO] +- org.fusesource.jansi:jansi:jar:1.11:compile
[INFO] +- nz.ac.waikato.cms.weka:weka-dev:jar:3.9.0:compile
[INFO] |  +- nz.ac.waikato.cms.weka.thirdparty:java-cup-11b:jar:2015.03.26:compile
[INFO] |  +- nz.ac.waikato.cms.weka.thirdparty:java-cup-11b-runtime:jar:2015.03.26:compile
[INFO] |  +- nz.ac.waikato.cms.weka.thirdparty:bounce:jar:0.18:compile
[INFO] |  +- com.googlecode.matrix-toolkits-java:mtj:jar:1.0.4:compile
[INFO] |  |  \- com.github.fommil.netlib:all:pom:1.1.2:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_ref-osx-x86_64:jar:natives:1.1:compile
[INFO] |  |     |  \- com.github.fommil.netlib:native_ref-java:jar:1.1:compile
[INFO] |  |     |     \- com.github.fommil:jniloader:jar:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_ref-linux-x86_64:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_ref-linux-i686:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_ref-win-x86_64:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_ref-win-i686:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_ref-linux-armhf:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_system-osx-x86_64:jar:natives:1.1:compile
[INFO] |  |     |  \- com.github.fommil.netlib:native_system-java:jar:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_system-linux-x86_64:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_system-linux-i686:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_system-linux-armhf:jar:natives:1.1:compile
[INFO] |  |     +- com.github.fommil.netlib:netlib-native_system-win-x86_64:jar:natives:1.1:compile
[INFO] |  |     \- com.github.fommil.netlib:netlib-native_system-win-i686:jar:natives:1.1:compile
[INFO] |  +- net.sourceforge.f2j:arpack_combined_all:jar:0.1:compile
[INFO] |  \- com.googlecode.netlib-java:netlib-java:jar:1.1:compile
[INFO] |     \- com.github.fommil.netlib:core:jar:1.1:compile
[INFO] +- org.apache.httpcomponents:fluent-hc:jar:4.5.1:compile
[INFO] |  \- commons-logging:commons-logging:jar:1.2:compile
[INFO] +- eu.medsea.mimeutil:mime-util:jar:2.1.3:compile
[INFO] \- com.sparkjava:spark-core:jar:2.8.0:compile
[INFO]    +- org.eclipse.jetty:jetty-server:jar:9.4.12.v20180830:compile
[INFO]    |  +- javax.servlet:javax.servlet-api:jar:3.1.0:compile
[INFO]    |  +- org.eclipse.jetty:jetty-http:jar:9.4.12.v20180830:compile
[INFO]    |  |  \- org.eclipse.jetty:jetty-util:jar:9.4.12.v20180830:compile
[INFO]    |  \- org.eclipse.jetty:jetty-io:jar:9.4.12.v20180830:compile
[INFO]    +- org.eclipse.jetty:jetty-webapp:jar:9.4.12.v20180830:compile
[INFO]    |  +- org.eclipse.jetty:jetty-xml:jar:9.4.12.v20180830:compile
[INFO]    |  \- org.eclipse.jetty:jetty-servlet:jar:9.4.12.v20180830:compile
[INFO]    |     \- org.eclipse.jetty:jetty-security:jar:9.4.12.v20180830:compile
[INFO]    +- org.eclipse.jetty.websocket:websocket-server:jar:9.4.12.v20180830:compile
[INFO]    |  +- org.eclipse.jetty.websocket:websocket-common:jar:9.4.12.v20180830:compile
[INFO]    |  \- org.eclipse.jetty.websocket:websocket-client:jar:9.4.12.v20180830:compile
[INFO]    |     \- org.eclipse.jetty:jetty-client:jar:9.4.12.v20180830:compile
[INFO]    \- org.eclipse.jetty.websocket:websocket-servlet:jar:9.4.12.v20180830:compile
[INFO]       \- org.eclipse.jetty.websocket:websocket-api:jar:9.4.12.v20180830:compile
[INFO] 
[INFO] ------------------< org.aksw.limes:limes-debian-cli >-------------------
[INFO] Building limes-debian-cli 1.7.7-SNAPSHOT                           [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from maven.aksw.internal: https://maven.aksw.org/repository/internal/org/aksw/limes/limes-core/1.7.7-SNAPSHOT/maven-metadata.xml
Downloading from maven.aksw.snapshots: https://maven.aksw.org/repository/snapshots/org/aksw/limes/limes-core/1.7.7-SNAPSHOT/maven-metadata.xml
[INFO] 
[INFO] --- maven-dependency-plugin:3.0.2:tree (default-cli) @ limes-debian-cli ---
