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TheJacksonLaboratory / HPOworkbench

Human Phenotype Ontology Workbench
http://hpo-workbench.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
15 stars 8 forks source link

Unable to compile on Linux #70

Open oleraj opened 2 years ago

oleraj commented 2 years ago

Hi @pnrobinson,

I'm unable to compile the HPOWorkbench on Linux. I'm using maven v3.6.2.

Here is the error report:

mvn clean package
[INFO] Scanning for projects...
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-starter-parent/2.5.1/spring-boot-starter-parent-2.5.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-starter-parent/2.5.1/spring-boot-starter-parent-2.5.1.pom (8.6 kB at 25 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-dependencies/2.5.1/spring-boot-dependencies-2.5.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-dependencies/2.5.1/spring-boot-dependencies-2.5.1.pom (109 kB at 2.4 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/datastax/oss/java-driver-bom/4.11.1/java-driver-bom-4.11.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/datastax/oss/java-driver-bom/4.11.1/java-driver-bom-4.11.1.pom (4.1 kB at 207 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-bom/4.1.22/metrics-bom-4.1.22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-bom/4.1.22/metrics-bom-4.1.22.pom (5.3 kB at 332 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-parent/4.1.22/metrics-parent-4.1.22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-parent/4.1.22/metrics-parent-4.1.22.pom (17 kB at 948 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/groovy/groovy-bom/3.0.8/groovy-bom-3.0.8.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/groovy/groovy-bom/3.0.8/groovy-bom-3.0.8.pom (26 kB at 825 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/infinispan/infinispan-bom/12.1.4.Final/infinispan-bom-12.1.4.Final.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/infinispan/infinispan-bom/12.1.4.Final/infinispan-bom-12.1.4.Final.pom (18 kB at 840 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/infinispan/infinispan-build-configuration-parent/12.1.4.Final/infinispan-build-configuration-parent-12.1.4.Final.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/infinispan/infinispan-build-configuration-parent/12.1.4.Final/infinispan-build-configuration-parent-12.1.4.Final.pom (14 kB at 614 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/jboss/jboss-parent/36/jboss-parent-36.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/jboss/jboss-parent/36/jboss-parent-36.pom (66 kB at 2.3 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/jackson-bom/2.12.3/jackson-bom-2.12.3.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/jackson-bom/2.12.3/jackson-bom-2.12.3.pom (17 kB at 906 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/jackson-parent/2.12/jackson-parent-2.12.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/jackson/jackson-parent/2.12/jackson-parent-2.12.pom (7.5 kB at 228 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/fasterxml/oss-parent/41/oss-parent-41.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/fasterxml/oss-parent/41/oss-parent-41.pom (23 kB at 1.3 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/glassfish/jersey/jersey-bom/2.33/jersey-bom-2.33.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/glassfish/jersey/jersey-bom/2.33/jersey-bom-2.33.pom (19 kB at 1.1 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/eclipse/ee4j/project/1.0.6/project-1.0.6.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/ee4j/project/1.0.6/project-1.0.6.pom (13 kB at 833 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/eclipse/jetty/jetty-bom/9.4.42.v20210604/jetty-bom-9.4.42.v20210604.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/jetty/jetty-bom/9.4.42.v20210604/jetty-bom-9.4.42.v20210604.pom (18 kB at 802 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/junit/junit-bom/5.7.2/junit-bom-5.7.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/junit/junit-bom/5.7.2/junit-bom-5.7.2.pom (5.1 kB at 268 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/jetbrains/kotlin/kotlin-bom/1.5.10/kotlin-bom-1.5.10.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/jetbrains/kotlin/kotlin-bom/1.5.10/kotlin-bom-1.5.10.pom (9.3 kB at 519 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/jetbrains/kotlinx/kotlinx-coroutines-bom/1.5.0/kotlinx-coroutines-bom-1.5.