New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ADAM-743] exclude conflicting jackson dependencies #744

Merged
merged 1 commit into from Jul 27, 2015

Conversation

Projects
None yet
2 participants
@heuermh
Member

heuermh commented Jul 27, 2015

Fixes #743

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 27, 2015

Member

What are the conflicting jackson dependencies used for in utils?
Nit: can you prefix the commit message with [ADAM-774]?

Member

fnothaft commented Jul 27, 2015

What are the conflicting jackson dependencies used for in utils?
Nit: can you prefix the commit message with [ADAM-774]?

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Jul 27, 2015

Member

HEAD contains versions 2.1.x and 2.3.x

$ mvn dependency:tree
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.10: CLI 0.17.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ adam-cli_2.10 ---
[INFO] org.bdgenomics.adam:adam-cli_2.10:jar:0.17.1-SNAPSHOT
...
[INFO] +- org.apache.spark:spark-core_2.10:jar:1.2.0:provided
...
[INFO] |  +- org.json4s:json4s-jackson_2.10:jar:3.2.10:provided
[INFO] |  |  +- org.json4s:json4s-core_2.10:jar:3.2.10:provided
[INFO] |  |  |  +- org.json4s:json4s-ast_2.10:jar:3.2.10:provided
[INFO] |  |  |  \- org.scala-lang:scalap:jar:2.10.0:provided
[INFO] |  |  |     \- org.scala-lang:scala-compiler:jar:2.10.0:provided
[INFO] |  |  \- com.fasterxml.jackson.core:jackson-databind:jar:2.3.1:provided
...
[INFO] +- org.bdgenomics.utils:utils-io_2.10:jar:0.2.2:compile
[INFO] |  +- org.bdgenomics.utils:utils-misc_2.10:jar:0.2.2:compile
[INFO] |  +- org.apache.httpcomponents:httpclient:jar:4.3.2:compile
[INFO] |  |  \- org.apache.httpcomponents:httpcore:jar:4.3.1:compile
[INFO] |  \- com.amazonaws:aws-java-sdk:jar:1.7.5:provided
[INFO] |     +- com.fasterxml.jackson.core:jackson-core:jar:2.1.1:provided
[INFO] |     +- com.fasterxml.jackson.core:jackson-annotations:jar:2.1.1:provided
...

vs. 2.3.x for this pull request

$ mvn dependency:tree
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.10: CLI 0.17.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ adam-cli_2.10 ---
[INFO] org.bdgenomics.adam:adam-cli_2.10:jar:0.17.1-SNAPSHOT
...
[INFO] +- org.apache.spark:spark-core_2.10:jar:1.2.0:provided
...
[INFO] |  +- org.json4s:json4s-jackson_2.10:jar:3.2.10:provided
[INFO] |  |  +- org.json4s:json4s-core_2.10:jar:3.2.10:provided
[INFO] |  |  |  +- org.json4s:json4s-ast_2.10:jar:3.2.10:provided
[INFO] |  |  |  \- org.scala-lang:scalap:jar:2.10.0:provided
[INFO] |  |  |     \- org.scala-lang:scala-compiler:jar:2.10.0:provided
[INFO] |  |  \- com.fasterxml.jackson.core:jackson-databind:jar:2.3.1:provided
[INFO] |  |     +- com.fasterxml.jackson.core:jackson-annotations:jar:2.3.0:provided
[INFO] |  |     \- com.fasterxml.jackson.core:jackson-core:jar:2.3.1:provided
[INFO] +- org.bdgenomics.utils:utils-io_2.10:jar:0.2.2:compile
[INFO] |  +- org.bdgenomics.utils:utils-misc_2.10:jar:0.2.2:compile
[INFO] |  +- org.apache.httpcomponents:httpclient:jar:4.3.2:compile
[INFO] |  |  \- org.apache.httpcomponents:httpcore:jar:4.3.1:compile
[INFO] |  \- com.amazonaws:aws-java-sdk:jar:1.7.5:provided
...
Member

