It also gives error (mvn version installation)

[DSRYU]

Hello,

I am trying to install using maven. This version also gives the error as below messages:

[ERROR] Failed to execute goal on project matchbox: Could not resolve dependencies for project org.broadinstitute.macarthurlab:matchbox:jar:0.1.0: The following artifacts could not be resolved: org.monarchinitiative.exomiser:exomiser-spring-boot-starter:jar:11.0.0, org.monarchinitiative.exomiser:exomiser-spring-boot-test:jar:11.0.0: Could not find artifact org.monarchinitiative.exomiser:exomiser-spring-boot-starter:jar:11.0.0 in central (https://repo.maven.apache.org/maven2) -> [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

The version of maven is Apache Maven 3.3.9 . root@ubuntu:~/.m2/matchbox# mvn -version Apache Maven 3.3.9 Maven home: /usr/share/maven Java version: 1.8.0_181, vendor: Oracle Corporation Java home: /usr/lib/jvm/java-8-openjdk-amd64/jre Default locale: ko_KR, platform encoding: UTF-8 OS name: "linux", version: "4.4.0-96-generic", arch: "amd64", family: "unix"

The Exomiser directory structure is as follows: root@ubuntu:~/.m2# tree -L 1 Exomiser Exomiser ├── 1807_phenotype ├── 1807_phenotype.tar.gz ├── LICENCE ├── LOGO_IRDIRCRR_RVB.jpg ├── README.md ├── docs ├── exomiser-cli ├── exomiser-core ├── exomiser-data-genome ├── exomiser-data-phenotype ├── exomiser-rest-prioritiser ├── exomiser-spring-boot-autoconfigure ├── exomiser-spring-boot-starter ├── exomiser-spring-boot-test ├── exomiser-web ├── mvnw ├── mvnw.cmd └── pom.xml

I also edited the part of application.properties file. root@ubuntu:~/.m2# vi matchbox/src/main/resources/application.properties

matchbox.gene-symbol-to-id-mappings=${user.dir}/config/gene_symbol_to_ensembl_id_map.txt matchbox.connected-nodes=${user.dir}/config/nodes.json exomiser.data-directory=/home/sysadm/.m2/Exomiser exomiser.phenotype.data-version=1807

I used below command for installation. root@ubuntu:~/.m2/matchbox# mvn clean install package

Could you help me?

[northwestwitch]

I remember experiencing an error like this..

After cloning Exomiser have you installed it? mvn clean install package from inside the cloned repo?

[DSRYU]

I tried it but it gives error. root@ubuntu:/data/reference_data/Exomiser# ls -al ~/.m2/ total 12 drwxr-xr-x 2 root root 4096 11월 22 18:29 . drwxr-xr-x 18 sysadm sysadm 4096 11월 22 18:31 .. -rw-r--r-- 1 root root 86 11월 22 18:29 settings.xml setting.xml < settings>

${user.home}/.m2/repository

root@ubuntu:/data/reference_data/Exomiser# ls -al total 228 drwxr-xr-x 15 root root 4096 11월 22 18:31 . drwxr-xr-x 3 root root 4096 11월 22 18:28 .. drwxr-xr-x 2 root root 4096 11월 22 18:28 .circleci drwxr-xr-x 8 root root 4096 11월 22 18:28 .git -rw-r--r-- 1 root root 447 11월 22 18:28 .gitattributes -rw-r--r-- 1 root root 841 11월 22 18:28 .gitignore drwxr-xr-x 3 root root 4096 11월 22 18:28 .mvn -rw-r--r-- 1 root root 34519 11월 22 18:28 LICENCE -rw-r--r-- 1 root root 83957 11월 22 18:28 LOGO_IRDIRCRR_RVB.jpg -rw-r--r-- 1 root root 9366 11월 22 18:28 README.md drwxr-xr-x 2 root root 4096 11월 22 18:28 docs drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-cli drwxr-xr-x 5 root root 4096 11월 22 18:31 exomiser-core drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-data-genome drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-data-phenotype drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-rest-prioritiser drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-spring-boot-autoconfigure drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-spring-boot-starter drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-spring-boot-test drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-web -rw-r--r-- 1 root root 6468 11월 22 18:28 mvnw -rw-r--r-- 1 root root 4994 11월 22 18:28 mvnw.cmd -rw-r--r-- 1 root root 11680 11월 22 18:28 pom.xml