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/jetbrains/kotlinx/kotlinx-coroutines-bom/1.5.0/kotlinx-coroutines-bom-1.5.0.pom (4.1 kB at 216 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/logging/log4j/log4j-bom/2.14.1/log4j-bom-2.14.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/logging/log4j/log4j-bom/2.14.1/log4j-bom-2.14.1.pom (8.1 kB at 450 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/logging/logging-parent/3/logging-parent-3.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/logging/logging-parent/3/logging-parent-3.pom (3.1 kB at 224 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/apache/23/apache-23.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/apache/23/apache-23.pom (18 kB at 921 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/micrometer/micrometer-bom/1.7.0/micrometer-bom-1.7.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/micrometer/micrometer-bom/1.7.0/micrometer-bom-1.7.0.pom (6.8 kB at 400 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/netty/netty-bom/4.1.65.Final/netty-bom-4.1.65.Final.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/netty/netty-bom/4.1.65.Final/netty-bom-4.1.65.Final.pom (8.8 kB at 462 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/oss/oss-parent/7/oss-parent-7.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/oss/oss-parent/7/oss-parent-7.pom (4.8 kB at 268 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/oracle/database/jdbc/ojdbc-bom/21.1.0.0/ojdbc-bom-21.1.0.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/oracle/database/jdbc/ojdbc-bom/21.1.0.0/ojdbc-bom-21.1.0.0.pom (12 kB at 730 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/r2dbc/r2dbc-bom/Arabba-SR10/r2dbc-bom-Arabba-SR10.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/r2dbc/r2dbc-bom/Arabba-SR10/r2dbc-bom-Arabba-SR10.pom (4.3 kB at 360 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/projectreactor/reactor-bom/2020.0.7/reactor-bom-2020.0.7.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/projectreactor/reactor-bom/2020.0.7/reactor-bom-2020.0.7.pom (4.5 kB at 347 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/rsocket/rsocket-bom/1.1.1/rsocket-bom-1.1.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/rsocket/rsocket-bom/1.1.1/rsocket-bom-1.1.1.pom (2.6 kB at 220 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/data/spring-data-bom/2021.0.1/spring-data-bom-2021.0.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/data/spring-data-bom/2021.0.1/spring-data-bom-2021.0.1.pom (5.7 kB at 379 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/spring-framework-bom/5.3.8/spring-framework-bom-5.3.8.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/spring-framework-bom/5.3.8/spring-framework-bom-5.3.8.pom (5.6 kB at 469 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/integration/spring-integration-bom/5.5.0/spring-integration-bom-5.5.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/integration/spring-integration-bom/5.5.0/spring-integration-bom-5.5.0.pom (9.5 kB at 559 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/security/spring-security-bom/5.5.0/spring-security-bom-5.5.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/security/spring-security-bom/5.5.0/spring-security-bom-5.5.0.pom (5.7 kB at 238 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/session/spring-session-bom/2021.0.0/spring-session-bom-2021.0.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/session/spring-session-bom/2021.0.0/spring-session-bom-2021.0.0.pom (2.7 kB at 151 kB/s)
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-cli/pom.xml, line 9, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-gui:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-gui/pom.xml, line 13, column 14
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[WARNING] The project org.monarchinitiative.hpoworkbench:hpoworkbench:pom:2.1.1 uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] HPOworkbench                                                       [pom]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core               [jar]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli                [jar]
[INFO] hpoworkbench-gui                                                   [jar]
[INFO] 
[INFO] ----------< org.monarchinitiative.hpoworkbench:hpoworkbench >-----------
[INFO] Building HPOworkbench 2.1.1                                        [1/4]
[INFO] --------------------------------[ pom ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/3.1.0/maven-clean-plugin-3.1.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/3.1.0/maven-clean-plugin-3.1.0.pom (5.2 kB at 369 kB/s)
[snipped]

Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.2.1/maven-profile-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.2.1/maven-profile-2.2.1.pom (2.2 kB at 217 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.2.1/maven-artifact-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.2.1/maven-artifact-2.2.1.pom (1.6 kB at 144 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.2.1/maven-repository-metadata-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.2.1/maven-repository-metadata-2.2.1.pom (1.9 kB at 89 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.2.1/maven-error-diagnostics-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.2.1/maven-error-diagnostics-2.2.1.pom (1.7 kB at 155 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.2.1/maven-project-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.2.1/maven-project-2.2.1.pom (2.8 kB at 99 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.2.1/maven-artifact-manager-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.2.1/maven-artifact-manager-2.2.1.pom (3.1 kB at 282 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/backport-util-concurrent/backport-util-concurrent/3.1/backport-util-concurrent-3.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/backport-util-concurrent/backport-util-concurrent/3.1/backport-util-concurrent-3.1.pom (880 B at 68 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-registry/2.2.1/maven-plugin-registry-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-registry/2.2.1/maven-plugin-registry-2.2.1.pom (1.9 kB at 161 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.2.1/maven-plugin-descriptor-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.2.1/maven-plugin-descriptor-2.2.1.pom (2.1 kB at 188 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-monitor/2.2.1/maven-monitor-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-monitor/2.2.1/maven-monitor-2.2.1.pom (1.3 kB at 105 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-utils/0.1/maven-shared-utils-0.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-utils/0.1/maven-shared-utils-0.1.pom (4.0 kB at 311 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/18/maven-shared-components-18.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/18/maven-shared-components-18.pom (4.9 kB at 449 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/22/maven-parent-22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/22/maven-parent-22.pom (30 kB at 2.3 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/apache/11/apache-11.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/apache/11/apache-11.pom (15 kB at 1.1 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/google/code/findbugs/jsr305/2.0.1/jsr305-2.0.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/google/code/findbugs/jsr305/2.0.1/jsr305-2.0.1.pom (965 B at 96 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/0.9.10/plexus-java-0.9.10.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/0.9.10/plexus-java-0.9.10.pom (5.1 kB at 464 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-languages/0.9.10/plexus-languages-0.9.10.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-languages/0.9.10/plexus-languages-0.9.10.pom (4.1 kB at 345 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2/asm-6.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2/asm-6.2.pom (2.9 kB at 294 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M9/qdox-2.0-M9.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M9/qdox-2.0-M9.pom (16 kB at 1.2 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-api/2.8.4/plexus-compiler-api-2.8.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-api/2.8.4/plexus-compiler-api-2.8.4.pom (867 B at 62 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler/2.8.4/plexus-compiler-2.8.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler/2.8.4/plexus-compiler-2.8.4.pom (6.0 kB at 502 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-components/4.0/plexus-components-4.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-components/4.0/plexus-components-4.0.pom (2.7 kB at 204 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.0.22/plexus-utils-3.0.22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/3.0.22/plexus-utils-3.0.22.pom (3.8 kB at 383 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/3.3.1/plexus-3.3.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/3.3.1/plexus-3.3.1.pom (20 kB at 1.7 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-manager/2.8.4/plexus-compiler-manager-2.8.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-manager/2.8.4/plexus-compiler-manager-2.8.4.pom (692 B at 63 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-javac/2.8.4/plexus-compiler-javac-2.8.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-javac/2.8.4/plexus-compiler-javac-2.8.4.pom (771 B at 45 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compilers/2.8.4/plexus-compilers-2.8.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compilers/2.8.4/plexus-compilers-2.8.4.pom (1.3 kB at 122 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/3.0/maven-core-3.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model-builder/3.0/maven-model-builder-3.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/3.0/maven-repository-metadata-3.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings-builder/3.0/maven-settings-builder-3.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/3.0/maven-settings-3.0.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/3.0/maven-repository-metadata-3.0.jar (30 kB at 1.3 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-aether-provider/3.0/maven-aether-provider-3.0.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings-builder/3.0/maven-settings-builder-3.0.jar (38 kB at 1.5 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-impl/1.7/aether-impl-1.7.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/3.0/maven-settings-3.0.jar (47 kB at 1.7 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-spi/1.7/aether-spi-1.7.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-spi/1.7/aether-spi-1.7.jar (14 kB at 261 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-api/1.7/aether-api-1.7.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-aether-provider/3.0/maven-aether-provider-3.0.jar (51 kB at 914 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-util/1.7/aether-util-1.7.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model-builder/3.0/maven-model-builder-3.0.jar (148 kB at 2.1 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.14/plexus-interpolation-1.14.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-impl/1.7/aether-impl-1.7.jar (106 kB at 1.4 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-incremental/1.1/maven-shared-incremental-1.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-api/1.7/aether-api-1.7.jar (74 kB at 873 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/0.9.10/plexus-java-0.9.10.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-incremental/1.1/maven-shared-incremental-1.1.jar (14 kB at 137 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2/asm-6.2.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/0.9.10/plexus-java-0.9.10.jar (39 kB at 362 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M9/qdox-2.0-M9.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.14/plexus-interpolation-1.14.jar (61 kB at 550 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-api/2.8.4/plexus-compiler-api-2.8.4.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-util/1.7/aether-util-1.7.jar (108 kB at 947 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-manager/2.8.4/plexus-compiler-manager-2.8.4.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-manager/2.8.4/plexus-compiler-manager-2.8.4.jar (4.7 kB at 36 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-api/2.8.4/plexus-compiler-api-2.8.4.jar (27 kB at 205 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-javac/2.8.4/plexus-compiler-javac-2.8.4.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/3.0/maven-core-3.0.jar (527 kB at 3.8 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2/asm-6.2.jar (111 kB at 783 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-javac/2.8.4/plexus-compiler-javac-2.8.4.jar (21 kB at 143 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M9/qdox-2.0-M9.jar (317 kB at 1.9 MB/s)
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 21 source files to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HPOworkbench 2.1.1:
[INFO] 
[INFO] HPOworkbench ....................................... SUCCESS [  0.997 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core FAILURE [ 12.296 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli  SKIPPED
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  15.128 s
[INFO] Finished at: 2022-04-05T18:34:28-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project hpoworkbench-core: Fatal error compiling: invalid target release: 17 -> [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/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :hpoworkbench-core

