Type SparkFunSuite in package org.bdgenomics.utils.misc is not available #1193

Closed
heuermh opened this Issue Oct 3, 2016 · 8 comments

Comments

Projects
None yet
3 participants
@heuermh
Member

heuermh commented Oct 3, 2016

Not sure what this is supposed to mean

$ mvn clean install
...
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-snpeff_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.5
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] Compiling 1 Scala source to /Users/heuermh/working/adam-snpeff/target/scala-2.10.5/test-classes...
[ERROR] bad symbolic reference. A signature in ADAMFunSuite.class refers to type SparkFunSuite
in package org.bdgenomics.utils.misc which is not available.
It may be completely missing from the current classpath, or the version on
the classpath might be incompatible with the version used when compiling ADAMFunSuite.class.
[ERROR] /Users/heuermh/working/adam-snpeff/src/test/scala/com/github/heuermh/adam/snpeff/AdamSnpEffSuite.scala:30: not found: value sparkTest
[ERROR]   sparkTest("load vcf and pipe through SnpEff") {
[ERROR]   ^
[ERROR] two errors found
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------

I also tried with version Scala 2.10.4

$ mvn clean install
...
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-snpeff_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.1 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] Compiling 1 Scala source to /Users/heuermh/working/adam-snpeff/target/scala-2.10.4/test-classes...
[ERROR] bad symbolic reference. A signature in ADAMFunSuite.class refers to type SparkFunSuite
in package org.bdgenomics.utils.misc which is not available.
It may be completely missing from the current classpath, or the version on
the classpath might be incompatible with the version used when compiling ADAMFunSuite.class.
[ERROR] /Users/heuermh/working/adam-snpeff/src/test/scala/com/github/heuermh/adam/snpeff/AdamSnpEffSuite.scala:30: not found: value sparkTest
[ERROR]   sparkTest("load vcf and pipe through SnpEff") {
[ERROR]   ^
[ERROR] two errors found
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------

I'm depending on fnothaft issues/1112-pipes-api branch per #1114.

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Oct 3, 2016

Member

Can you push your branch? I tried building from ToT --> heuermh/adam-snpeff@7336bb4 but the pom.xml is missing. I have a thought as to what is missing.

Member

fnothaft commented Oct 3, 2016

Can you push your branch? I tried building from ToT --> heuermh/adam-snpeff@7336bb4 but the pom.xml is missing. I have a thought as to what is missing.

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Oct 3, 2016

Member

If I add an explicit test scoped dependency on utils test-jar, then it works. I don't understand why that isn't pulled in as a transitive dependency. Will push shortly.

Member

heuermh commented Oct 3, 2016

If I add an explicit test scoped dependency on utils test-jar, then it works. I don't understand why that isn't pulled in as a transitive dependency. Will push shortly.

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Oct 3, 2016

Member

Yeah, that's what I was going to say to add. I don't think you get transitive dependencies in the test scope, no?

Member

fnothaft commented Oct 3, 2016

Yeah, that's what I was going to say to add. I don't think you get transitive dependencies in the test scope, no?

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Oct 3, 2016

Member

I don't think you get transitive dependencies in the test scope, no?

I don't know. Why not? :)

Member

heuermh commented Oct 3, 2016

I don't think you get transitive dependencies in the test scope, no?

I don't know. Why not? :)

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Oct 3, 2016

Member

I don't think you get transitive dependencies in the test scope, no?

I don't know. Why not? :)

Agreed, I'm not sure why.

Member

fnothaft commented Oct 3, 2016

I don't think you get transitive dependencies in the test scope, no?

I don't know. Why not? :)

Agreed, I'm not sure why.

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Oct 3, 2016

Member

WontFix

Member

heuermh commented Oct 3, 2016

WontFix

@heuermh heuermh closed this Oct 3, 2016

@ryan-williams

This comment has been minimized.

Show comment
Hide comment
@ryan-williams

ryan-williams Oct 4, 2016

Member

I've run in to this before; test dependencies are included in the "test-jar" but not the "jar"; if you want to depend on a library + its test deps, it has to have published a "test-jar" (usually *-tests.jar) that you depend on, otomh.

Member

ryan-williams commented Oct 4, 2016

I've run in to this before; test dependencies are included in the "test-jar" but not the "jar"; if you want to depend on a library + its test deps, it has to have published a "test-jar" (usually *-tests.jar) that you depend on, otomh.

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Oct 4, 2016

Member

Yeah that is what we have, a <type>test-jar</type> for adam-core
https://github.com/heuermh/adam-snpeff/blob/master/pom.xml#L336

It has a transitive dependency on the test-jar from bdg-utils, but for some reason that isn't brought in. I had to add a separate direct dependency on the utils test-jar
https://github.com/heuermh/adam-snpeff/blob/master/pom.xml#L342

Member

heuermh commented Oct 4, 2016

Yeah that is what we have, a <type>test-jar</type> for adam-core
https://github.com/heuermh/adam-snpeff/blob/master/pom.xml#L336

It has a transitive dependency on the test-jar from bdg-utils, but for some reason that isn't brought in. I had to add a separate direct dependency on the utils test-jar
https://github.com/heuermh/adam-snpeff/blob/master/pom.xml#L342

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