root@ubuntu:/data/reference_data/Exomiser# mvn clean install package [INFO] Results: [INFO] [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] exomiser ........................................... SUCCESS [ 0.570 s] [INFO] exomiser-core ...................................... FAILURE [ 9.206 s] [INFO] exomiser-spring-boot-autoconfigure ................. SKIPPED [INFO] exomiser-spring-boot-starter ....................... SKIPPED [INFO] exomiser-spring-boot-test .......................... SKIPPED [INFO] exomiser-cli ....................................... SKIPPED [INFO] exomiser-data-genome ............................... SKIPPED [INFO] exomiser-data-phenotype ............................ SKIPPED [INFO] exomiser-rest-prioritiser .......................... SKIPPED [INFO] exomiser-web ....................................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 10.598 s [INFO] Finished at: 2018-11-22T18:37:50+09:00 [INFO] Final Memory: 52M/656M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.0:test (default-test) on project exomiser-core: There are test failures. [ERROR] [ERROR] Please refer to /data/reference_data/Exomiser/exomiser-core/target/surefire-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream. [ERROR] ExecutionException The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd /data/reference_data/Exomiser/exomiser-core && /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java '-javaagent:/root/.m2/repository/org/jacoco/org.jacoco.agent/0.8.1/org.jacoco.agent-0.8.1-runtime.jar=destfile=/data/reference_data/Exomiser/exomiser-core/target/jacoco.exec,excludes=/resources/:/assemble/' -jar /data/reference_data/Exomiser/exomiser-core/target/surefire/surefirebooter3160720047109604265.jar /data/reference_data/Exomiser/exomiser-core/target/surefire 2018-11-22T18-37-49_419-jvmRun1 surefire4075254641124906505tmp surefire_05707736014213914957tmp [ERROR] Error occurred in starting fork, check output in log .... [ERROR] Caused by: org.apache.maven.surefire.booter.SurefireBooterForkException: The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd /data/reference_data/Exomiser/exomiser-core && /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java '-javaagent:/root/.m2/repository/org/jacoco/org.jacoco.agent/0.8.1/org.jacoco.agent-0.8.1-runtime.jar=destfile=/data/reference_data/Exomiser/exomiser-core/target/jacoco.exec,excludes=/resources/:/assemble/' -jar /data/reference_data/Exomiser/exomiser-core/target/surefire/surefirebooter2589335864457829238.jar /data/reference_data/Exomiser/exomiser-core/target/surefire 2018-11-22T18-31-52_099-jvmRun2 surefire607711632266005679tmp surefire_26777377948123787022tmp [ERROR] Error occurred in starting fork, check output in log [ERROR] Process Exit Code: 1 [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:671) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:533) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.access$600(ForkStarter.java:115) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter$1.call(ForkStarter.java:362) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter$1.call(ForkStarter.java:342) [ERROR] at java.util.concurrent.FutureTask.run(FutureTask.java:266) [ERROR] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [ERROR] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [ERROR] at java.lang.Thread.run(Thread.java:748) [ERROR] -> [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]

[northwestwitch]

Hi again. Under the ~/.m2/ folder I have these settings:

<settings>
        <localRepository>${user.home}/.m3/repository</localRepository>
</settings>

Maybe this helps?

[julesjacobsen]

You're running whatever maven version is installed on your system. This can cause problems, so Exomiser has a bundled maven binary to prevent these issues. Run it like this:

./mvnw clean install -DskipTests=true -Dmaven.javadoc.skip=true -B -V

[DSRYU]

Thank northwestwitch for kind reply.

Dear julesjacobsen.

You're right. -DskipTests enable to compile Exomiser.

Thanks again ^^.

INFO] Reactor Summary: [INFO] [INFO] exomiser ........................................... SUCCESS [ 3.849 s] [INFO] exomiser-core ...................................... SUCCESS [ 11.169 s] [INFO] exomiser-spring-boot-autoconfigure ................. SUCCESS [ 39.635 s] [INFO] exomiser-spring-boot-starter ....................... SUCCESS [ 0.032 s] [INFO] exomiser-spring-boot-test .......................... SUCCESS [ 0.149 s] [INFO] exomiser-cli ....................................... SUCCESS [ 42.698 s] [INFO] exomiser-data-genome ............................... SUCCESS [ 43.924 s] [INFO] exomiser-data-phenotype ............................ SUCCESS [ 4.553 s] [INFO] exomiser-rest-prioritiser .......................... SUCCESS [ 45.370 s] [INFO] exomiser-web ....................................... SUCCESS [ 19.012 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------

[DSRYU]

Thanks to julesjacobsen, the Exomiser has been successfully compiled. But I have another error in compiling matchbox with mvn.

I edited pom.xml and GenotypeSimilarityServiceImplTest.java as recommended: The added infromation in pom.xml is like this(In the case of 1.9.5 version, I tried both cases, commetend or uncommented):

org.mockito mockito-all 1.9.5 test

            <dependency>
                    <groupId>org.mockito</groupId>
                    <artifactId>mockito-all</artifactId>
                    <version>2.0.2-beta</version>
            </dependency>

But matchbox maven could not recognize GenotypeSimilarityServiceImplTest class. The edited GenotypeSimilarityServiceImplTest.java is like this: //assertThat(commonGenes, equalTo(expected)); DecimalFormat df = new DecimalFormat("0.##"); assertThat(df.format(genotypeSimilarityScore.getScore()), equalTo("0.94"));

before editing GenotypeSimilarityServiceImplTest.java, it gives below error:

[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ matchbox --- [INFO] Surefire report directory: /home/sysadm/matchbox/target/surefire-reports

---

T E S T S

오류: 기본 클래스 org.apache.maven.surefire.booter.ForkedBooter을(를) 찾거나 로드할 수 없습니다. ==> This means "Error: basic class, org.apache.maven.surefire.booter.ForkedBooter is not founded or loaded. Results :

Tests run: 0, Failures: 0, Errors: 0, Skipped: 0

[INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3.277 s [INFO] Finished at: 2018-11-23T13:41:36+09:00 [INFO] Final Memory: 37M/284M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test (default-test) on project matchbox: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test failed: The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd /home/sysadm/matchbox && /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java -jar /home/sysadm/matchbox/target/surefire/surefirebooter6380962758114387402.jar /home/sysadm/matchbox/target/surefire/surefire5390621855385802781tmp /home/sysadm/matchbox/target/surefire/surefire_06289007752142453377tmp [ERROR] -> [Help 1] [ERROR]

Could you look at this more?

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:testCompile (default-testCompile) on project matchbox: Compilation failure [ERROR] /home/sysadm/matchbox/src/test/java/org/broadinstitute/macarthurlab/matchbox/match/GenotypeSimilarityServiceImplTest.java:[173,30] cannot find symbol [ERROR] symbol: variable genotypeSimilarityScore [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.match.GenotypeSimilarityServiceImplTest [ERROR] -> [Help 1]

[northwestwitch]

About the failing test, It's due to a bug that I described in another issue (#54) and has to be fixed before having a full functioning version of the software. But if you want to install Matchbox to test it you should modify this test first, otherwise it doesn't install.

[DSRYU]

Thanks northwestiwitch.

About the matchbox compile, it has been successfully compiled without test process. When I run the compiled matchbox with below command, it gave other errors like belows: root@ubuntu:~/matchbox# java -jar target/matchbox-0.1.0.jar --server.port=9020 I think it would be caused by converting modules gene symbols to ensembl id. How can I solve it? Best regards, 2018-11-26 16:24:25.446 INFO 12055 --- [ main] o.m.e.a.DataDirectoryAutoConfiguration : Exomiser data directory set to: /data/reference_data/Exomiser 2018-11-26 16:24:25.471 INFO 12055 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1807 - Started. 2018-11-26 16:24:25.919 ERROR 12055 --- [ main] o.b.m.matchbox.metrics.BaseMetric : Error reading gene symbol to emsembl id map:java.lang.NullPointerException : null

.... 2018-11-26 16:24:26.441 INFO 12055 --- [ main] org.mongodb.driver.connection : Opened connection [connectionId{localValue:2, serverValue:26}] to 147.47.106.196:27017 2018-11-26 16:24:26.493 ERROR 12055 --- [ main] o.b.m.matchbox.metrics.BaseMetric : Error reading gene symbol to emsembl id map:java.lang.NullPointerException : null 2018-11-26 16:24:26.496 ERROR 12055 --- [ main] o.b.m.matchbox.metrics.BaseMetric : Error reading gene symbol to emsembl id map:java.lang.NullPointerException : null 2018-11-26 16:24:26.511 INFO 12055 --- [ main] o.b.m.m.config.MatchMakerNodeConfig : Reading MME nodes from /home/sysadm/matchbox/config/nodes.json

[northwestwitch]

Hi, I see the same error when I launch the server. I don't know what the cause!