After switching to develop branch and re-running, here is the output:

[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-cli/pom.xml, line 9, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-gui:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-gui/pom.xml, line 13, column 14
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[WARNING] The project org.monarchinitiative.hpoworkbench:hpoworkbench:pom:2.1.1 uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] HPOworkbench                                                       [pom]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core               [jar]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli                [jar]
[INFO] hpoworkbench-gui                                                   [jar]
[INFO] 
[INFO] ----------< org.monarchinitiative.hpoworkbench:hpoworkbench >-----------
[INFO] Building HPOworkbench 2.1.1                                        [1/4]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench ---
[INFO] 
[INFO] --------< org.monarchinitiative.hpoworkbench:hpoworkbench-core >--------
[INFO] Building org.monarchinitiative.hpoworkbench:hpoworkbench-core 2.1.1 [2/4]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.pom (6.3 kB at 18 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.pom (3.5 kB at 184 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.pom (20 kB at 897 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.pom (2.6 kB at 173 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.pom (4.6 kB at 288 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.pom (20 kB at 505 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.pom (4.4 kB at 258 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.jar (2.2 MB at 7.9 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.jar (1.0 MB at 3.3 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.jar
Downloaded from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.jar (112 kB at 278 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.jar (327 kB at 788 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.jar (2.9 MB at 6.8 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.jar (2.0 MB at 4.4 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.jar (5.8 MB at 12 MB/s)
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench-core ---
[INFO] Deleting /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/target
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ hpoworkbench-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] skip non existing resourceDirectory /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hpoworkbench-core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 21 source files to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HPOworkbench 2.1.1:
[INFO] 
[INFO] HPOworkbench ....................................... SUCCESS [  0.156 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core FAILURE [  2.028 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli  SKIPPED
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  2.443 s
[INFO] Finished at: 2022-04-05T18:54:14-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project hpoworkbench-core: Fatal error compiling: invalid target release: 17 -> [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/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :hpoworkbench-core

Note that I don't have any experience with compiling Java code, so this could be a very simple error.

Any ideas?

Thanks!

Andrew

pnrobinson commented 2 years ago

Can you let us know what version you are on?

java -version

Possibly installing Java 17 is the issue, https://www.azul.com/downloads/

oleraj commented 2 years ago

Yes, it appears we have an earlier version of java as default on our cluster: java version "1.8.0_92"

I'll see if I can get Java 17.

oleraj commented 2 years ago

Okay, I tried again this time using Java 17. I was able to get past the previous error, however I'm getting a new error:

[INFO] Reactor Summary for HPOworkbench 2.1.1:
[INFO] 
[INFO] HPOworkbench ....................................... SUCCESS [  0.329 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core FAILURE [  7.413 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli  SKIPPED
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  8.164 s
[INFO] Finished at: 2022-04-08T17:41:56-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project hpoworkbench-core: Compilation failure: Compilation failure: 
[ERROR] /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/analysis/HpoStats.java:[8,56] package org.monarchinitiative.phenol.annotations.obo.hpo does not exist
[ERROR] /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/analysis/AnnotationTlc.java:[53,59] cannot find symbol
[ERROR]   symbol:   method getName()
...