Downloading from maven.aksw.internal: https://maven.aksw.org/repository/internal/org/aksw/limes/limes-core/1.7.7-SNAPSHOT/limes-core-1.7.7-SNAPSHOT.jar
Downloading from maven.aksw.snapshots: https://maven.aksw.org/repository/snapshots/org/aksw/limes/limes-core/1.7.7-SNAPSHOT/limes-core-1.7.7-SNAPSHOT.jar
[INFO] org.aksw.limes:limes-debian-cli:jar:1.7.7-SNAPSHOT
[INFO] \- org.aksw.limes:limes-core:jar:1.7.7-SNAPSHOT:compile
[INFO]    +- org.slf4j:slf4j-api:jar:1.7.21:compile
[INFO]    +- de.vandermeer:asciitable:jar:0.3.2:compile
[INFO]    |  +- de.vandermeer:ascii-utf-themes:jar:0.0.1:compile
[INFO]    |  |  \- de.vandermeer:skb-interfaces:jar:0.0.1:compile
[INFO]    |  |     +- org.antlr:ST4:jar:4.0.8:compile
[INFO]    |  |     |  \- org.antlr:antlr-runtime:jar:3.5.2:compile
[INFO]    |  |     \- org.antlr:antlr4:jar:4.5.1:compile
[INFO]    |  \- de.vandermeer:char-translation:jar:0.0.2:compile
[INFO]    +- org.apache.commons:commons-math3:jar:3.3:compile
[INFO]    +- org.apache.logging.log4j:log4j-slf4j-impl:jar:2.6.1:compile
[INFO]    +- org.slf4j:log4j-over-slf4j:jar:1.7.21:compile
[INFO]    +- org.slf4j:jcl-over-slf4j:jar:1.7.21:compile
[INFO]    +- org.apache.logging.log4j:log4j-api:jar:2.17.1:compile
[INFO]    +- org.apache.logging.log4j:log4j-core:jar:2.17.1:compile
[INFO]    +- commons-codec:commons-codec:jar:1.11:compile
[INFO]    +- org.apache.jena:apache-jena-libs:pom:4.2.0:compile
[INFO]    |  +- org.apache.jena:jena-shacl:jar:4.2.0:compile
[INFO]    |  +- org.apache.jena:jena-shex:jar:4.2.0:compile
[INFO]    |  |  \- org.apache.jena:jena-arq:jar:tests:4.2.0:compile
[INFO]    |  |     +- com.apicatalog:titanium-json-ld:jar:1.1.0:compile
[INFO]    |  |     \- org.glassfish:jakarta.json:jar:2.0.1:compile
[INFO]    |  +- org.apache.jena:jena-tdb:jar:4.2.0:compile
[INFO]    |  +- org.apache.jena:jena-tdb2:jar:4.2.0:compile
[INFO]    |  |  \- org.apache.jena:jena-dboe-storage:jar:4.2.0:compile
[INFO]    |  |     \- org.apache.jena:jena-dboe-trans-data:jar:4.2.0:compile
[INFO]    |  |        +- org.apache.jena:jena-dboe-transaction:jar:4.2.0:compile
[INFO]    |  |        |  \- org.apache.jena:jena-dboe-base:jar:4.2.0:compile
[INFO]    |  |        \- org.apache.jena:jena-dboe-index:jar:4.2.0:compile
[INFO]    |  \- org.apache.jena:jena-rdfconnection:jar:4.2.0:compile
[INFO]    +- org.aksw.jena-sparql-api:jena-sparql-api-cache-h2:jar:3.9.0-1:compile
[INFO]    |  +- org.aksw.jena-sparql-api:jena-sparql-api-resources:jar:3.9.0-1:compile
[INFO]    |  \- com.h2database:h2:jar:1.4.196:compile
[INFO]    +- org.aksw.jena-sparql-api:jena-sparql-api-core:jar:3.9.0-1:compile
[INFO]    |  +- org.aksw.jena-sparql-api:jena-sparql-api-mapper-annotations:jar:3.9.0-1:compile
[INFO]    |  +- org.aksw.jena-sparql-api:jena-sparql-api-utils:jar:3.9.0-1:compile
[INFO]    |  |  +- org.apache.jena:jena-sdb:jar:3.9.0:compile
[INFO]    |  |  |  \- org.apache.jena:jena-cmds:jar:3.9.0:compile
[INFO]    |  |  +- org.aksw.commons:aksw-commons-util:jar:0.8.10:compile
[INFO]    |  |  |  \- net.sourceforge.collections:collections-generic:jar:4.01:compile
[INFO]    |  |  \- com.google.code.gson:gson:jar:2.8.2:compile
[INFO]    |  +- org.aksw.jena-sparql-api:jena-sparql-api-vocabs:jar:3.9.0-1:compile
[INFO]    |  +- org.aksw.jena-sparql-api:jena-sparql-api-sparql-ext:jar:3.9.0-1:compile
[INFO]    |  |  +- net.sf.jopt-simple:jopt-simple:jar:5.0.4:compile
[INFO]    |  |  +- com.jayway.jsonpath:json-path:jar:2.4.0:compile
[INFO]    |  |  |  \- net.minidev:json-smart:jar:2.3:compile
[INFO]    |  |  |     \- net.minidev:accessors-smart:jar:1.2:compile
[INFO]    |  |  |        \- org.ow2.asm:asm:jar:5.0.4:compile
[INFO]    |  |  +- commons-validator:commons-validator:jar:1.6:compile
[INFO]    |  |  |  +- commons-beanutils:commons-beanutils:jar:1.9.2:compile
[INFO]    |  |  |  \- commons-digester:commons-digester:jar:1.8.1:compile
[INFO]    |  |  +- com.vividsolutions:jts-core:jar:1.14.0:compile
[INFO]    |  |  +- com.vividsolutions:jts-io:jar:1.14.0:compile
[INFO]    |  |  |  \- com.googlecode.json-simple:json-simple:jar:1.1:compile
[INFO]    |  |  \- org.codehaus.plexus:plexus-utils:jar:3.1.0:compile
[INFO]    |  +- io.reactivex.rxjava2:rxjava:jar:2.1.14:compile
[INFO]    |  |  \- org.reactivestreams:reactive-streams:jar:1.0.2:compile
[INFO]    |  +- com.github.davidmoten:rxjava2-extras:jar:0.1.28:compile
[INFO]    |  |  \- com.github.davidmoten:guava-mini:jar:0.1.1:compile
[INFO]    |  +- org.apache.jena:jena-iri:jar:3.9.0:compile
[INFO]    |  +- org.aksw.commons:aksw-commons-collections:jar:0.8.10:compile
[INFO]    |  |  \- com.codepoetics:protonpack:jar:1.11:compile
[INFO]    |  +- com.google.guava:guava:jar:24.0-jre:compile
[INFO]    |  |  +- com.google.code.findbugs:jsr305:jar:1.3.9:compile
[INFO]    |  |  +- org.checkerframework:checker-compat-qual:jar:2.0.0:compile
[INFO]    |  |  +- com.google.errorprone:error_prone_annotations:jar:2.1.3:compile
[INFO]    |  |  +- com.google.j2objc:j2objc-annotations:jar:1.1:compile
[INFO]    |  |  \- org.codehaus.mojo:animal-sniffer-annotations:jar:1.14:compile
[INFO]    |  +- org.apache.commons:commons-compress:jar:1.15:compile
[INFO]    |  |  \- org.objenesis:objenesis:jar:2.6:compile
[INFO]    |  +- org.aksw.jena-sparql-api:jena-sparql-api-resources-test-config:jar:3.9.0-1:compile
[INFO]    |  \- com.nurkiewicz.asyncretry:asyncretry-jdk7:jar:0.0.6:compile
[INFO]    +- org.apache.jena:jena-core:jar:3.9.0:compile
[INFO]    |  +- commons-cli:commons-cli:jar:1.4:compile
[INFO]    |  \- org.apache.jena:jena-base:jar:3.9.0:compile
[INFO]    |     +- org.apache.commons:commons-csv:jar:1.5:compile
[INFO]    |     +- commons-io:commons-io:jar:2.6:compile
[INFO]    |     \- com.github.andrewoma.dexx:collection:jar:0.7:compile
[INFO]    +- org.apache.jena:jena-arq:jar:3.9.0:compile
[INFO]    |  +- org.apache.jena:jena-shaded-guava:jar:3.9.0:compile
[INFO]    |  +- org.apache.httpcomponents:httpclient:jar:4.5.5:compile
[INFO]    |  |  \- org.apache.httpcomponents:httpcore:jar:4.4.9:compile
[INFO]    |  +- com.github.jsonld-java:jsonld-java:jar:0.12.1:compile
[INFO]    |  |  +- com.fasterxml.jackson.core:jackson-core:jar:2.9.6:compile
[INFO]    |  |  \- com.fasterxml.jackson.core:jackson-databind:jar:2.9.6:compile
[INFO]    |  |     \- com.fasterxml.jackson.core:jackson-annotations:jar:2.9.0:compile
[INFO]    |  +- org.apache.httpcomponents:httpclient-cache:jar:4.5.5:compile
[INFO]    |  +- org.apache.thrift:libthrift:jar:0.10.0:compile
[INFO]    |  \- org.apache.commons:commons-lang3:jar:3.4:compile
[INFO]    +- org.apache.jena:jena-jdbc-driver-mem:jar:3.6.0:compile
[INFO]    |  \- org.apache.jena:jena-jdbc-core:jar:3.6.0:compile
[INFO]    +- org.apache.jena:jena-jdbc-driver-remote:jar:3.6.0:compile
[INFO]    +- org.apache.jena:jena-jdbc-driver-tdb:jar:3.6.0:compile
[INFO]    +- org.locationtech.jts:jts:pom:1.16.0:compile
[INFO]    +- org.locationtech.jts:jts-core:jar:1.16.0:compile
[INFO]    +- algorithms.edjoin:edjoin-plus:jar:2011:compile
[INFO]    +- uk.ac.shef.wit:simmetrics:jar:1.6.2:compile
[INFO]    +- com.opencsv:opencsv:jar:3.7:compile
[INFO]    +- commons-lang:commons-lang:jar:2.5:compile
[INFO]    +- edu.mit:jwi:jar:2.4.0:compile
[INFO]    +- jgraphx:jgraphx:jar:1.0:compile
[INFO]    +- commons-collections:commons-collections:jar:3.2.2:compile
[INFO]    +- ssjoin:ssjoin:jar:1.0:compile
[INFO]    +- junit:junit:jar:4.12:compile
[INFO]    |  \- org.hamcrest:hamcrest-core:jar:1.3:compile
[INFO]    +- fr.ign.cogit:geoxygene-api:jar:1.6:compile
[INFO]    +- fr.ign.cogit:geoxygene-spatial:jar:1.6:compile
[INFO]    +- net.sf.jgap:jgap:jar:3.4.4:compile
[INFO]    |  +- net.sf.trove4j:trove4j:jar:2.0.2:compile