heuermh commented Jul 27, 2015

HEAD contains versions 2.1.x and 2.3.x

$ mvn dependency:tree
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.10: CLI 0.17.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ adam-cli_2.10 ---
[INFO] org.bdgenomics.adam:adam-cli_2.10:jar:0.17.1-SNAPSHOT
...
[INFO] +- org.apache.spark:spark-core_2.10:jar:1.2.0:provided
...
[INFO] |  +- org.json4s:json4s-jackson_2.10:jar:3.2.10:provided
[INFO] |  |  +- org.json4s:json4s-core_2.10:jar:3.2.10:provided
[INFO] |  |  |  +- org.json4s:json4s-ast_2.10:jar:3.2.10:provided
[INFO] |  |  |  \- org.scala-lang:scalap:jar:2.10.0:provided
[INFO] |  |  |     \- org.scala-lang:scala-compiler:jar:2.10.0:provided
[INFO] |  |  \- com.fasterxml.jackson.core:jackson-databind:jar:2.3.1:provided
...
[INFO] +- org.bdgenomics.utils:utils-io_2.10:jar:0.2.2:compile
[INFO] |  +- org.bdgenomics.utils:utils-misc_2.10:jar:0.2.2:compile
[INFO] |  +- org.apache.httpcomponents:httpclient:jar:4.3.2:compile
[INFO] |  |  \- org.apache.httpcomponents:httpcore:jar:4.3.1:compile
[INFO] |  \- com.amazonaws:aws-java-sdk:jar:1.7.5:provided
[INFO] |     +- com.fasterxml.jackson.core:jackson-core:jar:2.1.1:provided
[INFO] |     +- com.fasterxml.jackson.core:jackson-annotations:jar:2.1.1:provided
...

vs. 2.3.x for this pull request

$ mvn dependency:tree
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.10: CLI 0.17.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ adam-cli_2.10 ---
[INFO] org.bdgenomics.adam:adam-cli_2.10:jar:0.17.1-SNAPSHOT
...
[INFO] +- org.apache.spark:spark-core_2.10:jar:1.2.0:provided
...
[INFO] |  +- org.json4s:json4s-jackson_2.10:jar:3.2.10:provided
[INFO] |  |  +- org.json4s:json4s-core_2.10:jar:3.2.10:provided
[INFO] |  |  |  +- org.json4s:json4s-ast_2.10:jar:3.2.10:provided
[INFO] |  |  |  \- org.scala-lang:scalap:jar:2.10.0:provided
[INFO] |  |  |     \- org.scala-lang:scala-compiler:jar:2.10.0:provided
[INFO] |  |  \- com.fasterxml.jackson.core:jackson-databind:jar:2.3.1:provided
[INFO] |  |     +- com.fasterxml.jackson.core:jackson-annotations:jar:2.3.0:provided
[INFO] |  |     \- com.fasterxml.jackson.core:jackson-core:jar:2.3.1:provided
[INFO] +- org.bdgenomics.utils:utils-io_2.10:jar:0.2.2:compile
[INFO] |  +- org.bdgenomics.utils:utils-misc_2.10:jar:0.2.2:compile
[INFO] |  +- org.apache.httpcomponents:httpclient:jar:4.3.2:compile
[INFO] |  |  \- org.apache.httpcomponents:httpcore:jar:4.3.1:compile
[INFO] |  \- com.amazonaws:aws-java-sdk:jar:1.7.5:provided
...
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 27, 2015

Member

Ah. I was more going for, what code in utils has the jackson dependency? I think we may be able to fix that in utils by removing or upgrading the Jackson dep; it may be old?

Member

fnothaft commented Jul 27, 2015

Ah. I was more going for, what code in utils has the jackson dependency? I think we may be able to fix that in utils by removing or upgrading the Jackson dep; it may be old?

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Jul 27, 2015

Member

From what I can see there isn't a direct dependency. It appears to be a transitive dependency where old versions are pulled in by aws-java-sdk in the module utils-io.

The class in the stack trace is part of Apache Spark
https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/metrics/sink/MetricsServlet.scala

Member

heuermh commented Jul 27, 2015

From what I can see there isn't a direct dependency. It appears to be a transitive dependency where old versions are pulled in by aws-java-sdk in the module utils-io.

The class in the stack trace is part of Apache Spark
https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/metrics/sink/MetricsServlet.scala

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 27, 2015

Member

Ah, OK! SGTM.

Member

fnothaft commented Jul 27, 2015

Ah, OK! SGTM.

fnothaft added a commit that referenced this pull request Jul 27, 2015

Merge pull request #744 from heuermh/issue-743
[ADAM-743] exclude conflicting jackson dependencies

@fnothaft fnothaft merged commit ec13bd9 into bigdatagenomics:master Jul 27, 2015

1 check passed

default Merged build finished.
Details
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 27, 2015

Member

Merged! Thanks @heuermh!

Member

fnothaft commented Jul 27, 2015

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:issue-743 branch Jul 28, 2015

@heuermh heuermh referenced this pull request Aug 3, 2015

Closed

upgrade to Spark 1.3.1 #690

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment