Why did I use Maven build cbioportal v6.1.0,6.2.0,6.2.1 and get failed ?

Harry Sun

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Apr 15, 2025, 12:45:49 PMApr 15

to cBioPortal for Cancer Genomics Discussion Group

I downloaded cBioportal v6.1.0,6.2.0,6.2.1, then used Maven to build it(mvn -DskipTests clean install), I got failure as the below (my java 21.0.2,maven 3.9.9)

Failed to execute goal on project cbioportal: Could not resolve dependencies for project io.github.cbioportal:cbioportal:jar:6.2.1-SNAPSHOT

[ERROR] dependency: com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 (test)

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 was not found in https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of jboss-third-party has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 was not found in https://build.shibboleth.net/nexus/content/repositories/releases/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of shiboleth has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 was not found in https://repo1.maven.org/maven2/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of maven-central has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 was not found in https://repo.maven.apache.org/maven2 during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of central has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 was not found in https://repository.jboss.org/nexus/content/groups/public/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of jboss-public-repository-group has elapsed or updates are forced

[ERROR] dependency: com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 (test)

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 was not found in https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of jboss-third-party has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 was not found in https://build.shibboleth.net/nexus/content/repositories/releases/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of shiboleth has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 was not found in https://repo1.maven.org/maven2/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of maven-central has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 was not found in https://repo.maven.apache.org/maven2 during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of central has elapsed or updates are forced

[ERROR] com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 was not found in https://repository.jboss.org/nexus/content/groups/public/ during a previous attempt. This failure was cached in the local repository and resolution is not reattempted until the update interval of jboss-public-repository-group has elapsed or updates are forced

de Bruijn, Ino

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Apr 16, 2025, 10:56:21 AMApr 16

to Harry Sun, cBioPortal for Cancer Genomics Discussion Group

Hi Harry,

Thanks for reaching out! Sorry to hear you are having some issues. Many of the errors look related to common java packages, e.g.:

https://mvnrepository.com/artifact/com.github.java-json-tools/jackson-coreutils

Are you sure the machine has access to the internet etc? Maybe try to build with removing all cache too `mvn -U -DskipTests clean install`

Hope that helps!

Best wishes,

Ino

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Harry Sun <hds...@gmail.com>
Date: Tuesday, April 15, 2025 at 12:45 PM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Why did I use Maven build cbioportal v6.1.0,6.2.0,6.2.1 and get failed ?

I downloaded cBioportal v6. 1. 0,6. 2. 0,6. 2. 1, then used Maven to build it(mvn -DskipTests clean install), I got failure as the below (my java 21. 0. 2,maven 3. 9. 9) Failed to execute goal on project cbioportal: Could not resolve dependencies for

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Harry Sun

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Apr 16, 2025, 11:33:35 AMApr 16

to cBioPortal for Cancer Genomics Discussion Group

Hi Ino,

Surely, my server is able to access Internet. No problem if I mvn -DskipTests clean install` cbioportal 6.0.x or older version.

I checked pom.xml, no any jackson-coreutils found.

I used your mvn -U -DskipTests clean install,still got the below failure:

[hsun4@r1prlcbio cbioportal621]$ mvn -U -DskipTests clean install

[INFO] Scanning for projects...

[WARNING]

[WARNING] Some problems were encountered while building the effective model for io.github.cbioportal:cbioportal:jar:6.2.1-SNAPSHOT

[WARNING] 'profiles.profile[maven-central].plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-source-plugin @ line 794, column 29

[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]

[INFO]

[INFO] ------------------< io.github.cbioportal:cbioportal >-------------------

[INFO] Building io.github.cbioportal:cbioportal 6.2.1-SNAPSHOT

[INFO] from pom.xml

[INFO] --------------------------------[ jar ]---------------------------------

[INFO] Artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:pom:2.0 is present in the local repository, but cached from a remote repository ID that is unavailable in current build context, verifying that is downloadable from [jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/, default, releases+snapshots), shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/, default, releases+snapshots), maven-central (https://repo1.maven.org/maven2/, default, releases+snapshots), central (https://repo.maven.apache.org/maven2, default, releases), sonatype-snapshots (https://oss.sonatype.org/content/repositories/snapshots, default, snapshots), sonatype-releases (https://oss.sonatype.org/content/repositories/releases, default, releases), sonatype-nexus-snapshots (https://oss.sonatype.org/content/repositories/snapshots, default, snapshots)]