This seems to be the important clue: package org.monarchinitiative.phenol.annotations.obo.hpo does not exist

Is this a prerequisite I need?

oleraj commented 2 years ago

I just realized I forgot to switch to develop branch.

Here's the error message I get when I try to compile on the develop branch:

[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-cli/pom.xml, line 9, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-gui:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-gui/pom.xml, line 13, column 14
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[WARNING] The project org.monarchinitiative.hpoworkbench:hpoworkbench:pom:2.1.1 uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] HPOworkbench                                                       [pom]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core               [jar]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli                [jar]
[INFO] hpoworkbench-gui                                                   [jar]
[INFO] 
[INFO] ----------< org.monarchinitiative.hpoworkbench:hpoworkbench >-----------
[INFO] Building HPOworkbench 2.1.1                                        [1/4]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench ---
[INFO] 
[INFO] --------< org.monarchinitiative.hpoworkbench:hpoworkbench-core >--------
[INFO] Building org.monarchinitiative.hpoworkbench:hpoworkbench-core 2.1.1 [2/4]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench-core ---
[INFO] Deleting /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/target
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ hpoworkbench-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] skip non existing resourceDirectory /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hpoworkbench-core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 21 source files to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/target/classes
[INFO] /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/analysis/HpoStats.java: /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/analysis/HpoStats.java uses or overrides a deprecated API.
[INFO] /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/analysis/HpoStats.java: Recompile with -Xlint:deprecation for details.
[INFO] /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/github/GitHubIssueRetriever.java: Some input files use unchecked or unsafe operations.
[INFO] /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/github/GitHubIssueRetriever.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:testResources (default-testResources) @ hpoworkbench-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ hpoworkbench-core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/target/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M5:test (default-test) @ hpoworkbench-core ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/3.0.0-M5/maven-surefire-common-3.0.0-M5.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/3.0.0-M5/maven-surefire-common-3.0.0-M5.pom (9.6 kB at 31 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/3.0.0-M5/surefire-api-3.0.0-M5.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/3.0.0-M5/surefire-api-3.0.0-M5.pom (3.2 kB at 169 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/3.0.0-M5/surefire-logger-api-3.0.0-M5.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/3.0.0-M5/surefire-logger-api-3.0.0-M5.pom (3.7 kB at 231 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-shared-utils/3.0.0-M4/surefire-shared-utils-3.0.0-M4.pom
...
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.monarchinitiative.hpoworkbench.io.HPOParserTest
18:27:31.491 [main] DEBUG org.monarchinitiative.phenol.io.OntologyLoader - Read first bytes: format-version: 
18:27:31.494 [main] DEBUG org.monarchinitiative.phenol.io.OntologyLoader - Looks like a OBO/OWL file...
18:27:31.494 [main] ERROR org.monarchinitiative.phenol.io.OntologyLoader - OBO/OWL support was removed since 2.0.0
[ERROR] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.224 s <<< FAILURE! - in org.monarchinitiative.hpoworkbench.io.HPOParserTest
[ERROR] org.monarchinitiative.hpoworkbench.io.HPOParserTest.testInputOntology  Time elapsed: 0.203 s  <<< ERROR!
org.monarchinitiative.phenol.base.PhenolRuntimeException: OBO/OWL support was removed since 2.0.0, use JSON instead
    at org.monarchinitiative.hpoworkbench.io.HPOParserTest.testInputOntology(HPOParserTest.java:21)

[INFO] 
[INFO] Results:
[INFO] 
[ERROR] Errors: 
[ERROR]   HPOParserTest.testInputOntology:21 » PhenolRuntime OBO/OWL support was removed...
[INFO] 
[ERROR] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HPOworkbench 2.1.1:
[INFO] 
[INFO] HPOworkbench ....................................... SUCCESS [  0.160 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core FAILURE [  7.385 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli  SKIPPED
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  7.811 s
[INFO] Finished at: 2022-04-08T18:27:31-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:3.0.0-M5:test (default-test) on project hpoworkbench-core: There are test failures.
[ERROR] 
[ERROR] Please refer to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream.
[ERROR] -> [Help 1]

Thanks

pnrobinson commented 2 years ago

@oleraj -- please see this file in the Releases section -- hpoworkbench_2.2.2-1_amd64.deb This is an independent program and does not need Java to be preinstalled. Alternatively the JAR file will run if you have Java 17 installed.