[INFO]    |  +- com.thoughtworks.xstream:xstream:jar:1.2.2:compile
[INFO]    |  |  \- xpp3:xpp3_min:jar:1.1.3.4.O:compile
[INFO]    |  +- xpp3:xpp3:jar:1.1.3.4.O:compile
[INFO]    |  +- tablelayout:TableLayout:jar:20050920:compile
[INFO]    |  +- net.sf.jcgrid:jcgrid:jar:0.05:compile
[INFO]    |  \- junit-addons:junit-addons:jar:1.4:compile
[INFO]    |     +- xerces:xercesImpl:jar:2.6.2:compile
[INFO]    |     \- xerces:xmlParserAPIs:jar:2.6.2:compile
[INFO]    +- org.fusesource.jansi:jansi:jar:1.11:compile
[INFO]    +- nz.ac.waikato.cms.weka:weka-dev:jar:3.9.0:compile
[INFO]    |  +- nz.ac.waikato.cms.weka.thirdparty:java-cup-11b:jar:2015.03.26:compile
[INFO]    |  +- nz.ac.waikato.cms.weka.thirdparty:java-cup-11b-runtime:jar:2015.03.26:compile
[INFO]    |  +- nz.ac.waikato.cms.weka.thirdparty:bounce:jar:0.18:compile
[INFO]    |  +- com.googlecode.matrix-toolkits-java:mtj:jar:1.0.4:compile
[INFO]    |  |  \- com.github.fommil.netlib:all:pom:1.1.2:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_ref-osx-x86_64:jar:natives:1.1:compile
[INFO]    |  |     |  \- com.github.fommil.netlib:native_ref-java:jar:1.1:compile
[INFO]    |  |     |     \- com.github.fommil:jniloader:jar:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_ref-linux-x86_64:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_ref-linux-i686:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_ref-win-x86_64:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_ref-win-i686:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_ref-linux-armhf:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_system-osx-x86_64:jar:natives:1.1:compile
[INFO]    |  |     |  \- com.github.fommil.netlib:native_system-java:jar:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_system-linux-x86_64:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_system-linux-i686:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_system-linux-armhf:jar:natives:1.1:compile
[INFO]    |  |     +- com.github.fommil.netlib:netlib-native_system-win-x86_64:jar:natives:1.1:compile
[INFO]    |  |     \- com.github.fommil.netlib:netlib-native_system-win-i686:jar:natives:1.1:compile
[INFO]    |  +- net.sourceforge.f2j:arpack_combined_all:jar:0.1:compile
[INFO]    |  \- com.googlecode.netlib-java:netlib-java:jar:1.1:compile
[INFO]    |     \- com.github.fommil.netlib:core:jar:1.1:compile
[INFO]    +- org.apache.httpcomponents:fluent-hc:jar:4.5.1:compile
[INFO]    |  \- commons-logging:commons-logging:jar:1.2:compile
[INFO]    +- eu.medsea.mimeutil:mime-util:jar:2.1.3:compile
[INFO]    \- com.sparkjava:spark-core:jar:2.8.0:compile
[INFO]       +- org.eclipse.jetty:jetty-server:jar:9.4.12.v20180830:compile
[INFO]       |  +- javax.servlet:javax.servlet-api:jar:3.1.0:compile
[INFO]       |  +- org.eclipse.jetty:jetty-http:jar:9.4.12.v20180830:compile
[INFO]       |  |  \- org.eclipse.jetty:jetty-util:jar:9.4.12.v20180830:compile
[INFO]       |  \- org.eclipse.jetty:jetty-io:jar:9.4.12.v20180830:compile
[INFO]       +- org.eclipse.jetty:jetty-webapp:jar:9.4.12.v20180830:compile
[INFO]       |  +- org.eclipse.jetty:jetty-xml:jar:9.4.12.v20180830:compile
[INFO]       |  \- org.eclipse.jetty:jetty-servlet:jar:9.4.12.v20180830:compile
[INFO]       |     \- org.eclipse.jetty:jetty-security:jar:9.4.12.v20180830:compile
[INFO]       +- org.eclipse.jetty.websocket:websocket-server:jar:9.4.12.v20180830:compile
[INFO]       |  +- org.eclipse.jetty.websocket:websocket-common:jar:9.4.12.v20180830:compile
[INFO]       |  \- org.eclipse.jetty.websocket:websocket-client:jar:9.4.12.v20180830:compile
[INFO]       |     \- org.eclipse.jetty:jetty-client:jar:9.4.12.v20180830:compile
[INFO]       \- org.eclipse.jetty.websocket:websocket-servlet:jar:9.4.12.v20180830:compile
[INFO]          \- org.eclipse.jetty.websocket:websocket-api:jar:9.4.12.v20180830:compile

KonradHoeffner · 2022-02-07T12:36:51Z

limes$ ack "log4j" -t xml
limes-core/pom.xml
85:            <groupId>org.apache.logging.log4j</groupId>
86:            <artifactId>log4j-slf4j-impl</artifactId>
92:            <artifactId>log4j-over-slf4j</artifactId>
103:            <groupId>org.apache.logging.log4j</groupId>
104:            <artifactId>log4j-api</artifactId>
109:            <groupId>org.apache.logging.log4j</groupId>
110:            <artifactId>log4j-core</artifactId>
150:            <groupId>org.apache.logging.log4j</groupId>
151:            <artifactId>log4j-web</artifactId>
165:                    <artifactId>slf4j-log4j12</artifactId>
185:                    <artifactId>slf4j-log4j12</artifactId>
200:                    <artifactId>slf4j-log4j12</artifactId>
219:                    <artifactId>slf4j-log4j12</artifactId>
223:                    <artifactId>log4j</artifactId>
224:                    <groupId>log4j</groupId>
238:                    <artifactId>slf4j-log4j12</artifactId>
242:                    <artifactId>log4j</artifactId>
243:                    <groupId>log4j</groupId>
257:                    <artifactId>slf4j-log4j12</artifactId>
261:                    <artifactId>log4j</artifactId>
262:                    <groupId>log4j</groupId>
363:                    <groupId>log4j</groupId>
364:                    <artifactId>log4j</artifactId>
400:                    <artifactId>slf4j-log4j12</artifactId>
404:                    <artifactId>log4j</artifactId>
405:                    <groupId>log4j</groupId>

KonradHoeffner · 2022-02-07T12:44:12Z

Updating dependencies

+++ b/limes-core/pom.xml
@@ -84,19 +84,19 @@
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j-impl</artifactId>
-            <version>2.6.1</version>
+            <version>2.17.1</version>
         </dependency>
 
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>log4j-over-slf4j</artifactId>
-            <version>1.7.21</version>
+            <version>1.7.35</version>
         </dependency>
 
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>jcl-over-slf4j</artifactId>
-            <version>1.7.21</version>
+            <version>1.7.35</version>
         </dependency>
 
         <dependency>
@@ -149,7 +149,7 @@
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-web</artifactId>
-            <version>2.6.2</version>
+            <version>2.17.1</version>
             <scope>test</scope>
         </dependency>
         <dependency>

This seems to fix the problem.

KonradHoeffner · 2022-02-07T12:58:52Z

However now there is:

Exception in thread "main" java.lang.NoSuchFieldError: SHACLC
	at org.apache.jena.shacl.compact.SHACLC.init(SHACLC.java:57)
	at org.apache.jena.shacl.sys.InitShacl.start(InitShacl.java:30)
	at org.apache.jena.sys.JenaSystem.lambda$init$2(JenaSystem.java:116)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
	at org.apache.jena.sys.JenaSystem.forEach(JenaSystem.java:191)
	at org.apache.jena.sys.JenaSystem.forEach(JenaSystem.java:168)
	at org.apache.jena.sys.JenaSystem.init(JenaSystem.java:114)
	at org.apache.jena.graph.NodeFactory.<clinit>(NodeFactory.java:32)
	at org.apache.jena.rdf.model.impl.ResourceImpl.fresh(ResourceImpl.java:135)
	at org.apache.jena.rdf.model.impl.ResourceImpl.<init>(ResourceImpl.java:85)
	at org.apache.jena.rdf.model.ResourceFactory$Impl.createResource(ResourceFactory.java:297)
	at org.apache.jena.rdf.model.ResourceFactory.createResource(ResourceFactory.java:92)
	at org.apache.jena.vocabulary.OWL.<clinit>(OWL.java:46)
	at org.aksw.limes.core.io.mapping.AMapping.<init>(AMapping.java:48)
	at org.aksw.limes.core.io.mapping.MemoryMapping.<init>(MemoryMapping.java:44)
	at org.aksw.limes.core.io.mapping.MappingFactory.createDefaultMapping(MappingFactory.java:36)
	at org.aksw.limes.core.execution.engine.SimpleExecutionEngine.execute(SimpleExecutionEngine.java:523)
	at org.aksw.limes.core.controller.LSPipeline.execute(LSPipeline.java:110)
	at org.aksw.limes.core.controller.LSPipeline.execute(LSPipeline.java:69)
	at org.aksw.limes.core.controller.Controller.getMapping(Controller.java:224)
	at org.aksw.limes.core.controller.Controller.getMapping(Controller.java:187)
	at org.aksw.limes.core.controller.Controller.main(Controller.java:97)

KonradHoeffner · 2022-02-07T13:08:54Z

I tried the following but there is still the error with "SHACLC":

