Unable to compile on Linux

[kohjy2000]

Hi @pnrobinson,

I'm unable to compile the HPOWorkbench on Linux. I'm using maven v3.8.5.

I'm also using java version 17.0.3

openjdk 17.0.3 2022-04-19 OpenJDK Runtime Environment (build 17.0.3+7-Ubuntu-0ubuntu0.20.04.1) OpenJDK 64-Bit Server VM (build 17.0.3+7-Ubuntu-0ubuntu0.20.04.1, mixed mode, sharing)

Here is the error report:

june-young@DESKTOP-PJI8A90:~/HPOworkbench$ mvn clean package [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.4 [WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /home/june-young/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.4 [WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /home/june-young/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:2.1.4 [WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /home/june-young/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:2.1.4 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 2.1.4 [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 2.1.4 [2/4] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench-core --- [INFO] Deleting /home/june-young/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 /home/june-young/HPOworkbench/hpoworkbench-core/src/main/resources [INFO] skip non existing resourceDirectory /home/june-young/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 19 source files to /home/june-young/HPOworkbench/hpoworkbench-core/target/classes [INFO] /home/june-young/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/github/GitHubLabelRetriever.java: Some input files use unchecked or unsafe operations. [INFO] /home/june-young/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/github/GitHubLabelRetriever.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] skip non existing resourceDirectory /home/june-young/HPOworkbench/hpoworkbench-core/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ hpoworkbench-core --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M5:test (default-test) @ hpoworkbench-core --- [INFO] No tests to run. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ hpoworkbench-core --- [INFO] Building jar: /home/june-young/HPOworkbench/hpoworkbench-core/target/hpoworkbench-core-2.1.4.jar [INFO] [INFO] --------< org.monarchinitiative.hpoworkbench:hpoworkbench-cli >--------- [INFO] Building org.monarchinitiative.hpoworkbench:hpoworkbench-cli 2.1.4 [3/4] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for org.phenopackets.phenotools:phenotools-converter:jar:0.0.2-SNAPSHOT is missing, no dependency information available [WARNING] The POM for org.phenopackets.phenotools:phenotools-builder:jar:0.0.2-SNAPSHOT is missing, no dependency information available [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for HPOworkbench 2.1.4: [INFO] [INFO] HPOworkbench ....................................... SUCCESS [ 0.124 s] [INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core SUCCESS [ 2.343 s] [INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli FAILURE [ 0.180 s] [INFO] hpoworkbench-gui ................................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2.835 s [INFO] Finished at: 2022-05-31T14:50:39+09:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal on project hpoworkbench-cli: Could not resolve dependencies for project org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.4: The following artifacts could not be resolved: org.phenopackets.phenotools:phenotools-converter:jar:0.0.2-SNAPSHOT, org.phenopackets.phenotools:phenotools-builder:jar:0.0.2-SNAPSHOT: Could not find artifact org.phenopackets.phenotools:phenotools-converter:jar:0.0.2-SNAPSHOT -> [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/DependencyResolutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :hpoworkbench-cli

Any ideas?

Thanks!

June-Young

[kohjy2000]

Also, I want to ask to try using the HPO workbanch on older versions of Windows?

Thank you for your cooperation.

[pnrobinson]

Now I see what the problem is. We are in the process of updating some dependencies in our libraries. I think this should work again by the end of the week after the latest version is on maven central. HPOWorkbench is not a published project it is more of a prototyping tool that we made public in case it is of interest!

[pnrobinson]

@kohjy2000 I think I have been able to fix this problem, please let me know if this works now for you.

[pnrobinson]

Note that this package needs to be installed localled with mvn install https://github.com/phenopackets/phenopacket-tools

We are putting this onto laven central next week.

[kohjy2000]

Thank you for solving the problem. After this update, the previous error has been resolved. I'm currently getting an error, but this is a Java version issue for our Linux server and I'm discussing a Java version upgrade with our server manager. Thank you very much