Downloading from jboss-third-party: https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.pom

Downloading from shiboleth: https://build.shibboleth.net/nexus/content/repositories/releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.pom

Downloading from maven-central: https://repo1.maven.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.pom

Downloading from central: https://repo.maven.apache.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.pom

Downloading from sonatype-releases: https://oss.sonatype.org/content/repositories/releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.pom

[WARNING] The POM for com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 is missing, no dependency information available

[INFO] Artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:pom:2.0 is present in the local repository, but cached from a remote repository ID that is unavailable in current build context, verifying that is downloadable from [jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/, default, releases+snapshots), shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/, default, releases+snapshots), maven-central (https://repo1.maven.org/maven2/, default, releases+snapshots), central (https://repo.maven.apache.org/maven2, default, releases), sonatype-snapshots (https://oss.sonatype.org/content/repositories/snapshots, default, snapshots), sonatype-releases (https://oss.sonatype.org/content/repositories/releases, default, releases), sonatype-nexus-snapshots (https://oss.sonatype.org/content/repositories/snapshots, default, snapshots)]

Downloading from jboss-third-party: https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.pom

Downloading from shiboleth: https://build.shibboleth.net/nexus/content/repositories/releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.pom

Downloading from maven-central: https://repo1.maven.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.pom

Downloading from central: https://repo.maven.apache.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.pom

Downloading from sonatype-releases: https://oss.sonatype.org/content/repositories/releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.pom

[WARNING] The POM for com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 is missing, no dependency information available

[INFO] Artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 is present in the local repository, but cached from a remote repository ID that is unavailable in current build context, verifying that is downloadable from [jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/, default, releases+snapshots), shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/, default, releases+snapshots), maven-central (https://repo1.maven.org/maven2/, default, releases+snapshots), central (https://repo.maven.apache.org/maven2, default, releases), jboss-public-repository-group (https://repository.jboss.org/nexus/content/groups/public/, default, releases+snapshots)]

[INFO] Artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 is present in the local repository, but cached from a remote repository ID that is unavailable in current build context, verifying that is downloadable from [jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/, default, releases+snapshots), shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/, default, releases+snapshots), maven-central (https://repo1.maven.org/maven2/, default, releases+snapshots), central (https://repo.maven.apache.org/maven2, default, releases), jboss-public-repository-group (https://repository.jboss.org/nexus/content/groups/public/, default, releases+snapshots)]

[INFO] Artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 is present in the local repository, but cached from a remote repository ID that is unavailable in current build context, verifying that is downloadable from [jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/, default, releases+snapshots), shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/, default, releases+snapshots), maven-central (https://repo1.maven.org/maven2/, default, releases+snapshots), central (https://repo.maven.apache.org/maven2, default, releases), jboss-public-repository-group (https://repository.jboss.org/nexus/content/groups/public/, default, releases+snapshots)]

[INFO] Artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 is present in the local repository, but cached from a remote repository ID that is unavailable in current build context, verifying that is downloadable from [jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/, default, releases+snapshots), shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/, default, releases+snapshots), maven-central (https://repo1.maven.org/maven2/, default, releases+snapshots), central (https://repo.maven.apache.org/maven2, default, releases), jboss-public-repository-group (https://repository.jboss.org/nexus/content/groups/public/, default, releases+snapshots)]

Downloading from jboss-third-party: https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.jar

Downloading from jboss-third-party: https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.jar

Downloading from shiboleth: https://build.shibboleth.net/nexus/content/repositories/releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.jar

Downloading from shiboleth: https://build.shibboleth.net/nexus/content/repositories/releases/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.jar

Downloading from maven-central: https://repo1.maven.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.jar

Downloading from maven-central: https://repo1.maven.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.jar

Downloading from central: https://repo.maven.apache.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.jar

Downloading from central: https://repo.maven.apache.org/maven2/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.jar