--- a/limes-core/pom.xml
+++ b/limes-core/pom.xml
@@ -84,19 +84,19 @@
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j-impl</artifactId>
-            <version>2.6.1</version>
+            <version>2.17.1</version>
         </dependency>
 
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>log4j-over-slf4j</artifactId>
-            <version>1.7.21</version>
+            <version>1.7.35</version>
         </dependency>
 
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>jcl-over-slf4j</artifactId>
-            <version>1.7.21</version>
+            <version>1.7.35</version>
         </dependency>
 
         <dependency>
@@ -110,7 +110,11 @@
             <artifactId>log4j-core</artifactId>
             <version>2.17.1</version>
         </dependency>
-
+               <dependency>
+            <groupId>org.aksw.commons</groupId>
+                       <artifactId>aksw-commons-util</artifactId>
+                       <version>0.8.14</version>
+        </dependency>
         <!--<dependency>-->
         <!--<groupId>com.ibm.icu</groupId>-->
         <!--<artifactId>icu4j</artifactId>-->
@@ -132,13 +136,13 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>apache-jena-libs</artifactId>
-            <version>4.2.0</version>
+            <version>4.4.0</version>
             <type>pom</type>
         </dependency>
         <dependency>
             <groupId>org.aksw.jena-sparql-api</groupId>
             <artifactId>jena-sparql-api-cache-h2</artifactId>
-            <version>3.9.0-1</version>
+            <version>3.17.0-1</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.aksw.jena-sparql-api</groupId>
@@ -149,13 +153,13 @@
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-web</artifactId>
-            <version>2.6.2</version>
+            <version>2.17.1</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.aksw.jena-sparql-api</groupId>
             <artifactId>jena-sparql-api-core</artifactId>
-            <version>3.9.0-1</version>
+            <version>3.17.0-1</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>

KonradHoeffner · 2022-02-07T13:41:42Z

Maybe Maven master @LorenzBuehmann can help out?

KonradHoeffner · 2022-02-07T17:39:03Z

The dependencies seem seriously out of tune. After updating all the Jena dependencies the error goes away, however now there is:

ERROR StatusLogger Caught java.lang.AbstractMethodError setting feature http://xml.org/sax/features/external-general-entities to false on DocumentBuilderFactory org.apache.xerces.jaxp.DocumentBuilderFactoryImpl@7dc222ae: java.lang.AbstractMethodError: Receiver class org.apache.xerces.jaxp.DocumentBuilderFactoryImpl does not define or inherit an implementation of the resolved method 'abstract void setFeature(java.lang.String, boolean)' of abstract class javax.xml.parsers.DocumentBuilderFactory.
 java.lang.AbstractMethodError: Receiver class org.apache.xerces.jaxp.DocumentBuilderFactoryImpl does not define or inherit an implementation of the resolved method 'abstract void setFeature(java.lang.String, boolean)' of abstract class javax.xml.parsers.DocumentBuilderFactory.
	at org.apache.logging.log4j.core.config.xml.XmlConfiguration.setFeature(XmlConfiguration.java:204)
	at org.apache.logging.log4j.core.config.xml.XmlConfiguration.disableDtdProcessing(XmlConfiguration.java:197)
	at org.apache.logging.log4j.core.config.xml.XmlConfiguration.newDocumentBuilder(XmlConfiguration.java:186)
	at org.apache.logging.log4j.core.config.xml.XmlConfiguration.<init>(XmlConfiguration.java:89)
	at org.apache.logging.log4j.core.config.xml.XmlConfigurationFactory.getConfiguration(XmlConfigurationFactory.java:46)
	at org.apache.logging.log4j.core.config.ConfigurationFactory$Factory.getConfiguration(ConfigurationFactory.java:557)
	at org.apache.logging.log4j.core.config.ConfigurationFactory$Factory.getConfiguration(ConfigurationFactory.java:481)
	at org.apache.logging.log4j.core.config.ConfigurationFactory.getConfiguration(ConfigurationFactory.java:323)
	at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:695)
	at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
	at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
	at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:245)
	at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
	at org.apache.logging.log4j.LogManager.getContext(LogManager.java:176)
	at org.apache.logging.slf4j.Log4jLoggerFactory.getContext(Log4jLoggerFactory.java:54)
	at org.apache.logging.log4j.spi.AbstractLoggerAdapter.getLogger(AbstractLoggerAdapter.java:47)
	at org.apache.logging.slf4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:33)
	at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:358)
	at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:383)
	at org.aksw.limes.core.controller.Controller.main(Controller.java:75)

This seems to be another log4j issue, maybe caused by Junit. Upgrading Junit to 4.13.2.
This wasn't enough, excluding junit-addon from jgap because that brings in xerces.

KonradHoeffner · 2022-02-07T17:50:31Z

Hooray, a new error

$ java -jar ~/projekte/java/limes/limes-core/target/limes-core-1.7.7-SNAPSHOT.jar catalogue.xml 
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
18:49:30.475 [main] [] INFO  org.aksw.limes.core.io.cache.HybridCache:125 - Checking for file /home/konrad/projekte/hito/ontology/scripts/limes/cache/-98907991.ser
18:49:30.482 [main] [] INFO  org.aksw.limes.core.io.cache.HybridCache:142 - No cached data found for c1
18:49:30.483 [main] [] INFO  org.aksw.limes.core.io.query.QueryModuleFactory:35 - Generating <TURTLE> reader
Exception in thread "main" java.lang.ExceptionInInitializerError
	at org.aksw.limes.core.io.query.FileQueryModule.<init>(FileQueryModule.java:53)
	at org.aksw.limes.core.io.query.QueryModuleFactory.getQueryModule(QueryModuleFactory.java:52)
	at org.aksw.limes.core.io.cache.HybridCache.getData(HybridCache.java:143)
	at org.aksw.limes.core.io.cache.HybridCache.getData(HybridCache.java:106)
	at org.aksw.limes.core.controller.Controller.getMapping(Controller.java:196)
	at org.aksw.limes.core.controller.Controller.getMapping(Controller.java:187)
	at org.aksw.limes.core.controller.Controller.main(Controller.java:97)
Caused by: java.lang.RuntimeException: java.lang.reflect.InaccessibleObjectException: Unable to make java.lang.invoke.MethodHandles$Lookup(java.lang.Class) accessible: module java.base does not "opens java.lang.invoke" to unnamed module @5d20b857
	at org.aksw.jena_sparql_api.mapper.proxy.MapperProxyUtils.createProxyFactory(MapperProxyUtils.java:1403)
	at org.aksw.jena_sparql_api.mapper.proxy.JenaPluginUtils.createImplementation(JenaPluginUtils.java:219)
	at org.aksw.jena_sparql_api.mapper.proxy.JenaPluginUtils.createImplementation(JenaPluginUtils.java:205)
	at org.aksw.jena_sparql_api.mapper.proxy.JenaPluginUtils.registerResourceClass(JenaPluginUtils.java:258)
	at org.aksw.jena_sparql_api.mapper.proxy.JenaPluginUtils.registerResourceClass(JenaPluginUtils.java:237)
	at org.aksw.jena_sparql_api.mapper.proxy.JenaPluginUtils.registerResourceClasses(JenaPluginUtils.java:179)
	at org.aksw.jena_sparql_api.mapper.proxy.JenaPluginUtils.registerResourceClasses(JenaPluginUtils.java:174)
	at org.aksw.jena_sparql_api.core.plugin.JenaPluginJsaCore.init(JenaPluginJsaCore.java:22)
	at org.aksw.jena_sparql_api.core.plugin.JenaPluginJsaCore.start(JenaPluginJsaCore.java:14)
	at org.apache.jena.base.module.Subsystem.lambda$initialize$2(Subsystem.java:117)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.apache.jena.base.module.Subsystem.forEach(Subsystem.java:193)
	at org.apache.jena.base.module.Subsystem.forEach(Subsystem.java:169)
	at org.apache.jena.base.module.Subsystem.initialize(Subsystem.java:115)
	at org.apache.jena.sys.JenaSystem.init(JenaSystem.java:88)
	at org.apache.jena.rdf.model.ModelFactory.<clinit>(ModelFactory.java:48)
	... 7 more
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make java.lang.invoke.MethodHandles$Lookup(java.lang.Class) accessible: module java.base does not "opens java.lang.invoke" to unnamed module @5d20b857
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:357)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Constructor.checkCanSetAccessible(Constructor.java:188)
	at java.base/java.lang.reflect.Constructor.setAccessible(Constructor.java:181)
	at org.aksw.jena_sparql_api.mapper.proxy.MapperProxyUtils.proxyDefaultMethod(MapperProxyUtils.java:2048)
	at org.aksw.jena_sparql_api.mapper.proxy.MapperProxyUtils.createProxyFactory(MapperProxyUtils.java:1401)
	... 22 more

KonradHoeffner · 2022-02-07T17:53:34Z

This seems to be caused by Java 16, see SmartDataAnalytics/jena-sparql-api#43.

KonradHoeffner · 2022-02-07T17:54:39Z

$ java --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED -jar ~/projekte/java/limes/limes-core/target/limes-core-1.7.7-SNAPSHOT.jar catalogue.xml 
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
18:53:52.006 [main] [] INFO  org.aksw.limes.core.io.cache.HybridCache:125 - Checking for file /home/konrad/projekte/hito/ontology/scripts/limes/cache/-98907991.ser
18:53:52.013 [main] [] INFO  org.aksw.limes.core.io.cache.HybridCache:142 - No cached data found for c1
18:53:52.013 [main] [] INFO  org.aksw.limes.core.io.query.QueryModuleFactory:35 - Generating <TURTLE> reader
Trying to get reader TURTLE
18:53:52.415 [main] [] WARN  org.apache.jena.riot:110 - [line: 37, col: 21] Lexical form '2021-07-29' not valid for datatype XSD gYear
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/codec/digest/MurmurHash3
	at org.apache.jena.riot.lang.BlankNodeAllocatorHash.alloc(BlankNodeAllocatorHash.java:138)
	at org.apache.jena.riot.lang.BlankNodeAllocatorHash.create(BlankNodeAllocatorHash.java:111)
	at org.apache.jena.riot.lang.LabelToNode$Alloc.create(LabelToNode.java:187)
	at org.apache.jena.riot.lang.LabelToNode$Alloc.create(LabelToNode.java:178)
	at org.apache.jena.riot.system.MapWithScope.create(MapWithScope.java:86)
	at org.apache.jena.riot.system.FactoryRDFStd.createBlankNode(FactoryRDFStd.java:97)
	at org.apache.jena.riot.system.ParserProfileStd.createBlankNode(ParserProfileStd.java:220)
	at org.apache.jena.riot.lang.LangTurtleBase.triplesBlankNode(LangTurtleBase.java:495)
	at org.apache.jena.riot.lang.LangTurtleBase.triplesNodeCompound(LangTurtleBase.java:484)
	at org.apache.jena.riot.lang.LangTurtleBase.triplesNode(LangTurtleBase.java:469)
	at org.apache.jena.riot.lang.LangTurtleBase.objectList(LangTurtleBase.java:419)
	at org.apache.jena.riot.lang.LangTurtleBase.predicateObjectItem(LangTurtleBase.java:352)
	at org.apache.jena.riot.lang.LangTurtleBase.predicateObjectList(LangTurtleBase.java:345)
	at org.apache.jena.riot.lang.LangTurtleBase.triples(LangTurtleBase.java:314)
	at org.apache.jena.riot.lang.LangTurtleBase.triplesSameSubject(LangTurtleBase.java:178)
	at org.apache.jena.riot.lang.LangTurtle.oneTopLevelElement(LangTurtle.java:46)
	at org.apache.jena.riot.lang.LangTurtleBase.runParser(LangTurtleBase.java:79)
	at org.apache.jena.riot.lang.LangBase.parse(LangBase.java:43)
	at org.apache.jena.riot.RDFParserRegistry$ReaderRIOTLang.read(RDFParserRegistry.java:186)
	at org.apache.jena.riot.RDFParser.read(RDFParser.java:366)
	at org.apache.jena.riot.RDFParser.parseURI(RDFParser.java:335)
	at org.apache.jena.riot.RDFParser.parse(RDFParser.java:310)
	at org.apache.jena.riot.RDFParserBuilder.parse(RDFParserBuilder.java:552)
	at org.apache.jena.riot.RDFDataMgr.parseFromURI(RDFDataMgr.java:737)
	at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:193)
	at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:161)
	at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:148)
	at org.apache.jena.riot.adapters.RDFReaderRIOT.read(RDFReaderRIOT.java:76)
	at org.apache.jena.rdf.model.impl.ModelCom.read(ModelCom.java:229)
	at org.aksw.limes.core.io.query.FileQueryModule.<init>(FileQueryModule.java:56)
	at org.aksw.limes.core.io.query.QueryModuleFactory.getQueryModule(QueryModuleFactory.java:52)
	at org.aksw.limes.core.io.cache.HybridCache.getData(HybridCache.java:143)
	at org.aksw.limes.core.io.cache.HybridCache.getData(HybridCache.java:106)
	at org.aksw.limes.core.controller.Controller.getMapping(Controller.java:196)
	at org.aksw.limes.core.controller.Controller.getMapping(Controller.java:187)
	at org.aksw.limes.core.controller.Controller.main(Controller.java:97)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.codec.digest.MurmurHash3
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:636)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:182)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:519)
	... 36 more

KonradHoeffner · 2022-02-07T18:03:28Z

This seems to be this error: https://www.mail-archive.com/dev@jena.apache.org/msg27968.html caused by a missing commons-code dependency in jena-arq, adding it manually in version 1.15.

IT WORKS!

Disclaimer: On Java 16 only when called like this: java --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED -jar ~/projekte/java/limes/limes-core/target/limes-core-1.7.7-SNAPSHOT.jar catalogue.xml

This was referenced Feb 2, 2022

Add WordNet Dockerfile. #270

Closed

LIMES does not work anymore: java.lang.NoClassDefFoundError #272

Closed

KonradHoeffner mentioned this issue Feb 7, 2022

Fix NoClassDefError. #273

Merged

MSherif closed this as completed in #273 Mar 4, 2022

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Docker: NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil #271

Docker: NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil #271

KonradHoeffner commented Feb 2, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022 •

edited

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022 •

edited

KonradHoeffner commented Feb 7, 2022 •

edited

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022 •

edited

Docker: NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil #271

Docker: NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil #271

Comments

KonradHoeffner commented Feb 2, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022 • edited

Updating dependencies

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022 • edited

KonradHoeffner commented Feb 7, 2022 • edited

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022

KonradHoeffner commented Feb 7, 2022 • edited

IT WORKS!

KonradHoeffner commented Feb 7, 2022 •

edited

KonradHoeffner commented Feb 7, 2022 •

edited

KonradHoeffner commented Feb 7, 2022 •

edited

KonradHoeffner commented Feb 7, 2022 •

edited