Downloading from jboss-public-repository-group: https://repository.jboss.org/nexus/content/groups/public/com/github/java-json-tools/jackson-coreutils/jackson-coreutils/2.0/jackson-coreutils-2.0.jar

Downloading from jboss-public-repository-group: https://repository.jboss.org/nexus/content/groups/public/com/github/java-json-tools/jackson-coreutils/jackson-coreutils-equivalence/2.0/jackson-coreutils-equivalence-2.0.jar

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 8.221 s

[INFO] Finished at: 2025-04-16T10:15:50-05:00

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal on project cbioportal: Could not resolve dependencies for project io.github.cbioportal:cbioportal:jar:6.2.1-SNAPSHOT

[ERROR] dependency: com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 (test)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 in jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 in shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 in maven-central (https://repo1.maven.org/maven2/)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 in central (https://repo.maven.apache.org/maven2)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils:jar:2.0 in jboss-public-repository-group (https://repository.jboss.org/nexus/content/groups/public/)

[ERROR] dependency: com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 (test)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 in jboss-third-party (https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 in shiboleth (https://build.shibboleth.net/nexus/content/repositories/releases/)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 in maven-central (https://repo1.maven.org/maven2/)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 in central (https://repo.maven.apache.org/maven2)

[ERROR] Could not find artifact com.github.java-json-tools.jackson-coreutils:jackson-coreutils-equivalence:jar:2.0 in jboss-public-repository-group (https://repository.jboss.org/nexus/content/groups/public/)

[ERROR]

[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/DependencyResolutionException

de Bruijn, Ino

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Apr 16, 2025, 12:16:54 PMApr 16

to Harry Sun, cBioPortal for Cancer Genomics Discussion Group

Thanks Harry! Looks like I’m also seeing this error. Looking into it

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Harry Sun <hds...@gmail.com>

Date: Wednesday, April 16, 2025 at 11:33 AM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>

Subject: [EXTERNAL] Re: [cbioportal] Why did I use Maven build cbioportal v6.1.0,6.2.0,6.2.1 and get failed ?

Hi Ino, Surely, my server is able to access Internet. No problem if I mvn -DskipTests clean install` cbioportal 6. 0. x or older version. I checked pom. xml, no any jackson-coreutils found. I used your mvn -U -DskipTests clean install,still got

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/24a4cfe0-34f6-433c-8643-5932d1fbb7e6n%40googlegroups.com.

Harry Sun

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Apr 16, 2025, 12:31:07 PMApr 16

to cBioPortal for Cancer Genomics Discussion Group

Ino,

I found cbioportal 2.x to download Jackson-coreutils by those URLs not existing. It didn't download from https://mvnrepository.com/artifact/com.github.java-json-tools/jackson-coreutils

Thanks,

Harry

On Wednesday, April 16, 2025 at 9:56:21 AM UTC-5 de Bruijn, Ino wrote:

de Bruijn, Ino

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Apr 16, 2025, 2:57:29 PMApr 16

to Harry Sun, cBioPortal for Cancer Genomics Discussion Group

Hi Harry,

It seems like some odd caching issue. If I delete the entirety of my ~/.m2 folder and then rerun “mvn clean install”, it works

Hope that works for you as well!

Best wishes

Ino

de Bruijn, Ino

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Apr 16, 2025, 4:02:01 PMApr 16

to Harry Sun, cbiop...@googlegroups.com

Awesome! Thanks for reporting!

From: Harry Sun <hds...@gmail.com>
Sent: Wednesday, April 16, 2025 3:58:37 PM
To: de Bruijn, Ino <debr...@mskcc.org>

Subject: [EXTERNAL] Re: [cbioportal] Why did I use Maven build cbioportal v6.1.0,6.2.0,6.2.1 and get failed ?

Hi Ino,

Yes , I did the same thing as you did. It works.

Thanks a lot.

Harry

Harry Sun

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Apr 17, 2025, 5:35:09 PMApr 17

to cBioPortal for Cancer Genomics Discussion Group

Ino,

cBioportal v6.2.1 doesn't work after I completed "mvn -DskipTests clean install"

cBioportal v6.2.0 work.

Best,

Harry

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